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diff --git a/.clang-tidy b/.clang-tidy
index d973c6bbf..59ad5a5e7 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -1,4 +1,12 @@
-Checks: 'modernize-use-*, -modernize-use-trailing-return-type*, performance-*, mpi-*, openmp-*, readability-*, cppcoreguidelines-*, -cppcoreguidelines-pro-bounds-array-to-pointer-decay*, -cppcoreguidelines-macro-usage*'
+Checks: "
+ modernize-use-*, -modernize-use-trailing-return-type*,
+ performance-*,
+ mpi-*,
+ openmp-*,
+ bugprone-*,
+ readability-*, -readability-magic-numbers, -readability-redundant-access-specifiers,
+ -clang-analyzer-*
+ "
AnalyzeTemporaryDtors: false
-HeaderFilterRegex: 'src/.*'
-FormatStyle: file
+HeaderFilterRegex: 'src/.*'
+FormatStyle: file
diff --git a/doc/dev-doc/manual/fe_engine.rst b/doc/dev-doc/manual/fe_engine.rst
index 4b4fa0e87..5e693213f 100644
--- a/doc/dev-doc/manual/fe_engine.rst
+++ b/doc/dev-doc/manual/fe_engine.rst
@@ -1,183 +1,183 @@
``FEEngine``
============
The ``FEEngine`` interface is dedicated to handle the
finite-element approximations and the numerical integration of the
weak form. As we will see in Chapter sect:smm, ``Model``
creates its own ``FEEngine`` object so the explicit creation of the
object is not required.
Mathematical Operations
-----------------------
Using the ``FEEngine`` object, one can compute a interpolation, an
integration or a gradient. A simple example is given below::
// having a FEEngine object
std::unique_ptr<FEEngine> fem =
std::make_unique<FEEngineTemplate<IntegratorGauss,ShapeLagrange>>(
my_mesh, dim, "my_fem");
// instead of this, a FEEngine object can be get using the model:
// model.getFEEngine()
//compute the gradient
Array<Real> u; //append the values you want
Array<Real> nablauq; //gradient array to be computed
// compute the gradient
fem->gradientOnIntegrationPoints(const Array<Real> &u,
Array<Real> &nablauq,
const UInt nb_degree_of_freedom,
- const ElementType & type);
+ ElementType type);
// interpolate
Array<Real> uq; //interpolated array to be computed
// compute the interpolation
fem->interpolateOnIntegrationPoints(const Array<Real> &u,
Array<Real> &uq,
UInt nb_degree_of_freedom,
- const ElementType & type);
+ ElementType type);
// interpolated function can be integrated over the elements
Array<Real> int_val_on_elem;
// integrate
fem->integrate(const Array<Real> &uq,
Array<Real> &int_uq,
UInt nb_degree_of_freedom,
- const ElementType & type);
+ ElementType type);
Another example below shows how to integrate stress and strain fields
over elements assigned to a particular material::
UInt sp_dim = 3; //spatial dimension
UInt m = 1; //material index of interest
const ElementType type = _tetrahedron_4; //element type
// get the stress and strain arrays associated to the material index m
const Array<Real> & strain_vec = model.getMaterial(m).getGradU(type);
const Array<Real> & stress_vec = model.getMaterial(m).getStress(type);
// get the element filter for the material index
const Array<UInt> & elem_filter = model.getMaterial(m).getElementFilter(type);
// initialize the integrated stress and strain arrays
Array<Real> int_strain_vec(elem_filter.getSize(),
sp_dim*sp_dim, "int_of_strain");
Array<Real> int_stress_vec(elem_filter.getSize(),
sp_dim*sp_dim, "int_of_stress");
// integrate the fields
model.getFEEngine().integrate(strain_vec, int_strain_vec,
sp_dim*sp_dim, type, _not_ghost, elem_filter);
model.getFEEngine().integrate(stress_vec, int_stress_vec,
sp_dim*sp_dim, type, _not_ghost, elem_filter);
Elements
--------
The base for every Finite-Elements computation is its mesh and the elements that
are used within that mesh. The element types that can be used depend on the
mesh, but also on the dimensionality of the problem (1D, 2D or 3D). In Akantu,
several isoparametric Lagrangian element types are supported (and one
serendipity element). Each of these types is discussed in some detail below,
starting with the 1D-elements all the way to the 3D-elements. More detailed
information (shape function, location of Gaussian quadrature points, and so on)
can be found in Appendix app:elements.
Isoparametric Elements
......................
1D
````
In Akantu, there are two types of isoparametric elements defined in 1D. These
element types are called ``_segment_2`` and ``_segment_3``, and are
depicted schematically in :numref:`fig:elements:1D`. Some of the basic
properties of these elements are listed in :numref:`tab:elements:1D`.
.. _fig:elements:1D:
.. figure:: figures/elements/segments.svg
:align: center
Schematic overview of the two 1D element types in Akantu. In each
element, the node numbering as used in Akantu is indicated and also the
quadrature points are highlighted (gray circles).
.. _tab:elements:1D:
.. table:: Some basic properties of the two 1D isoparametric elements in Akantu
+--------------+---------+------+------+
|Element |Order |#nodes|#quad |
|type | | |points|
+--------------+---------+------+------+
|``_segment_2``|linear |2 |1 |
+--------------+---------+------+------+
|``_segment_3``|quadratic|3 |2 |
+--------------+---------+------+------+
2D
````
In Akantu, there are four types of isoparametric elements defined in 2D. These
element types are called ``_triangle_3``, ``_triangle_6``,
``_quadrangle_4`` and ``_quadrangle_8``, and all of them are depicted
in :numref:`fig:elements:2D`. As with the 1D elements, some of the most basic
properties of these elements are listed in :numref:`tab:elements:2D`. It is
important to note that the first element is linear, the next two quadratic and
the last one cubic. Furthermore, the last element type (``_quadrangle_8``)
is not a Lagrangian but a serendipity element.
.. _fig:elements:2D:
.. figure:: figures/elements/elements_2d.svg
:align: center
Schematic overview of the four 2D element types in Akantu. In each
element, the node numbering as used in Akantu is indicated and also the
quadrature points are highlighted (gray circles).
.. _tab:elements:2D:
.. table:: Some basic properties of the 2D isoparametric elements in Akantu
+--------------------+----------+------+------+
|Element |Order |#nodes|#quad |
|type | | |points|
+--------------------+----------+------+------+
|``_triangle_3`` |linear |3 |1 |
+--------------------+----------+------+------+
|``_triangle_6`` |quadratic |6 |3 |
+--------------------+----------+------+------+
|``_quadrangle_4`` |linear |4 |4 |
+--------------------+----------+------+------+
|``_quadrangle_8`` |quadratic |8 |9 |
+--------------------+----------+------+------+
3D
````
In Akantu, there are three types of isoparametric elements defined in 3D. These
element types are called ``_tetrahedron_4``, ``_tetrahedron_10`` and
``_hexahedron_8``, and all of them are depicted schematically in
:numref:`fig:elements:3D`. As with the 1D and 2D elements some of the most
basic properties of these elements are listed in :numref:`tab:elements:3D`.
.. _fig:elements:3D:
.. figure:: figures/elements/elements_3d.svg
:align: center
Schematic overview of the three 3D element types in Akantu. In each
element, the node numbering as used in Akantu is indicated and also the
quadrature points are highlighted (gray circles).
.. _tab:elements:3D:
.. table:: Some basic properties of the 3D isoparametric elements in Akantu
+--------------------+----------+------+------+
|Element |Order |#nodes|#quad |
|type | | |points|
+--------------------+----------+------+------+
|``_tetrahedron_4`` |linear |4 |1 |
+--------------------+----------+------+------+
|``_tetrahedron_10`` |quadratic |10 |4 |
+--------------------+----------+------+------+
|``_hexadedron_8`` |cubic |8 |8 |
+--------------------+----------+------+------+
diff --git a/doc/manual/manual-feengine.tex b/doc/manual/manual-feengine.tex
index 9c221b578..415b15d1e 100644
--- a/doc/manual/manual-feengine.tex
+++ b/doc/manual/manual-feengine.tex
@@ -1,75 +1,75 @@
\chapter{FEEngine\index{FEEngine}}
\label{chap:feengine}
The \code{FEEngine} interface is dedicated to handle the
finite-element approximations and the numerical integration of the
weak form. As we will see in Chapter \ref{sect:smm}, \code{Model}
creates its own \code{FEEngine} object so the explicit creation of the
object is not required.
\section{Mathematical Operations\label{sect:fe:mathop}}
Using the \code{FEEngine} object, one can compute a interpolation, an
integration or a gradient. A simple example is given below.
\begin{cpp}
// having a FEEngine object
FEEngine *fem = new FEEngineTemplate<IntegratorGauss,ShapeLagrange>(my_mesh,
dim,
"my_fem");
// instead of this, a FEEngine object can be get using the model:
// model.getFEEngine()
//compute the gradient
Array<Real> u; //append the values you want
Array<Real> nablauq; //gradient array to be computed
// compute the gradient
fem->gradientOnIntegrationPoints(const Array<Real> &u,
Array<Real> &nablauq,
const UInt nb_degree_of_freedom,
- const ElementType & type);
+ ElementType type);
// interpolate
Array<Real> uq; //interpolated array to be computed
// compute the interpolation
fem->interpolateOnIntegrationPoints(const Array<Real> &u,
Array<Real> &uq,
UInt nb_degree_of_freedom,
- const ElementType & type);
+ ElementType type);
// interpolated function can be integrated over the elements
Array<Real> int_val_on_elem;
// integrate
fem->integrate(const Array<Real> &uq,
Array<Real> &int_uq,
UInt nb_degree_of_freedom,
- const ElementType & type);
+ ElementType type);
\end{cpp}
Another example below shows how to integrate stress and strain fields
over elements assigned to a particular material.
\begin{cpp}
UInt sp_dim = 3; //spatial dimension
UInt m = 1; //material index of interest
const ElementType type = _tetrahedron_4; //element type
// get the stress and strain arrays associated to the material index m
const Array<Real> & strain_vec = model.getMaterial(m).getGradU(type);
const Array<Real> & stress_vec = model.getMaterial(m).getStress(type);
// get the element filter for the material index
const Array<UInt> & elem_filter = model.getMaterial(m).getElementFilter(type);
// initialize the integrated stress and strain arrays
Array<Real> int_strain_vec(elem_filter.getSize(),
sp_dim*sp_dim, "int_of_strain");
Array<Real> int_stress_vec(elem_filter.getSize(),
sp_dim*sp_dim, "int_of_stress");
// integrate the fields
model.getFEEngine().integrate(strain_vec, int_strain_vec,
sp_dim*sp_dim, type, _not_ghost, elem_filter);
model.getFEEngine().integrate(stress_vec, int_stress_vec,
sp_dim*sp_dim, type, _not_ghost, elem_filter);
\end{cpp}
-\input{manual-elements}
\ No newline at end of file
+\input{manual-elements}
diff --git a/doc/manual/manual-solidmechanicsmodel.tex b/doc/manual/manual-solidmechanicsmodel.tex
index 95e0d5692..f0fe8760f 100644
--- a/doc/manual/manual-solidmechanicsmodel.tex
+++ b/doc/manual/manual-solidmechanicsmodel.tex
@@ -1,1138 +1,1138 @@
\chapter{Solid Mechanics Model\index{SolidMechanicsModel}\label{sect:smm}}
The solid mechanics model is a specific implementation of the
\code{Model} interface dedicated to handle the equations of motion or
equations of equilibrium. The model is created for a given mesh. It
will create its own \code{FEEngine} object to compute the interpolation,
gradient, integration and assembly operations. A
\code{SolidMechanicsModel} object can simply be created like this:
\begin{cpp}
SolidMechanicsModel model(mesh);
\end{cpp}
where \code{mesh} is the mesh for which the equations are to be
solved. A second parameter called \code{spatial\_dimension} can be
added after \code{mesh} if the spatial dimension of the problem is
different than that of the mesh.
This model contains at least the following six \code{Arrays}:
\begin{description}
\item[blocked\_dofs] contains a Boolean value for each degree of
freedom specifying whether that degree is blocked or not. A
Dirichlet boundary condition can be prescribed by setting the
\textbf{blocked\_dofs} value of a degree of freedom to \code{true}.
A Neumann boundary condition can be applied by setting the
\textbf{blocked\_dofs} value of a degree of freedom to \code{false}.
The \textbf{displacement}, \textbf{velocity} and
\textbf{acceleration} are computed for all degrees of freedom for
which the \textbf{blocked\_dofs} value is set to \code{false}. For
the remaining degrees of freedom, the imposed values (zero by
default after initialization) are kept.
\item[displacement] contains the displacements of all degrees of
freedom. It can be either a computed displacement for free degrees
of freedom or an imposed displacement in case of blocked ones
($\vec{u}$ in the following).
\item[velocity] contains the velocities of all degrees of freedom. As
\textbf{displacement}, it contains computed or imposed velocities
depending on the nature of the degrees of freedom ($\dot{\vec{u}}$
in the following).
\item[acceleration] contains the accelerations of all degrees of
freedom. As \textbf{displacement}, it contains computed or imposed
accelerations depending on the nature of the degrees of freedom
($\ddot{\vec{u}}$ in the following).
\item[external\_force] contains the external forces applied on the nodes
($\vec{f}_{\st{ext}}$ in the following).
\item[internal\_force] contains the internal forces on the nodes
($\vec{f}_{\st{int}}$ in the following).
\end{description}
Some examples to help to understand how to use this model will be
presented in the next sections.
\section{Model Setup}
\subsection{Setting Initial Conditions \label{sect:smm:initial_condition}}
For a unique solution of the equations of motion, initial
displacements and velocities for all degrees of freedom must be
specified:
\begin{eqnarray}
\vec{u}(t=0) = \vec{u}_0\\
\dot{\vec u}(t=0) =\vec{v}_0
\end{eqnarray} The solid mechanics model can be initialized as
follows:
\begin{cpp}
model.initFull()
\end{cpp}
This function initializes the internal arrays and sets them to
zero. Initial displacements and velocities that are not equal to zero
can be prescribed by running a loop over the total number of
nodes. Here, the initial displacement in $x$-direction and the
initial velocity in $y$-direction for all nodes is set to $0.1$ and $1$,
respectively.
\begin{cpp}
auto & disp = model.getDisplacement();
auto & velo = model.getVelocity();
for (UInt node = 0; node < mesh.getNbNodes(); ++node) {
disp(node, 0) = 0.1;
velo(node, 1) = 1.;
}
\end{cpp}
\subsection{Setting Boundary Conditions\label{sect:smm:boundary}}
This section explains how to impose Dirichlet or Neumann boundary
conditions. A Dirichlet boundary condition specifies the values that
the displacement needs to take for every point $x$ at the boundary
($\Gamma_u$) of the problem domain (Fig.~\ref{fig:smm:boundaries}):
\begin{equation}
\vec{u} = \bar{\vec u} \quad \forall \vec{x}\in
\Gamma_{u}
\end{equation}
A Neumann boundary condition imposes the value of the gradient of the
solution at the boundary $\Gamma_t$ of the problem domain
(Fig.~\ref{fig:smm:boundaries}):
\begin{equation}
\vec{t} = \mat{\sigma} \vec{n} = \bar{\vec t} \quad
\forall \vec{x}\in \Gamma_{t}
\end{equation}
\begin{figure} \centering
\def\svgwidth{0.5\columnwidth}
\input{figures/problemDomain.pdf_tex}
\caption{Problem domain $\Omega$ with boundary in three
dimensions. The Dirchelet and the Neumann regions of the boundary
are denoted with $\Gamma_u$ and $\Gamma_t$,
respecitvely.\label{fig:smm:boundaries}}
\label{fig:problemDomain}
\end{figure}
Different ways of imposing these boundary conditions exist. A basic
way is to loop over nodes or elements at the boundary and apply local
values. A more advanced method consists of using the notion of the
boundary of the mesh. In the following both ways are presented.
Starting with the basic approach, as mentioned, the Dirichlet boundary
conditions can be applied by looping over the nodes and assigning the
required values. Figure~\ref{fig:smm:dirichlet_bc} shows a beam with a
fixed support on the left side. On the right end of the beam, a load
is applied. At the fixed support, the displacement has a given
value. For this example, the displacements in both the $x$ and the
$y$-direction are set to zero. Implementing this displacement boundary
condition is similar to the implementation of initial displacement
conditions described above. However, in order to impose a displacement
boundary condition for all time steps, the corresponding nodes need to
be marked as boundary nodes using the function \code{blocked}. While,
in order to impose a load on the right side, the nodes are not marked.
The detail codes are shown as follows:
\begin{cpp}
auto & blocked = model.getBlockedDOFs();
const auto & pos = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
for (UInt node = 0; node < nb_nodes; ++node) {
if(Math::are_float_equal(pos(node, _x), 0)) {
blocked(node, _x) = true; // block dof in x-direction
blocked(node, _y) = true; // block dof in y-direction
disp(node, _x) = 0.; // fixed displacement in x-direction
disp(node, _y) = 0.; // fixed displacement in y-direction
} else if (Math::are_float_equal(pos(node, _y), 0)) {
blocked(node, _x) = false; // unblock dof in x-direction
forces(node, _x) = 10.; // force in x-direction
}
}
\end{cpp}
\begin{figure}[!htb]
\centering
\includegraphics[scale=0.4]{figures/dirichlet}
\caption{Beam with fixed support and load.\label{fig:smm:dirichlet_bc}}
\end{figure}
For the more advanced approach, one needs the notion of a boundary in
the mesh. Therefore, the boundary should be created before boundary
condition functors can be applied. Generally the boundary can be
specified from the mesh file or the geometry. For the first case, the
function \code{createGroupsFromMeshData} is called. This function
can read any types of mesh data which are provided in the mesh
file. If the mesh file is created with Gmsh, the function takes one
input strings which is either \code{tag\_0}, \code{tag\_1} or
\code{physical\_names}. The first two tags are assigned by Gmsh to
each element which shows the physical group that they belong to. In
Gmsh, it is also possible to consider strings for different groups of
elements. These elements can be separated by giving a string
\code{physical\_names} to the function
\code{createGroupsFromMeshData}:
\begin{cpp}
mesh.createGroupsFromMeshData<std::string>("physical_names").
\end{cpp}
Boundary conditions support can also be
created from the geometry by calling
\code{createBoundaryGroupFromGeometry}. This function gathers all the
elements on the boundary of the geometry.
To apply the required boundary conditions, the function \code{applyBC}
needs to be called on a \code{SolidMechanicsModel}. This function
gets a Dirichlet or Neumann functor and a string which specifies the
desired boundary on which the boundary conditions is to be
applied. The functors specify the type of conditions to apply. Three
built-in functors for Dirichlet exist: \code{FlagOnly, FixedValue,}
and \code{IncrementValue}. The functor \code{FlagOnly} is used if a
point is fixed in a given direction. Therefore, the input parameter to
this functor is only the fixed direction. The \code{FixedValue}
functor is used when a displacement value is applied in a fixed
direction. The \code{IncrementValue} applies an increment to the
displacement in a given direction. The following code shows the
utilization of three functors for the top, bottom and side surface of
the mesh which were already defined in the Gmsh file:
\begin{cpp}
model.applyBC(BC::Dirichlet::FixedValue(13.0, _y), "Top");
model.applyBC(BC::Dirichlet::FlagOnly(_x), "Bottom");
model.applyBC(BC::Dirichlet::IncrementValue(13.0, _x), "Side");
\end{cpp}
To apply a Neumann boundary condition, the applied traction or stress
should be specified before. In case of specifying the traction on the
surface, the functor \code{FromTraction} of Neumann boundary
conditions is called. Otherwise, the functor \code{FromStress} should
be called which gets the stress tensor as an input parameter.
\begin{cpp}
Vector<Real> surface_traction = {0., 0., 1.};
auto surface_stress(3, 3) = Matrix<Real>::eye(3);
model.applyBC(BC::Neumann::FromTraction(surface_traction), "Bottom");
model.applyBC(BC::Neumann::FromStress(surface_stress), "Top");
\end{cpp}
If the boundary conditions need to be removed during the simulation, a
functor is called from the Neumann boundary condition to free those
boundary conditions from the desired boundary.
\begin{cpp}
model.applyBC(BC::Neumann::FreeBoundary(), "Side");
\end{cpp}
User specified functors can also be implemented. A full example for
setting both initial and boundary conditions can be found in
\shellcode{\examplesdir/boundary\_conditions.cc}. The problem solved
in this example is shown in Fig.~\ref{fig:smm:bc_and_ic}. It consists
of a plate that is fixed with movable supports on the left and bottom
side. On the right side, a traction, which increases linearly with the
number of time steps, is applied. The initial displacement and
velocity in $x$-direction at all free nodes is zero and two
respectively.
\begin{figure}[!htb]
\centering
\includegraphics[scale=0.8]{figures/bc_and_ic_example}
\caption{Plate on movable supports.\label{fig:smm:bc_and_ic}}
\end{figure}
As it is mentioned in Section \ref{sect:common:groups}, node and
element groups can be used to assign the boundary conditions. A
generic example is given below with a Dirichlet boundary condition.
\begin{cpp}
// create a node group
NodeGroup & node_group = mesh.createNodeGroup("nodes_fix");
/*
fill the node group with the nodes you want
*/
// create an element group using the existing node group
mesh.createElementGroupFromNodeGroup("el_fix", "nodes_fix", spatial_dimension-1);
// boundary condition can be applied using the element group name
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "el_fix");
\end{cpp}
\subsection{Material Selector\label{sect:smm:materialselector}}
If the user wants to assign different materials to different
finite elements groups in \akantu, a material selector has to be
used. By default, \akantu assigns the first valid material in the
material file to all elements present in the model (regular continuum
materials are assigned to the regular elements and cohesive materials
are assigned to cohesive elements or element facets).
To assign different materials to specific elements, mesh data
information such as tag information or specified physical names can be
used. \code{MeshDataMaterialSelector} class uses this information to
assign different materials. With the proper physical name or tag name
and index, different materials can be assigned as demonstrated in the
examples below.
\begin{cpp}
auto mat_selector = std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names", model);
model.setMaterialSelector(mat_selector);
\end{cpp}
In this example the physical names specified in a GMSH geometry file will by
used to match the material names in the input file.
Another example would be to use the first (\code{tag\_0}) or the second
(\code{tag\_1}) tag associated to each elements in the mesh:
\begin{cpp}
auto mat_selector = std::make_shared<MeshDataMaterialSelector<UInt>>(
"tag_1", model, first_index);
model.setMaterialSelector(*mat_selector);
\end{cpp}
where \code{first\_index} (default is 1) is the value of \code{tag\_1} that will
be associated to the first material in the material input file. The following
values of the tag will be associated with the following materials.
There are four different material selectors pre-defined in
\akantu. \code{MaterialSelector} and \code{DefaultMaterialSelector} is
used to assign a material to regular elements by default. For the
regular elements, as in the example above,
\code{MeshDataMaterialSelector} can be used to assign different
materials to different elements.
Apart from the \akantu's default material selectors, users can always
develop their own classes in the main code to tackle various
multi-material assignment situations.
% An application of \code{DefaultMaterialCohesiveSelector} and usage in
% a customly generated material selector class can be seen in
% \shellcode{\examplesdir/cohesive\_element/cohesive\_extrinsic\_IG\_TG/cohesive\_extrinsic\_IG\_TG.cc}.
\IfFileExists{manual-cohesive_elements_insertion.tex}{\input{manual-cohesive_elements_insertion}}{}
\section{Static Analysis\label{sect:smm:static}}
The \code{SolidMechanicsModel} class can handle different analysis
methods, the first one being presented is the static case. In this
case, the equation to solve is
\begin{equation}
\label{eqn:smm:static} \mat{K} \vec{u} =
\vec{f}_{\st{ext}}
\end{equation}
where $\mat{K}$ is the global stiffness matrix, $\vec{u}$ the
displacement vector and $\vec{f}_{\st{ext}}$ the vector of external
forces applied to the system.
To solve such a problem, the static solver of the
\code{SolidMechanicsModel}\index{SolidMechanicsModel} object is used.
First, a model has to be created and initialized. To create the
model, a mesh (which can be read from a file) is needed, as explained
in Section~\ref{sect:common:mesh}. Once an instance of a
\code{SolidMechanicsModel} is obtained, the easiest way to initialize
it is to use the \code{initFull}\index{SolidMechanicsModel!initFull}
method by giving the \code{SolidMechanicsModelOptions}. These options
specify the type of analysis to be performed and whether the materials
should be initialized with \code{initMaterials} or not.
\begin{cpp}
SolidMechanicsModel model(mesh);
model.initFull(_analysis_method = _static);
\end{cpp}
Here, a static analysis is chosen by passing the argument
\code{\_static} to the method. By default, the Boolean for no
initialization of the materials is set to false, so that they are
initialized during the \code{initFull}. The method \code{initFull}
also initializes all appropriate vectors to zero. Once the model is
created and initialized, the boundary conditions can be set as
explained in Section~\ref{sect:smm:boundary}. Boundary conditions
will prescribe the external forces for some free degrees of freedom
$\vec{f}_{\st{ext}}$ and displacements for some others. At this point
of the analysis, the function
\code{solveStep}\index{SolidMechanicsModel!solveStep} can be called:
\begin{cpp}
model.solveStep<_scm_newton_raphson_tangent_modified, SolveConvergenceCriteria::_residual>(1e-4, 1);
\end{cpp}
This function is templated by the solving method and the convergence
criterion and takes two arguments: the tolerance and the maximum
number of iterations (100 by default), which are $\num{1e-4}$ and $1$ for this example. The
modified Newton-Raphson method is chosen to solve the system. In this
method, the equilibrium equation (\ref{eqn:smm:static}) is modified in
order to apply a Newton-Raphson convergence algorithm:
\begin{align}\label{eqn:smm:static-newton-raphson}
\mat{K}^{i+1}\delta\vec{u}^{i+1} &= \vec{r} \\
&= \vec{f}_{\st{ext}} -\vec{f}_{\st{int}}\\
&= \vec{f}_{\st{ext}} - \mat{K}^{i} \vec{u}^{i}\\
\vec{u}^{i+1} &= \vec{u}^{i} + \delta\vec{u}^{i+1}~,\nonumber
\end{align}
where $\delta\vec{u}$ is the increment of displacement to be added
from one iteration to the other, and $i$ is the Newton-Raphson
iteration counter. By invoking the \code{solveStep} method in the
first step, the global stiffness matrix $\mat{K}$ from
Equation~(\ref{eqn:smm:static}) is automatically assembled. A
Newton-Raphson iteration is subsequently started, $\mat{K}$ is updated
according to the displacement computed at the previous iteration and
one loops until the forces are balanced (\code{SolveConvergenceCriteria::\_residual}), \ie
$||\vec{r}|| < \mbox{\code{SolveConvergenceCriteria::\_residual}}$. One can also iterate
until the increment of displacement is zero (\code{SolveConvergenceCriteria::\_increment})
which also means that the equilibrium is found. For a linear elastic
problem, the solution is obtained in one iteration and therefore the
maximum number of iterations can be set to one. But for a non-linear
case, one needs to iterate as long as the norm of the residual exceeds
the tolerance threshold and therefore the maximum number of iterations
has to be higher, e.g. $100$:
\begin{cpp}
model.solveStep<_scm_newton_raphson_tangent_modified,SolveConvergenceCriteria::_residual>(1e-4, 100)
\end{cpp}
At the end of the analysis, the final solution is stored in the
\textbf{displacement} vector. A full example of how to solve a static
problem is presented in the code \code{\examplesdir/static/static.cc}.
This example is composed of a 2D plate of steel, blocked with rollers
on the left and bottom sides as shown in Figure \ref{fig:smm:static}.
The nodes from the right side of the sample are displaced by $0.01\%$
of the length of the plate.
\begin{figure}[!htb]
\centering
\includegraphics[scale=1.05]{figures/static}
\caption{Numerical setup\label{fig:smm:static}}
\end{figure}
The results of this analysis is depicted in
Figure~\ref{fig:smm:implicit:static_solution}.
\begin{figure}[!htb]
\centering
\includegraphics[width=.7\linewidth]{figures/static_analysis}
\caption{Solution of the static analysis. Left: the initial
condition, right: the solution (deformation magnified 50 times)}
\label{fig:smm:implicit:static_solution}
\end{figure}
\subsection{Static implicit analysis with dynamic insertion of cohesive elements}
In order to solve problems with the extrinsic cohesive method in the
static implicit solution scheme, the function \code{solveStepCohesive}
has to be used:
\begin{cpp}
model.solveStepCohesive<_scm_newton_raphson_tangent, SolveConvergenceCriteria::_increment>(1e-13, error, 25, false, 1e5, true);
\end{cpp}
in which the arguments are: tolerance, error, max\_iteration,
load\_reduction, tol\_increase\_factor, do\_not\_factorize. This
function, first applies the Newton-Raphson procedure to solve the
problem. Then, it calls the method \code{checkCohesiveStress} to
check if cohesive elements have to be inserted. Since the approach is
implicit, only one element is added, the most stressed one (see
Section \ref{extrinsic_insertion}). After insertion, the
Newton-Raphson procedure is applied again to solve the same
incremental loading step, with the new inserted cohesive element. The
procedure loops in this way since no new cohesive elements have to be
inserted. At that point, the solution is saved, and the simulation
can advance to the next incremental loading step. In case the
convergence is not reached, the obtained solution is not saved and the
simulation return to the main file with the error given by the
solution saved in the argument of the function \emph{error}. In this
way, the user can intervene in the simulation in order to find anyhow
convergence. A possibility is, for instance, to reduce the last
incremental loading step. The variable \emph{load\_reduction} can be
used to identify if the load has been already reduced or not. At the
same time, with the variable \emph{tol\_increase\_factor} it is
possible to increase the tolerance by a factor defined by the user in
the main file, in order to accept a solution even with an error bigger
than the tolerance set at the beginning. It is possible to increase
the tolerance only in the phase of loading reduction, i.e., when
load\_reduction = true. A not converged solution is never saved. In
case the convergence is not reached even after the loading reduction
procedure, the displacement field is not updated and remains the one
of the last converged incremental steps. Also, cohesive elements are
inserted only if convergence is reached. An example of the extrinsic
cohesive method in the static implicit solution scheme is presented in
\shellcode{\examplesdir/cohesive\_element/cohesive\_extrinsic\_implicit}.
\section{Dynamic Methods} \label{sect:smm:Dynamic_methods}
Different ways to solve the equations of motion are implemented in the
solid mechanics model. The complete equations that should be solved
are:
\begin{equation}
\label{eqn:equation-motion}
\mat{M}\ddot{\vec{u}} +
\mat{C}\dot{\vec{u}} + \mat{K}\vec{u} = \vec{f}_{\st{ext}}~,
\end{equation}
where $\mat{M}$, $\mat{C}$ and $\mat{K}$ are the mass,
damping and stiffness matrices, respectively.
In the previous section, it has already been discussed how to solve this
equation in the static case, where $\ddot{\vec{u}} = \dot{\vec{u}} = 0$. Here
the method to solve this equation in the general case will be presented. For
this purpose, a time discretization has to be specified. The most common
discretization method in solid mechanics is the Newmark-$\beta$ method, which is
also the default in \akantu.
For the Newmark-$\beta$ method, (\ref{eqn:equation-motion}) becomes a
system of three equations (see \cite{curnier92a} \cite{hughes-83a} for
more details):
\begin{align}
\mat{M} \ddot{\vec{u}}_{n+1} + \mat{C}\dot{\vec{u}}_{n+1} + \mat{K} \vec{u}_{n+1} &={\vec{f}_{\st{ext}}}_{\, n+1}
\label{eqn:equation-motion-discret} \\
\vec{u}_{n+1} &=\vec{u}_{n} + \left(1 - \alpha\right) \Delta t \dot{\vec{u}}_{n} +
\alpha \Delta t \dot{\vec{u}}_{n+1} + \left(\frac{1}{2} -
\alpha\right) \Delta t^2
\ddot{\vec{u}}_{n} \label{eqn:finite-difference-1}\\
\dot{\vec{u}}_{n+1} &= \dot{\vec{u}}_{n} + \left(1 - \beta\right)
\Delta t \ddot{\vec{u}}_{n} + \beta \Delta t
\ddot{\vec{u}}_{n+1} \label{eqn:finite-difference-2}
\end{align}
In these new equations, $\ddot{\vec{u}}_{n}$, $\dot{\vec{u}}_{n}$ and
$\vec{u}_{n}$ are the approximations of $\ddot{\vec{u}}(t_n)$,
$\dot{\vec{u}}(t_n)$ and $\vec{u}(t_n)$.
Equation~(\ref{eqn:equation-motion-discret}) is the equation of motion
discretized in space (finite-element discretization), and equations
(\ref{eqn:finite-difference-1}) and (\ref{eqn:finite-difference-2})
are discretized in both space and time (Newmark discretization). The
$\alpha$ and $\beta$ parameters determine the stability and the
accuracy of the algorithm. Classical values for $\alpha$ and $\beta$
are usually $\beta = 1/2$ for no numerical damping and $0 < \alpha <
1/2$.
\begin{center}
\begin{tabular}{cll}
\toprule
$\alpha$ & Method ($\beta = 1/2$) & Type\\
\midrule
$0$ & central difference & explicit\\
$1/6$ & Fox-Goodwin (royal road) &implicit\\
$1/3$ & Linear acceleration &implicit\\
$1/2$ & Average acceleration (trapezoidal rule)& implicit\\
\bottomrule
\end{tabular}
\end{center}
The solution of this system of equations,
(\ref{eqn:equation-motion-discret})-(\ref{eqn:finite-difference-2}) is
split into a predictor and a corrector system of equations. Moreover,
in the case of a non-linear equations, an iterative algorithm such as
the Newton-Raphson method is applied. The system of equations can be
written as:
\begin{enumerate}
\item \textit{Predictor:}
\begin{align}
\vec{u}_{n+1}^{0} &= \vec{u}_{n} + \Delta t
\dot{\vec{u}}_{n} + \frac{\Delta t^2}{2} \ddot{\vec{u}}_{n} \\
\dot{\vec{u}}_{n+1}^{0} &= \dot{\vec{u}}_{n} + \Delta t
\ddot{\vec{u}}_{n} \\
\ddot{\vec{u}}_{n+1}^{0} &= \ddot{\vec{u}}_{n}
\end{align}
\item \textit{Solve:}
\begin{align}
\left(c \mat{M} + d \mat{C} + e \mat{K}_{n+1}^i\right)
\vec{w} = {\vec{f}_{\st{ext}}}_{\,n+1} - {\vec{f}_{\st{int}}}_{\,n+1}^i -
\mat{C} \dot{\vec{u}}_{n+1}^i - \mat{M} \ddot{\vec{u}}_{n+1}^i = \vec{r}_{n+1}^i
\end{align}
\item \textit{Corrector:}
\begin{align}
\ddot{\vec{u}}_{n+1}^{i+1} &= \ddot{\vec{u}}_{n+1}^{i} +c \vec{w} \\
\dot{\vec{u}}_{n+1}^{i+1} &= \dot{\vec{u}}_{n+1}^{i} + d\vec{w} \\
\vec{u}_{n+1}^{i+1} &= \vec{u}_{n+1}^{i} + e \vec{w}
\end{align}
\end{enumerate}
where $i$ is the Newton-Raphson iteration counter and $c$, $d$ and $e$
are parameters depending on the method used to solve the equations
\begin{center}
\begin{tabular}{lcccc}
\toprule
& $\vec{w}$ & $e$ & $d$ & $c$\\
\midrule
in acceleration &$ \delta\ddot{\vec{u}}$ & $\alpha \beta\Delta t^2$ &$\beta \Delta t$ &$1$\\
in velocity & $ \delta\dot{\vec{u}}$& $\alpha\Delta t$ & $1$ & $\frac{1}{\beta \Delta t}$\\
in displacement &$\delta\vec{u}$ & $ 1$ & $\frac{1}{\alpha \Delta t}$ & $\frac{1}{\alpha \beta \Delta t^2}$\\
\bottomrule
\end{tabular}
\end{center}
% \note{If you want to use the implicit solver \akantu should be compiled at
% least with one sparse matrix solver such as Mumps\cite{mumps}.}
\subsection{Implicit Time Integration}
To solve a problem with an implicit time integration scheme, first a
\code{SolidMechanicsModel} object has to be created and initialized.
Then the initial and boundary conditions have to be set. Everything
is similar to the example in the static case
(Section~\ref{sect:smm:static}), however, in this case the implicit
dynamic scheme is selected at the initialization of the model.
\begin{cpp}
SolidMechanicsModel model(mesh);
model.initFull(_analysis_method = _implicit_dynamic);
/*Boundary conditions see Section ~ %\ref{sect:smm:boundary}% */
\end{cpp}
Because a dynamic simulation is conducted, an integration time step
$\Delta t$ has to be specified. In the case of implicit simulations,
\akantu implements a trapezoidal rule by default. That is to say
$\alpha = 1/2$ and $\beta = 1/2$ which is unconditionally
stable. Therefore the value of the time step can be chosen arbitrarily
within reason. \index{SolidMechanicsModel!setTimeStep}
\begin{cpp}
model.setTimeStep(time_step);
\end{cpp}
Since the system has to be solved for a given amount of time steps, the
method \code{solveStep()}, (which has already been used in the static
example in Section~\ref{sect:smm:static}), is called inside a time
loop:
\begin{cpp}
/// time loop
Real time = 0.;
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", 100);
solver.set("threshold", 1e-12);
solver.set("convergence_type", SolveConvergenceCriteria::_solution);
for (UInt s = 1; time <max_time; ++s, time += time_step) {
model.solveStep();
}
\end{cpp}
An example of solid mechanics with an implicit time integration scheme
is presented in
\shellcode{\examplesdir/implicit/implicit\_dynamic.cc}. This example
consists of a 3D beam of
$\SI{10}{\metre}\,\times\,\SI{1}{\metre}\,\times\,\SI{1}{\metre}$
blocked on one side and is on a roller on the other side. A constant
force of \SI{5}{\kilo\newton} is applied in its middle.
Figure~\ref{fig:smm:implicit:dynamic} presents the geometry of this
case. The material used is a fictitious linear elastic material with a
density of \SI{1000}{\kilo\gram\per\cubic\metre}, a Young's Modulus of
\SI{120}{\mega\pascal} and Poisson's ratio of $0.3$. These values
were chosen to simplify the analytical solution.
An approximation of the dynamic response of the middle point of the
beam is given by:
\begin{equation}
\label{eqn:smm:implicit}
u\left(\frac{L}{2}, t\right)
= \frac{1}{\pi^4} \left(1 - cos\left(\pi^2 t\right) +
\frac{1}{81}\left(1 - cos\left(3^2 \pi^2 t\right)\right) +
\frac{1}{625}\left(1 - cos\left(5^2 \pi^2 t\right)\right)\right)
\end{equation}
\begin{figure}[!htb]
\centering
\includegraphics[scale=.6]{figures/implicit_dynamic}
\caption{Numerical setup}
\label{fig:smm:implicit:dynamic}
\end{figure}
Figure \ref{fig:smm:implicit:dynamic_solution} presents the deformed
beam at 3 different times during the simulation: time steps 0, 1000 and
2000.
\begin{figure}[!htb]
\centering
\setlength{\unitlength}{0.1\textwidth}
\begin{tikzpicture}
\node[above right] (img) at (0,0)
{\includegraphics[width=.6\linewidth]{figures/dynamic_analysis}};
\node[left] at (0pt,20pt) {$0$}; \node[left] at (0pt,60pt) {$1000$};
\node[left] at (0pt,100pt) {$2000$};
\end{tikzpicture}
\caption{Deformed beam at 3 different times (displacement are
magnified by a factor 10).}
\label{fig:smm:implicit:dynamic_solution}
\end{figure}
\subsection{Explicit Time Integration}
\label{ssect:smm:expl-time-integr}
The explicit dynamic time integration scheme is based on the
Newmark-$\beta$ scheme with $\alpha=0$ (see equations
\ref{eqn:equation-motion-discret}-\ref{eqn:finite-difference-2}). In
\akantu, $\beta$ is defaults to $\beta=1/2$, see section
\ref{sect:smm:Dynamic_methods}.
The initialization of the simulation is similar to the static and
implicit dynamic version. The model is created from the
\code{SolidMechanicsModel} class. In the initialization, the explicit
scheme is selected using the \code{\_explicit\_lumped\_mass} constant.
\begin{cpp}
SolidMechanicsModel model(mesh);
model.initFull(_analysis_method = _explicit_lumped_mass);
\end{cpp}
\index{SolidMechanicsModel!initFull}
\note{Writing \code{model.initFull()} or \code{model.initFull();} is
equivalent to use the \code{\_explicit\_lumped\_mass} keyword, as this
is the default case.}
The explicit time integration scheme implemented in \akantu uses a
lumped mass matrix $\mat{M}$ (reducing the computational cost). This
matrix is assembled by distributing the mass of each element onto its
nodes. The resulting $\mat{M}$ is therefore a diagonal matrix stored
in the \textbf{mass} vector of the model.
The explicit integration scheme is conditionally stable. The time step
has to be smaller than the stable time step which is obtained in
\akantu as follows:
\begin{cpp}
critical_time_step = model.getStableTimeStep();
\end{cpp} \index{SolidMechanicsModel!StableTimeStep}
The stable time step corresponds to the time the fastest wave (the compressive
wave) needs to travel the characteristic length of the mesh:
\begin{equation}
\label{eqn:smm:explicit:stabletime}
\Delta t_{\st{crit}} = \frac{\Delta x}{c}
\end{equation}
where $\Delta x$ is a characteristic length (\eg the inradius in the case of
linear triangle element) and $c$ is the celerity of the fastest wave in the
material. It is generally the compressive wave of celerity
$c = \sqrt{\frac{2 \mu + \lambda}{\rho}}$, $\mu$ and $\lambda$ are the first and
second Lame's coefficients and $\rho$ is the density. However, it is recommended
to impose a time step that is smaller than the stable time step, for instance,
by multiplying the stable time step by a safety factor smaller than one.
\begin{cpp}
const Real safety_time_factor = 0.8;
Real applied_time_step = critical_time_step * safety_time_factor;
model.setTimeStep(applied_time_step);
\end{cpp}
\index{SolidMechanicsModel!setTimeStep} The initial displacement and
velocity fields are, by default, equal to zero if not given
specifically by the user (see \ref{sect:smm:initial_condition}).
Like in implicit dynamics, a time loop is used in which the
displacement, velocity and acceleration fields are updated at each
time step. The values of these fields are obtained from the
Newmark$-\beta$ equations with $\beta=1/2$ and $\alpha=0$. In \akantu
these computations at each time step are invoked by calling the
function \code{solveStep}:
\begin{cpp}
for (UInt s = 1; (s-1)*applied_time_step < total_time; ++s) {
model.solveStep();
}
\end{cpp} \index{SolidMechanicsModel!solveStep}
The method
\code{solveStep} wraps the four following functions:
\begin{itemize}
\item \code{model.explicitPred()} allows to compute the displacement
field at $t+1$ and a part of the velocity field at $t+1$, denoted by
$\vec{\dot{u}^{\st{p}}}_{n+1}$, which will be used later in the method
\code{model.explicitCorr()}. The equations are:
\begin{align}
\vec{u}_{n+1} &= \vec{u}_{n} + \Delta t
\vec{\dot{u}}_{n} + \frac{\Delta t^2}{2} \vec{\ddot{u}}_{n}\\
\vec{\dot{u}^{\st{p}}}_{n+1} &= \vec{\dot{u}}_{n} + \Delta t
\vec{\ddot{u}}_{n}
\label{eqn:smm:explicit:onehalfvelocity}
\end{align}
\item \code{model.updateResidual()} and
\code{model.updateAcceleration()} compute the acceleration increment
$\delta \vec{\ddot{u}}$:
\begin{equation}
\left(\mat{M} + \frac{1}{2} \Delta t \mat{C}\right)
\delta \vec{\ddot{u}} = \vec{f_{\st{ext}}} - \vec{f}_{\st{int}\, n+1}
- \mat{C} \vec{\dot{u}^{\st{p}}}_{n+1} - \mat{M} \vec{\ddot{u}}_{n}
\end{equation}
\note{The internal force $\vec{f}_{\st{int}\, n+1}$ is computed from
the displacement $\vec{u}_{n+1}$ based on the constitutive law.}
\item \code{model.explicitCorr()} computes the velocity and
acceleration fields at $t+1$:
\begin{align}
\vec{\dot{u}}_{n+1} &= \vec{\dot{u}^{\st{p}}}_{n+1} + \frac{\Delta t}{2}
\delta \vec{\ddot{u}} \\ \vec{\ddot{u}}_{n+1} &=
\vec{\ddot{u}}_{n} + \delta \vec{\ddot{u}}
\end{align}
\end{itemize}
The use of an explicit time integration scheme is illustrated by the
example:\par
\noindent \shellcode{\examplesdir/explicit/explicit\_dynamic.cc}\par
\noindent This example models the propagation of a wave in a steel beam. The
beam and the applied displacement in the $x$ direction are shown in
Figure~\ref{fig:smm:explicit}.
\begin{figure}[!htb] \centering
\begin{tikzpicture}
\coordinate (c) at (0,2);
\draw[shift={(c)},thick, color=blue] plot [id=x, domain=-5:5, samples=50] ({\x, {(40 * sin(0.1*pi*3*\x) * exp(- (0.1*pi*3*\x)*(0.1*pi*3*\x) / 4))}});
\draw[shift={(c)},-latex] (-6,0) -- (6,0) node[right, below] {$x$};
\draw[shift={(c)},-latex] (0,-0.7) -- (0,1) node[right] {$u$};
\draw[shift={(c)}] (-0.1,0.6) node[left] {$A$}-- (1.5,0.6);
\coordinate (l) at (0,0.6);
\draw[shift={(0,-0.7)}] (-5, 0) -- (5,0) -- (5, 1) -- (-5, 1) -- cycle;
\draw[shift={(l)}, latex-latex] (-5,0)-- (5,0) node [midway, above] {$L$};
\draw[shift={(l)}] (5,0.2)-- (5,-0.2);
\draw[shift={(l)}] (-5,0.2)-- (-5,-0.2);
\coordinate (h) at (5.3,-0.7);
\draw[shift={(h)}, latex-latex] (0,0)-- (0,1) node [midway, right] {$h$};
\draw[shift={(h)}] (-0.2,1)-- (0.2,1);
\draw[shift={(h)}] (-0.2,0)-- (0.2,0);
\end{tikzpicture}
\caption{Numerical setup \label{fig:smm:explicit}}
\end{figure}
The length and height of the beam are $L=\SI{10}{\metre}$ and
$h = \SI{1}{\metre}$, respectively. The material is linear elastic,
homogeneous and isotropic (density:
\SI{7800}{\kilo\gram\per\cubic\metre}, Young's modulus:
\SI{210}{\giga\pascal} and Poisson's ratio: $0.3$). The imposed
displacement follow a Gaussian function with a maximum amplitude of $A = \SI{0.01}{\meter}$. The
potential, kinetic and total energies are computed. The safety factor
is equal to $0.8$.
\input{manual-constitutive-laws}
\section{Adding a New Constitutive Law}\index{Material!create a new
material}
There are several constitutive laws in \akantu as described in the
previous Section~\ref{sect:smm:CL}. It is also possible to use a
user-defined material for the simulation. These materials are referred
to as local materials since they are local to the example of the user
and not part of the \akantu library. To define a new local material,
two files (\code {material\_XXX.hh} and \code{material\_XXX.cc}) have
to be provided where \code{XXX} is the name of the new material. The
header file \code {material\_XXX.hh} defines the interface of your
custom material. Its implementation is provided in the
\code{material\_XXX.cc}. The new law must inherit from the
\code{Material} class or any other existing material class. It is
therefore necessary to include the interface of the parent material
in the header file of your local material and indicate the inheritance
in the declaration of the class:
\begin{cpp}
/* ---------------------------------------------------------------------- */
#include "material.hh"
/* ---------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_XXX_HH__
#define __AKANTU_MATERIAL_XXX_HH__
namespace akantu {
class MaterialXXX : public Material {
/// declare here the interface of your material
};
\end{cpp}
In the header file the user also needs to declare all the members of the new
material. These include the parameters that a read from the
material input file, as well as any other material parameters that will be
computed during the simulation and internal variables.
In the following the example of adding a new damage material will be
presented. In this case the parameters in the material will consist of the
Young's modulus, the Poisson coefficient, the resistance to damage and the
damage threshold. The material will then from these values compute its Lam\'{e}
coefficients and its bulk modulus. Furthermore, the user has to add a new
internal variable \code{damage} in order to store the amount of damage at each
quadrature point in each step of the simulation. For this specific material the
member declaration inside the class will look as follows:
\begin{cpp}
class LocalMaterialDamage : public Material {
/// declare constructors/destructors here
/// declare methods and accessors here
/* -------------------------------------------------------------------- */
/* Class Members */
/* -------------------------------------------------------------------- */
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
private:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lame coefficient
Real lambda;
/// Second Lame coefficient (shear modulus)
Real mu;
/// resistance to damage
Real Yd;
/// damage threshold
Real Sd;
/// Bulk modulus
Real kpa;
/// damage internal variable
InternalField<Real> damage;
};
\end{cpp}
In order to enable to print the material parameters at any point in
the user's example file using the standard output stream by typing:
\begin{cpp}
for (UInt m = 0; m < model.getNbMaterials(); ++m)
std::cout << model.getMaterial(m) << std::endl;
\end{cpp}
the standard output stream operator has to be redefined. This should be done at the end of the header file:
\begin{cpp}
class LocalMaterialDamage : public Material {
/// declare here the interace of your material
}:
/* ---------------------------------------------------------------------- */
/* inline functions */
/* ---------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const LocalMaterialDamage & _this)
{
_this.printself(stream);
return stream;
}
\end{cpp}
However, the user still needs to register the material parameters that
should be printed out. The registration is done during the call of the
constructor. Like all definitions the implementation of the
constructor has to be written in the \code{material\_XXX.cc}
file. However, the declaration has to be provided in the
\code{material\_XXX.hh} file:
\begin{cpp}
class LocalMaterialDamage : public Material {
/* -------------------------------------------------------------------- */
/* Constructors/Destructors */
/* -------------------------------------------------------------------- */
public:
LocalMaterialDamage(SolidMechanicsModel & model, const ID & id = "");
};
\end{cpp}
The user can now define the implementation of the constructor in the
\code{material\_XXX.cc} file:
\begin{cpp}
/* ---------------------------------------------------------------------- */
#include "local_material_damage.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* ---------------------------------------------------------------------- */
LocalMaterialDamage::LocalMaterialDamage(SolidMechanicsModel & model,
const ID & id) :
Material(model, id),
damage("damage", *this) {
AKANTU_DEBUG_IN();
this->registerParam("E", E, 0., _pat_parsable, "Young's modulus");
this->registerParam("nu", nu, 0.5, _pat_parsable, "Poisson's ratio");
this->registerParam("lambda", lambda, _pat_readable, "First Lame coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lame coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
this->registerParam("Yd", Yd, 50., _pat_parsmod);
this->registerParam("Sd", Sd, 5000., _pat_parsmod);
damage.initialize(1);
AKANTU_DEBUG_OUT();
}
\end{cpp}
During the intializer list the reference to the model and the material id are
assigned and the constructor of the internal field is called. Inside the scope
of the constructor the internal values have to be initialized and the
parameters, that should be printed out, are registered with the function:
\code{registerParam}\index{Material!registerParam}:
\begin{cpp}
void registerParam(name of the parameter (key in the material file),
member variable,
default value (optional parameter),
access permissions,
description);
\end{cpp}
The available access permissions are as follows:
\begin{itemize}
\item \code{\_pat\_internal}: Parameter can only be output when the material is printed.
\item \code{\_pat\_writable}: User can write into the parameter. The parameter is output when the material is printed.
\item \code{\_pat\_readable}: User can read the parameter. The parameter is output when the material is printed.
\item \code{\_pat\_modifiable}: Parameter is writable and readable.
\item \code{\_pat\_parsable}: Parameter can be parsed, \textit{i.e.} read from the input file.
\item \code{\_pat\_parsmod}: Parameter is modifiable and parsable.
\end{itemize}
In order to implement the new constitutive law the user needs to
specify how the additional material parameters, that are not
defined in the input material file, should be calculated. Furthermore,
it has to be defined how stresses and the stable time step should be
computed for the new local material. In the case of implicit
simulations, in addition, the computation of the tangent stiffness needs
to be defined. Therefore, the user needs to redefine the following
functions of the parent material:
\begin{cpp}
void initMaterial();
// for explicit and implicit simulations void
computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
// for implicit simulations
-void computeTangentStiffness(const ElementType & el_type,
+void computeTangentStiffness(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
// for explicit and implicit simulations
Real getStableTimeStep(Real h, const Element & element);
\end{cpp}
In the following a detailed description of these functions is provided:
\begin{itemize}
\item \code{initMaterial}:~ This method is called after the material
file is fully read and the elements corresponding to each material
are assigned. Some of the frequently used constant parameters are
calculated in this method. For example, the Lam\'{e} constants of
elastic materials can be considered as such parameters.
\item \code{computeStress}:~ In this method, the stresses are
computed based on the constitutive law as a function of the strains of the
quadrature points. For example, the stresses for the elastic
material are calculated based on the following formula:
\begin{equation}
\label{eqn:smm:constitutive_elastic}
\mat{\sigma } =\lambda\mathrm{tr}(\mat{\varepsilon})\mat{I}+2 \mu \mat{\varepsilon}
\end{equation}
Therefore, this method contains a loop on all quadrature points
assigned to the material using the two macros:\par
\code{MATERIAL\_STRESS\_QUADRATURE\_POINT\_LOOP\_BEGIN}\par
\code{MATERIAL\_STRESS\_QUADRATURE\_POINT\_LOOP\_END}
\begin{cpp}
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(element_type);
// sigma <- f(grad_u)
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
\end{cpp}
\note{The strain vector in \akantu contains the values of $\nabla
\vec{u}$, i.e. it is really the \emph{displacement gradient},}
\item \code{computeTangentStiffness}:~ This method is called when
the tangent to the stress-strain curve is desired (see Fig \ref
{fig:smm:AL:K}). For example, it is called in the implicit solver
when the stiffness matrix for the regular elements is assembled
based on the following formula:
\begin{equation}
\label{eqn:smm:constitutive_elasc} \mat{K }
=\int{\mat{B^T}\mat{D(\varepsilon)}\mat{B}}
\end{equation}
Therefore, in this method, the \code{tangent} matrix (\mat{D}) is
computed for a given strain.
\note{ The \code{tangent} matrix is a $4^{th}$ order tensor which is
stored as a matrix in Voigt notation.}
\begin{figure}[!htb]
\begin{center}
\includegraphics[width=0.4\textwidth,keepaspectratio=true]{figures/tangent.pdf}
\caption{Tangent to the stress-strain curve.}
\label{fig:smm:AL:K}
\end{center}
\end{figure}
\item \code{getCelerity}:~The stability criterion of the explicit integration scheme depend on the fastest wave celerity~\eqref{eqn:smm:explicit:stabletime}. This celerity depend on the material, and therefore the value of this velocity should be defined in this method for each new material. By default, the fastest wave speed is the compressive wave whose celerity can be defined in~\code{getPushWaveSpeed}.
\end{itemize}
Once the declaration and implementation of the new material has been
completed, this material can be used in the user's example by including the header file:
\begin{cpp}
#include "material_XXX.hh"
\end{cpp}
For existing materials, as mentioned in Section~\ref{sect:smm:CL}, by
default, the materials are initialized inside the method
\code{initFull}. If a local material should be used instead, the
initialization of the material has to be postponed until the local
material is registered in the model. Therefore, the model is
initialized with the boolean for skipping the material initialization
equal to true:
\begin{cpp}
/// model initialization
model.initFull(_analysis_method = _explicit_lumped_mass);
\end{cpp}
Once the model has been initialized, the local material needs
to be registered in the model:
\begin{cpp}
model.registerNewCustomMaterials<XXX>("name_of_local_material");
\end{cpp}
Only at this point the material can be initialized:
\begin{cpp}
model.initMaterials();
\end{cpp}
A full example for adding a new damage law can be found in
\shellcode{\examplesdir/new\_material}.
\subsection{Adding a New Non-Local Constitutive Law}\index{Material!create a new non-local material}
In order to add a new non-local material we first have to add the local constitutive law in \akantu (see above). We can then add the non-local version of the constitutive law by adding the two files (\code{material\_XXX\_non\_local.hh} and \code{material\_XXX\_non\_local.cc}) where \code{XXX} is the name of the corresponding local material. The new law must inherit from the two classes, non-local parent class, such as the \code{MaterialNonLocal} class, and from the local version of the constitutive law, \textit{i.e.} \code{MaterialXXX}. It is therefore necessary to include the interface of those classes in the header file of your custom material and indicate the inheritance in the declaration of the class:
\begin{cpp}
/* ---------------------------------------------------------------------- */
#include "material_non_local.hh" // the non-local parent
#include "material_XXX.hh"
/* ---------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_XXX_HH__
#define __AKANTU_MATERIAL_XXX_HH__
namespace akantu {
class MaterialXXXNonLocal : public MaterialXXX,
public MaterialNonLocal {
/// declare here the interface of your material
};
\end{cpp}
As members of the class we only need to add the internal fields to store the non-local quantities, which are obtained from the averaging process:
\begin{cpp}
/* -------------------------------------------------------------------------- */
/* Class members */
/* -------------------------------------------------------------------------- *
protected:
InternalField<Real> grad_u_nl;
\end{cpp}
The following four functions need to be implemented in the non-local material:
\begin{cpp}
/// initialization of the material
void initMaterial();
/// loop over all element and invoke stress computation
virtual void computeNonLocalStresses(GhostType ghost_type);
/// compute stresses after local quantities have been averaged
virtual void computeNonLocalStress(ElementType el_type, GhostType ghost_type)
/// compute all local quantities
void computeStress(ElementType el_type, GhostType ghost_type);
\end{cpp}
In the intialization of the non-local material we need to register the local quantity for the averaging process. In our example the internal field \emph{grad\_u\_nl} is the non-local counterpart of the gradient of the displacement field (\emph{grad\_u\_nl}):
\begin{cpp}
void MaterialXXXNonLocal::initMaterial() {
MaterialXXX::initMaterial();
MaterialNonLocal::initMaterial();
/// register the non-local variable in the manager
this->model->getNonLocalManager().registerNonLocalVariable(this->grad_u.getName(), this->grad_u_nl.getName(), spatial_dimension * spatial_dimension);
}
\end{cpp}
The function to register the non-local variable takes as parameters the name of the local internal field, the name of the non-local counterpart and the number of components of the field we want to average.
In the \emph{computeStress} we now need to compute all the quantities we want to average. We can then write a loop for the stress computation in the function \emph{computeNonLocalStresses} and then provide the constitutive law on each integration point in the function \emph{computeNonLocalStress}.
%%% Local Variables: %%% mode: latex %%% TeX-master: "manual" %%% End:
diff --git a/examples/io/dumper/dumpable_interface.cc b/examples/io/dumper/dumpable_interface.cc
index 75cdef7b3..f6a4b47a9 100644
--- a/examples/io/dumper/dumpable_interface.cc
+++ b/examples/io/dumper/dumpable_interface.cc
@@ -1,189 +1,189 @@
/**
* @file dumpable_interface.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 17 2015
* @date last modification: Mon Aug 31 2015
*
* @brief Example of dumpers::Dumpable interface.
*
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "group_manager_inline_impl.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include "dumpable_inline_impl.hh"
#include "dumper_iohelper_paraview.hh"
/* -------------------------------------------------------------------------- */
#include "locomotive_tools.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
/*
In this example, we present dumpers::Dumpable which is an interface
for other classes who want to dump themselves.
Several classes of Akantu inheritate from Dumpable (Model, Mesh, ...).
In this example we reproduce the same tasks as example_dumper_low_level.cc
using this time Dumpable interface inherted by Mesh, NodeGroup and
ElementGroup.
It is then advised to read first example_dumper_low_level.cc.
*/
initialize(argc, argv);
// To start let us load the swiss train mesh and its mesh data information.
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("swiss_train.msh");
/*
swiss_train.msh has the following physical groups that can be viewed with
GMSH:
"$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
6
2 1 "red"
2 2 "white"
2 3 "lwheel_1"
2 4 "lwheel_2"
2 5 "rwheel_2"
2 6 "rwheel_1"
$EndPhysicalNames
..."
*/
// Grouping nodes and elements belonging to train wheels (=four mesh data).
ElementGroup & wheels_elements =
mesh.createElementGroup("wheels", spatial_dimension);
wheels_elements.append(mesh.getElementGroup("lwheel_1"));
wheels_elements.append(mesh.getElementGroup("lwheel_2"));
wheels_elements.append(mesh.getElementGroup("rwheel_1"));
wheels_elements.append(mesh.getElementGroup("rwheel_2"));
const Array<UInt> & lnode_1 =
(mesh.getElementGroup("lwheel_1")).getNodeGroup().getNodes();
const Array<UInt> & lnode_2 =
(mesh.getElementGroup("lwheel_2")).getNodeGroup().getNodes();
const Array<UInt> & rnode_1 =
(mesh.getElementGroup("rwheel_1")).getNodeGroup().getNodes();
const Array<UInt> & rnode_2 =
(mesh.getElementGroup("rwheel_2")).getNodeGroup().getNodes();
Array<Real> & node = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
// This time a 2D Array is created and a padding size of 3 is passed to
// NodalField in order to warp train deformation on Paraview.
Array<Real> displacement(nb_nodes, spatial_dimension);
// Create an ElementTypeMapArray for the colour
ElementTypeMapArray<UInt> colour("colour");
colour.initialize(mesh, _with_nb_element = true);
/* ------------------------------------------------------------------------ */
/* Creating dumpers */
/* ------------------------------------------------------------------------ */
// Create dumper for the complete mesh and register it as default dumper.
auto && dumper = std::make_shared<DumperParaview>("train", "./paraview/dumpable", false);
mesh.registerExternalDumper(dumper, "train", true);
mesh.addDumpMesh(mesh);
// The dumper for the filtered mesh can be directly taken from the
// ElementGroup and then registered as "wheels_elements" dumper.
auto && wheels = mesh.getGroupDumper("paraview_wheels", "wheels");
mesh.registerExternalDumper(wheels.shared_from_this(), "wheels");
mesh.setDirectoryToDumper("wheels", "./paraview/dumpable");
// Arrays and ElementTypeMapArrays can be added as external fields directly
mesh.addDumpFieldExternal("displacement", displacement);
ElementTypeMapArrayFilter<UInt> filtered_colour(
colour, wheels_elements.getElements());
auto colour_field_wheel =
std::make_shared<dumpers::ElementalField<UInt, Vector, true>>(
filtered_colour);
mesh.addDumpFieldExternal("color", colour_field_wheel);
mesh.addDumpFieldExternalToDumper("wheels", "displacement", displacement);
mesh.addDumpFieldExternalToDumper("wheels", "colour", colour);
// For some specific cases the Fields should be created, as when you want to
// pad an array
auto displacement_vector_field =
mesh.createNodalField(&displacement, "all", 3);
mesh.addDumpFieldExternal("displacement_as_paraview_vector",
displacement_vector_field);
mesh.addDumpFieldExternalToDumper("wheels", "displacement_as_paraview_vector",
displacement_vector_field);
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
// Fill the ElementTypeMapArray colour.
fillColour(mesh, colour);
/// Apply displacement and wheels rotation.
Real tot_displacement = 50.;
Real radius = 1.;
UInt nb_steps = 100;
Real theta = tot_displacement / radius;
Vector<Real> l_center(spatial_dimension);
Vector<Real> r_center(spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
l_center(i) = node(14, i);
r_center(i) = node(2, i);
}
for (UInt i = 0; i < nb_steps; ++i) {
- displacement.clear();
+ displacement.zero();
Real step_ratio = Real(i) / Real(nb_steps);
Real angle = step_ratio * theta;
applyRotation(l_center, angle, node, displacement, lnode_1);
applyRotation(l_center, angle, node, displacement, lnode_2);
applyRotation(r_center, angle, node, displacement, rnode_1);
applyRotation(r_center, angle, node, displacement, rnode_2);
for (UInt j = 0; j < nb_nodes; ++j) {
displacement(j, _x) += step_ratio * tot_displacement;
}
/// Dump call is finally made through Dumpable interface.
mesh.dump();
mesh.dump("wheels");
}
finalize();
return 0;
}
diff --git a/examples/io/dumper/dumper_low_level.cc b/examples/io/dumper/dumper_low_level.cc
index 96463770a..ff18d8d9a 100644
--- a/examples/io/dumper/dumper_low_level.cc
+++ b/examples/io/dumper/dumper_low_level.cc
@@ -1,197 +1,197 @@
/**
* @file dumper_low_level.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 17 2015
*
* @brief Example of dumpers::DumperIOHelper low-level methods.
*
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "group_manager.hh"
#include "mesh.hh"
#include "dumper_elemental_field.hh"
#include "dumper_nodal_field.hh"
#include "dumper_iohelper_paraview.hh"
#include "locomotive_tools.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
/* This example aims at illustrating how to manipulate low-level methods of
DumperIOHelper.
The aims is to visualize a colorized moving train with Paraview */
initialize(argc, argv);
// To start let us load the swiss train mesh and its mesh data information.
// We aknowledge here a weel-known swiss industry for mesh donation.
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("swiss_train.msh");
Array<Real> & nodes = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
/* swiss_train.msh has the following physical groups that can be viewed with
GMSH:
"$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
6
2 1 "red"
2 2 "white"
2 3 "lwheel_1"
2 4 "lwheel_2"
2 5 "rwheel_2"
2 6 "rwheel_1"
$EndPhysicalNames
..."
*/
// Grouping nodes and elements belonging to train wheels (=four mesh data)
ElementGroup & wheels_elements =
mesh.createElementGroup("wheels", spatial_dimension);
wheels_elements.append(mesh.getElementGroup("lwheel_1"));
wheels_elements.append(mesh.getElementGroup("lwheel_2"));
wheels_elements.append(mesh.getElementGroup("rwheel_1"));
wheels_elements.append(mesh.getElementGroup("rwheel_2"));
const Array<UInt> & lnode_1 =
(mesh.getElementGroup("lwheel_1")).getNodeGroup().getNodes();
const Array<UInt> & lnode_2 =
(mesh.getElementGroup("lwheel_2")).getNodeGroup().getNodes();
const Array<UInt> & rnode_1 =
(mesh.getElementGroup("rwheel_1")).getNodeGroup().getNodes();
const Array<UInt> & rnode_2 =
(mesh.getElementGroup("rwheel_2")).getNodeGroup().getNodes();
/* Note this Array is constructed with three components in order to warp train
deformation on Paraview. A more appropriate way to do this is to set a
padding in the NodalField (See example_dumpable_interface.cc.) */
Array<Real> displacement(nb_nodes, 3);
// ElementalField are constructed with an ElementTypeMapArray.
ElementTypeMapArray<UInt> colour;
colour.initialize(mesh, _with_nb_element = true);
/* ------------------------------------------------------------------------ */
/* Dumper creation */
/* ------------------------------------------------------------------------ */
// Creation of two DumperParaview. One for full mesh, one for a filtered
// mesh.
DumperParaview dumper("train", "./paraview/dumper", false);
DumperParaview wheels("wheels", "./paraview/dumper", false);
// Register the full mesh
dumper.registerMesh(mesh);
// Register a filtered mesh limited to nodes and elements from wheels groups
wheels.registerFilteredMesh(mesh, wheels_elements.getElements(),
wheels_elements.getNodeGroup().getNodes());
// Generate an output file of the two mesh registered.
dumper.dump();
wheels.dump();
/* At this stage no fields are attached to the two dumpers. To do so, a
dumpers::Field object has to be created. Several types of dumpers::Field
exist. In this example we present two of them.
NodalField to describe nodal displacements of our train.
ElementalField handling the color of our different part.
*/
// NodalField are constructed with an Array.
auto displ_field = std::make_shared<dumpers::NodalField<Real>>(displacement);
auto colour_field = std::make_shared<dumpers::ElementalField<UInt>>(colour);
// Register the freshly created fields to our dumper.
dumper.registerField("displacement", displ_field);
dumper.registerField("colour", colour_field);
// For the dumper wheels, fields have to be filtered at registration.
// Filtered NodalField can be simply registered by adding an Array<UInt>
// listing the nodes.
auto displ_field_wheel = std::make_shared<dumpers::NodalField<Real, true>>(
displacement, 0, 0, &(wheels_elements.getNodeGroup().getNodes()));
wheels.registerField("displacement", displ_field_wheel);
// For the ElementalField, an ElementTypeMapArrayFilter has to be created.
ElementTypeMapArrayFilter<UInt> filtered_colour(
colour, wheels_elements.getElements());
auto colour_field_wheel =
std::make_shared<dumpers::ElementalField<UInt, Vector, true>>(
filtered_colour);
wheels.registerField("colour", colour_field_wheel);
/* ------------------------------------------------------------------------ */
// Now that the dumpers are created and the fields are associated, let's
// paint and move the train!
// Fill the ElementTypeMapArray colour according to mesh data information.
fillColour(mesh, colour);
// Apply displacement and wheels rotation.
Real tot_displacement = 50.;
Real radius = 1.;
UInt nb_steps = 100;
Real theta = tot_displacement / radius;
Vector<Real> l_center(3);
Vector<Real> r_center(3);
for (UInt i = 0; i < spatial_dimension; ++i) {
l_center(i) = nodes(14, i);
r_center(i) = nodes(2, i);
}
for (UInt i = 0; i < nb_steps; ++i) {
- displacement.clear();
+ displacement.zero();
Real angle = (Real)i / (Real)nb_steps * theta;
applyRotation(l_center, angle, nodes, displacement, lnode_1);
applyRotation(l_center, angle, nodes, displacement, lnode_2);
applyRotation(r_center, angle, nodes, displacement, rnode_1);
applyRotation(r_center, angle, nodes, displacement, rnode_2);
for (UInt j = 0; j < nb_nodes; ++j) {
displacement(j, 0) += (Real)i / (Real)nb_steps * tot_displacement;
}
// Output results after each moving steps for main and wheel dumpers.
dumper.dump();
wheels.dump();
}
finalize();
return 0;
}
diff --git a/examples/new_material/local_material_damage.hh b/examples/new_material/local_material_damage.hh
index bd6e41f0d..1161310de 100644
--- a/examples/new_material/local_material_damage.hh
+++ b/examples/new_material/local_material_damage.hh
@@ -1,117 +1,117 @@
/**
* @file local_material_damage.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 10 2015
* @date last modification: Mon Jan 18 2016
*
* @brief Material isotropic elastic
*
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_LOCAL_MATERIAL_DAMAGE_HH__
-#define __AKANTU_LOCAL_MATERIAL_DAMAGE_HH__
+#ifndef AKANTU_LOCAL_MATERIAL_DAMAGE_HH_
+#define AKANTU_LOCAL_MATERIAL_DAMAGE_HH_
namespace akantu {
class LocalMaterialDamage : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
LocalMaterialDamage(SolidMechanicsModel & model, const ID & id = "");
virtual ~LocalMaterialDamage(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the potential energy for all elements
void computePotentialEnergy(ElementType el_type) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real & damage);
/// compute the potential energy for on element
inline void computePotentialEnergyOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & epot);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// compute the celerity of the fastest wave in the material
inline Real getCelerity(const Element & element) const override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
private:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// resistance to damage
Real Yd;
/// damage threshold
Real Sd;
/// Bulk modulus
Real kpa;
/// damage internal variable
InternalField<Real> damage;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "local_material_damage_inline_impl.hh"
-#endif /* __AKANTU_LOCAL_MATERIAL_DAMAGE_HH__ */
+#endif /* AKANTU_LOCAL_MATERIAL_DAMAGE_HH_ */
diff --git a/examples/new_material/local_material_damage_inline_impl.hh b/examples/new_material/local_material_damage_inline_impl.hh
index ab2cbd34e..90f85a170 100644
--- a/examples/new_material/local_material_damage_inline_impl.hh
+++ b/examples/new_material/local_material_damage_inline_impl.hh
@@ -1,90 +1,90 @@
/**
* @file local_material_damage_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 10 2015
* @date last modification: Mon Jan 18 2016
*
* @brief Implementation of the inline functions of the material damage
*
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_LOCAL_MATERIAL_DAMAGE_INLINE_IMPL_HH__
-#define __AKANTU_LOCAL_MATERIAL_DAMAGE_INLINE_IMPL_HH__
+#ifndef AKANTU_LOCAL_MATERIAL_DAMAGE_INLINE_IMPL_HH_
+#define AKANTU_LOCAL_MATERIAL_DAMAGE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void LocalMaterialDamage::computeStressOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & sigma,
Real & dam) {
Real trace = grad_u.trace();
/// \sigma_{ij} = \lambda * (\nabla u)_{kk} * \delta_{ij} + \mu * (\nabla
/// u_{ij} + \nabla u_{ji})
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
sigma(i, j) =
(i == j) * lambda * trace + mu * (grad_u(i, j) + grad_u(j, i));
}
}
Real Y = 0;
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
Y += sigma(i, j) * grad_u(i, j);
}
}
Y *= 0.5;
Real Fd = Y - Yd - Sd * dam;
if (Fd > 0)
dam = (Y - Yd) / Sd;
dam = std::min(dam, 1.);
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
inline void LocalMaterialDamage::computePotentialEnergyOnQuad(
Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & epot) {
epot = 0.;
for (UInt i = 0, t = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j, ++t)
epot += sigma(i, j) * (grad_u(i, j) - (i == j));
epot *= .5;
}
/* -------------------------------------------------------------------------- */
inline Real LocalMaterialDamage::getCelerity(__attribute__((unused))
const Element & element) const {
// Here the fastest celerity is the push wave speed
return (std::sqrt((2 * mu + lambda) / rho));
}
} // namespace akantu
-#endif /* __AKANTU_LOCAL_MATERIAL_DAMAGE_INLINE_IMPL_HH__ */
+#endif /* AKANTU_LOCAL_MATERIAL_DAMAGE_INLINE_IMPL_HH_ */
diff --git a/examples/structural_mechanics/bernoulli_beam_2_exemple.cc b/examples/structural_mechanics/bernoulli_beam_2_exemple.cc
index ebf5020d6..b825f93e7 100644
--- a/examples/structural_mechanics/bernoulli_beam_2_exemple.cc
+++ b/examples/structural_mechanics/bernoulli_beam_2_exemple.cc
@@ -1,164 +1,164 @@
/**
* @file bernoulli_beam_2_exemple.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
*
* @date creation: Mon Jan 18 2016
*
* @brief Computation of the analytical exemple 1.1 in the TGC vol 6
*
*
* Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
* (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
#define TYPE _bernoulli_beam_2
using namespace akantu;
// Linear load function
static void lin_load(double * position, double * load,
__attribute__((unused)) Real * normal,
__attribute__((unused)) UInt surface_id) {
memset(load, 0, sizeof(Real) * 3);
if (position[0] <= 10) {
load[1] = -6000;
}
}
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
// Defining the mesh
Mesh beams(2);
UInt nb_nodes = 3;
UInt nb_nodes_1 = 1;
UInt nb_nodes_2 = nb_nodes - nb_nodes_1 - 1;
UInt nb_element = nb_nodes - 1;
Array<Real> & nodes = const_cast<Array<Real> &>(beams.getNodes());
nodes.resize(nb_nodes);
beams.addConnectivityType(_bernoulli_beam_2);
Array<UInt> & connectivity =
const_cast<Array<UInt> &>(beams.getConnectivity(_bernoulli_beam_2));
connectivity.resize(nb_element);
for (UInt i = 0; i < nb_nodes; ++i) {
nodes(i, 1) = 0;
}
for (UInt i = 0; i < nb_nodes_1; ++i) {
nodes(i, 0) = 10. * i / ((Real)nb_nodes_1);
}
nodes(nb_nodes_1, 0) = 10;
for (UInt i = 0; i < nb_nodes_2; ++i) {
nodes(nb_nodes_1 + i + 1, 0) = 10 + 8. * (i + 1) / ((Real)nb_nodes_2);
}
for (UInt i = 0; i < nb_element; ++i) {
connectivity(i, 0) = i;
connectivity(i, 1) = i + 1;
}
// Defining the materials
StructuralMechanicsModel model(beams);
StructuralMaterial mat1;
mat1.E = 3e10;
mat1.I = 0.0025;
mat1.A = 0.01;
model.addMaterial(mat1);
StructuralMaterial mat2;
mat2.E = 3e10;
mat2.I = 0.00128;
mat2.A = 0.01;
model.addMaterial(mat2);
// Defining the forces
model.initFull();
const Real M = -3600; // Momentum at 3
Array<Real> & forces = model.getForce();
Array<Real> & displacement = model.getDisplacement();
Array<bool> & boundary = model.getBlockedDOFs();
const Array<Real> & N_M = model.getStress(_bernoulli_beam_2);
Array<UInt> & element_material = model.getElementMaterial(_bernoulli_beam_2);
- forces.clear();
- displacement.clear();
+ forces.zero();
+ displacement.zero();
for (UInt i = 0; i < nb_nodes_2; ++i) {
element_material(i + nb_nodes_1) = 1;
}
forces(nb_nodes - 1, 2) += M;
model.computeForcesFromFunction<_bernoulli_beam_2>(lin_load, _bft_traction);
// Defining the boundary conditions
boundary(0, 0) = true;
boundary(0, 1) = true;
boundary(0, 2) = true;
boundary(nb_nodes_1, 1) = true;
boundary(nb_nodes - 1, 1) = true;
// Solve
Real error;
model.assembleStiffnessMatrix();
UInt count = 0;
model.addDumpFieldVector("displacement");
model.addDumpField("rotation");
model.addDumpFieldVector("force");
model.addDumpField("momentum");
do {
if (count != 0)
std::cerr << count << " - " << error << std::endl;
model.updateResidual();
model.solve();
count++;
} while (!model.testConvergenceIncrement(1e-10, error) && count < 10);
std::cerr << count << " - " << error << std::endl;
/* --------------------------------------------------------------------------
*/
// Post-Processing
model.computeStresses();
std::cout << " d1 = " << displacement(nb_nodes_1, 2) << std::endl;
std::cout << " d2 = " << displacement(nb_nodes - 1, 2) << std::endl;
std::cout << " M1 = " << N_M(0, 1) << std::endl;
std::cout << " M2 = " << N_M(2 * (nb_nodes - 2), 1) << std::endl;
model.dump();
finalize();
}
diff --git a/extra_packages/extra-materials/src/material_FE2/material_FE2.cc b/extra_packages/extra-materials/src/material_FE2/material_FE2.cc
index 00b5acf18..68dd33e7f 100644
--- a/extra_packages/extra-materials/src/material_FE2/material_FE2.cc
+++ b/extra_packages/extra-materials/src/material_FE2/material_FE2.cc
@@ -1,199 +1,199 @@
/**
* @file material_FE2.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @brief Material for multi-scale simulations. It stores an
* underlying RVE on each integration point of the material.
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material_FE2.hh"
#include "communicator.hh"
#include "solid_mechanics_model_RVE.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialFE2<spatial_dimension>::MaterialFE2(SolidMechanicsModel & model,
const ID & id)
: Parent(model, id), C("material_stiffness", *this) {
AKANTU_DEBUG_IN();
this->C.initialize(voigt_h::size * voigt_h::size);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialFE2<spatial_dimension>::~MaterialFE2() = default;
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialFE2<dim>::initialize() {
this->registerParam("element_type", el_type, _triangle_3,
_pat_parsable | _pat_modifiable,
"element type in RVE mesh");
this->registerParam("mesh_file", mesh_file, _pat_parsable | _pat_modifiable,
"the mesh file for the RVE");
this->registerParam("nb_gel_pockets", nb_gel_pockets,
_pat_parsable | _pat_modifiable,
"the number of gel pockets in each RVE");
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialFE2<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
Parent::initMaterial();
/// create a Mesh and SolidMechanicsModel on each integration point of the
/// material
auto C_it = this->C(this->el_type).begin(voigt_h::size, voigt_h::size);
for (auto && data :
enumerate(make_view(C(this->el_type), voigt_h::size, voigt_h::size))) {
auto q = std::get<0>(data);
auto & C = std::get<1>(data);
meshes.emplace_back(std::make_unique<Mesh>(
spatial_dimension, "RVE_mesh_" + std::to_string(q), q + 1));
auto & mesh = *meshes.back();
mesh.read(mesh_file);
RVEs.emplace_back(std::make_unique<SolidMechanicsModelRVE>(
mesh, true, this->nb_gel_pockets, _all_dimensions,
"SMM_RVE_" + std::to_string(q), q + 1));
auto & RVE = *RVEs.back();
RVE.initFull(_analysis_method = _static);
/// compute intial stiffness of the RVE
RVE.homogenizeStiffness(C);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialFE2<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
// Compute thermal stresses first
Parent::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator sigma_th_it =
this->sigma_th(el_type, ghost_type).begin();
// Wikipedia convention:
// 2*eps_ij (i!=j) = voigt_eps_I
// http://en.wikipedia.org/wiki/Voigt_notation
Array<Real>::const_matrix_iterator C_it =
this->C(el_type, ghost_type).begin(voigt_h::size, voigt_h::size);
// create vectors to store stress and strain in Voigt notation
// for efficient computation of stress
Vector<Real> voigt_strain(voigt_h::size);
Vector<Real> voigt_stress(voigt_h::size);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
const Matrix<Real> & C_mat = *C_it;
const Real & sigma_th = *sigma_th_it;
/// copy strains in Voigt notation
for (UInt I = 0; I < voigt_h::size; ++I) {
/// copy stress in
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_strain(I) = voigt_factor * (grad_u(i, j) + grad_u(j, i)) / 2.;
}
// compute stresses in Voigt notation
voigt_stress.mul<false>(C_mat, voigt_strain);
/// copy stresses back in full vectorised notation
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
sigma(i, j) = sigma(j, i) = voigt_stress(I) + (i == j) * sigma_th;
}
++C_it;
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialFE2<spatial_dimension>::computeTangentModuli(
- const ElementType & el_type, Array<Real> & tangent_matrix,
+ ElementType el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real>::const_matrix_iterator C_it =
this->C(el_type, ghost_type).begin(voigt_h::size, voigt_h::size);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
tangent.copy(*C_it);
++C_it;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialFE2<spatial_dimension>::advanceASR(
const Matrix<Real> & prestrain) {
AKANTU_DEBUG_IN();
for (auto && data :
zip(RVEs,
make_view(this->gradu(this->el_type), spatial_dimension,
spatial_dimension),
make_view(this->eigengradu(this->el_type), spatial_dimension,
spatial_dimension),
make_view(this->C(this->el_type), voigt_h::size, voigt_h::size),
this->delta_T(this->el_type))) {
auto & RVE = *(std::get<0>(data));
/// apply boundary conditions based on the current macroscopic displ.
/// gradient
RVE.applyBoundaryConditions(std::get<1>(data));
/// apply homogeneous temperature field to each RVE to obtain thermoelastic
/// effect
RVE.applyHomogeneousTemperature(std::get<4>(data));
/// advance the ASR in every RVE
RVE.advanceASR(prestrain);
/// compute the average eigen_grad_u
RVE.homogenizeEigenGradU(std::get<2>(data));
/// compute the new effective stiffness of the RVE
RVE.homogenizeStiffness(std::get<3>(data));
}
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(material_FE2, MaterialFE2);
} // namespace akantu
diff --git a/extra_packages/extra-materials/src/material_FE2/material_FE2.hh b/extra_packages/extra-materials/src/material_FE2/material_FE2.hh
index 126bb201a..084f40da7 100644
--- a/extra_packages/extra-materials/src/material_FE2/material_FE2.hh
+++ b/extra_packages/extra-materials/src/material_FE2/material_FE2.hh
@@ -1,111 +1,111 @@
/**
* @file material_FE2.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Material for multi-scale simulations. It stores an
* underlying RVE on each integration point of the material.
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "material_thermal.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_FE_2_HH__
-#define __AKANTU_MATERIAL_FE_2_HH__
+#ifndef AKANTU_MATERIAL_FE_2_HH_
+#define AKANTU_MATERIAL_FE_2_HH_
namespace akantu {
class SolidMechanicsModelRVE;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
/// /!\ This material works ONLY for meshes with a single element type!!!!!
/* -------------------------------------------------------------------------- */
/**
* MaterialFE2
*
* parameters in the material files :
* - mesh_file
*/
template <UInt DIM> class MaterialFE2 : public MaterialThermal<DIM> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
typedef MaterialThermal<DIM> Parent;
public:
MaterialFE2(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialFE2();
typedef VoigtHelper<DIM> voigt_h;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void initMaterial();
/// constitutive law for all element of a type
virtual void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// compute the tangent stiffness matrix for an element type
- void computeTangentModuli(const ElementType & el_type,
+ void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
/// advance alkali-silica reaction
void advanceASR(const Matrix<Real> & prestrain);
private:
void initialize();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Underlying RVE at each integration point
std::vector<std::unique_ptr<SolidMechanicsModelRVE>> RVEs;
/// Meshes for all RVEs
std::vector<std::unique_ptr<Mesh>> meshes;
/// the element type of the associated mesh (this material handles only one
/// type!!)
ElementType el_type;
/// the name of RVE mesh file
ID mesh_file;
/// Elastic stiffness tensor at each Gauss point (in voigt notation)
InternalField<Real> C;
/// number of gel pockets in each underlying RVE
UInt nb_gel_pockets;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_FE2_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_FE_2_HH__ */
+#endif /* AKANTU_MATERIAL_FE_2_HH_ */
diff --git a/extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.cc b/extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.cc
index 327760804..a7eaafa2e 100644
--- a/extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.cc
+++ b/extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.cc
@@ -1,603 +1,603 @@
/**
* @file solid_mechanics_model_RVE.cc
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Wed Jan 13 15:32:35 2016
*
* @brief Implementation of SolidMechanicsModelRVE
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_RVE.hh"
#include "element_group.hh"
#include "material_damage_iterative.hh"
#include "node_group.hh"
#include "non_linear_solver.hh"
#include "non_local_manager.hh"
#include "parser.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <string>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SolidMechanicsModelRVE::SolidMechanicsModelRVE(Mesh & mesh,
bool use_RVE_mat_selector,
UInt nb_gel_pockets, UInt dim,
const ID & id,
const MemoryID & memory_id)
: SolidMechanicsModel(mesh, dim, id, memory_id), volume(0.),
use_RVE_mat_selector(use_RVE_mat_selector),
nb_gel_pockets(nb_gel_pockets), nb_dumps(0) {
AKANTU_DEBUG_IN();
/// find the four corner nodes of the RVE
findCornerNodes();
/// remove the corner nodes from the surface node groups:
/// This most be done because corner nodes a not periodic
mesh.getElementGroup("top").removeNode(corner_nodes(2));
mesh.getElementGroup("top").removeNode(corner_nodes(3));
mesh.getElementGroup("left").removeNode(corner_nodes(3));
mesh.getElementGroup("left").removeNode(corner_nodes(0));
mesh.getElementGroup("bottom").removeNode(corner_nodes(1));
mesh.getElementGroup("bottom").removeNode(corner_nodes(0));
mesh.getElementGroup("right").removeNode(corner_nodes(2));
mesh.getElementGroup("right").removeNode(corner_nodes(1));
const auto & bottom = mesh.getElementGroup("bottom").getNodeGroup();
bottom_nodes.insert(bottom.begin(), bottom.end());
const auto & left = mesh.getElementGroup("left").getNodeGroup();
left_nodes.insert(left.begin(), left.end());
// /// enforce periodicity on the displacement fluctuations
// auto surface_pair_1 = std::make_pair("top", "bottom");
// auto surface_pair_2 = std::make_pair("right", "left");
// SurfacePairList surface_pairs_list;
// surface_pairs_list.push_back(surface_pair_1);
// surface_pairs_list.push_back(surface_pair_2);
// TODO: To Nicolas correct the PBCs
// this->setPBC(surface_pairs_list);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModelRVE::~SolidMechanicsModelRVE() = default;
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::initFullImpl(const ModelOptions & options) {
AKANTU_DEBUG_IN();
auto options_cp(options);
options_cp.analysis_method = AnalysisMethod::_static;
SolidMechanicsModel::initFullImpl(options_cp);
// this->initMaterials();
auto & fem = this->getFEEngine("SolidMechanicsFEEngine");
/// compute the volume of the RVE
GhostType gt = _not_ghost;
for (auto element_type :
this->mesh.elementTypes(spatial_dimension, gt, _ek_not_defined)) {
Array<Real> Volume(this->mesh.getNbElement(element_type) *
fem.getNbIntegrationPoints(element_type),
1, 1.);
this->volume = fem.integrate(Volume, element_type);
}
std::cout << "The volume of the RVE is " << this->volume << std::endl;
/// dumping
std::stringstream base_name;
base_name << this->id; // << this->memory_id - 1;
this->setBaseName(base_name.str());
this->addDumpFieldVector("displacement");
this->addDumpField("stress");
this->addDumpField("grad_u");
this->addDumpField("eigen_grad_u");
this->addDumpField("blocked_dofs");
this->addDumpField("material_index");
this->addDumpField("damage");
this->addDumpField("Sc");
this->addDumpField("external_force");
this->addDumpField("equivalent_stress");
this->addDumpField("internal_force");
this->addDumpField("delta_T");
this->dump();
this->nb_dumps += 1;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::applyBoundaryConditions(
const Matrix<Real> & displacement_gradient) {
AKANTU_DEBUG_IN();
/// get the position of the nodes
const Array<Real> & pos = mesh.getNodes();
/// storage for the coordinates of a given node and the displacement that will
/// be applied
Vector<Real> x(spatial_dimension);
Vector<Real> appl_disp(spatial_dimension);
/// fix top right node
UInt node = this->corner_nodes(2);
x(0) = pos(node, 0);
x(1) = pos(node, 1);
appl_disp.mul<false>(displacement_gradient, x);
(*this->blocked_dofs)(node, 0) = true;
(*this->displacement)(node, 0) = appl_disp(0);
(*this->blocked_dofs)(node, 1) = true;
(*this->displacement)(node, 1) = appl_disp(1);
// (*this->blocked_dofs)(node,0) = true; (*this->displacement)(node,0) = 0.;
// (*this->blocked_dofs)(node,1) = true; (*this->displacement)(node,1) = 0.;
/// apply Hx at all the other corner nodes; H: displ. gradient
node = this->corner_nodes(0);
x(0) = pos(node, 0);
x(1) = pos(node, 1);
appl_disp.mul<false>(displacement_gradient, x);
(*this->blocked_dofs)(node, 0) = true;
(*this->displacement)(node, 0) = appl_disp(0);
(*this->blocked_dofs)(node, 1) = true;
(*this->displacement)(node, 1) = appl_disp(1);
node = this->corner_nodes(1);
x(0) = pos(node, 0);
x(1) = pos(node, 1);
appl_disp.mul<false>(displacement_gradient, x);
(*this->blocked_dofs)(node, 0) = true;
(*this->displacement)(node, 0) = appl_disp(0);
(*this->blocked_dofs)(node, 1) = true;
(*this->displacement)(node, 1) = appl_disp(1);
node = this->corner_nodes(3);
x(0) = pos(node, 0);
x(1) = pos(node, 1);
appl_disp.mul<false>(displacement_gradient, x);
(*this->blocked_dofs)(node, 0) = true;
(*this->displacement)(node, 0) = appl_disp(0);
(*this->blocked_dofs)(node, 1) = true;
(*this->displacement)(node, 1) = appl_disp(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::applyHomogeneousTemperature(
const Real & temperature) {
for (UInt m = 0; m < this->getNbMaterials(); ++m) {
Material & mat = this->getMaterial(m);
const ElementTypeMapArray<UInt> & filter_map = mat.getElementFilter();
// Loop over all element types
for (auto && type : filter_map.elementTypes(spatial_dimension)) {
const Array<UInt> & filter = filter_map(type);
if (filter.size() == 0)
continue;
Array<Real> & delta_T = mat.getArray<Real>("delta_T", type);
Array<Real>::scalar_iterator delta_T_it = delta_T.begin();
Array<Real>::scalar_iterator delta_T_end = delta_T.end();
for (; delta_T_it != delta_T_end; ++delta_T_it) {
*delta_T_it = temperature;
}
}
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::findCornerNodes() {
AKANTU_DEBUG_IN();
// find corner nodes
const auto & position = mesh.getNodes();
const auto & lower_bounds = mesh.getLowerBounds();
const auto & upper_bounds = mesh.getUpperBounds();
AKANTU_DEBUG_ASSERT(spatial_dimension == 2, "This is 2D only!");
corner_nodes.resize(4);
corner_nodes.set(UInt(-1));
for (auto && data : enumerate(make_view(position, spatial_dimension))) {
auto node = std::get<0>(data);
const auto & X = std::get<1>(data);
auto distance = X.distance(lower_bounds);
// node 1
if (Math::are_float_equal(distance, 0)) {
corner_nodes(0) = node;
}
// node 2
else if (Math::are_float_equal(X(_x), upper_bounds(_x)) &&
Math::are_float_equal(X(_y), lower_bounds(_y))) {
corner_nodes(1) = node;
}
// node 3
else if (Math::are_float_equal(X(_x), upper_bounds(_x)) &&
Math::are_float_equal(X(_y), upper_bounds(_y))) {
corner_nodes(2) = node;
}
// node 4
else if (Math::are_float_equal(X(_x), lower_bounds(_x)) &&
Math::are_float_equal(X(_y), upper_bounds(_y))) {
corner_nodes(3) = node;
}
}
for (UInt i = 0; i < corner_nodes.size(); ++i) {
if (corner_nodes(i) == UInt(-1))
AKANTU_ERROR("The corner node " << i + 1 << " wasn't found");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::advanceASR(const Matrix<Real> & prestrain) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(spatial_dimension == 2, "This is 2D only!");
/// apply the new eigenstrain
for (auto element_type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
Array<Real> & prestrain_vect =
const_cast<Array<Real> &>(this->getMaterial("gel").getInternal<Real>(
"eigen_grad_u")(element_type));
auto prestrain_it =
prestrain_vect.begin(spatial_dimension, spatial_dimension);
auto prestrain_end =
prestrain_vect.end(spatial_dimension, spatial_dimension);
for (; prestrain_it != prestrain_end; ++prestrain_it)
(*prestrain_it) = prestrain;
}
/// advance the damage
MaterialDamageIterative<2> & mat_paste =
dynamic_cast<MaterialDamageIterative<2> &>(*this->materials[1]);
MaterialDamageIterative<2> & mat_aggregate =
dynamic_cast<MaterialDamageIterative<2> &>(*this->materials[0]);
UInt nb_damaged_elements = 0;
Real max_eq_stress_aggregate = 0;
Real max_eq_stress_paste = 0;
auto & solver = this->getNonLinearSolver();
solver.set("max_iterations", 2);
solver.set("threshold", 1e-6);
solver.set("convergence_type", SolveConvergenceCriteria::_solution);
do {
this->solveStep();
/// compute damage
max_eq_stress_aggregate = mat_aggregate.getNormMaxEquivalentStress();
max_eq_stress_paste = mat_paste.getNormMaxEquivalentStress();
nb_damaged_elements = 0;
if (max_eq_stress_aggregate > max_eq_stress_paste)
nb_damaged_elements = mat_aggregate.updateDamage();
else if (max_eq_stress_aggregate < max_eq_stress_paste)
nb_damaged_elements = mat_paste.updateDamage();
else
nb_damaged_elements =
(mat_paste.updateDamage() + mat_aggregate.updateDamage());
std::cout << "the number of damaged elements is " << nb_damaged_elements
<< std::endl;
} while (nb_damaged_elements);
if (this->nb_dumps % 10 == 0) {
this->dump();
}
this->nb_dumps += 1;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModelRVE::averageTensorField(UInt row_index, UInt col_index,
const ID & field_type) {
AKANTU_DEBUG_IN();
auto & fem = this->getFEEngine("SolidMechanicsFEEngine");
Real average = 0;
GhostType gt = _not_ghost;
for (auto element_type :
mesh.elementTypes(spatial_dimension, gt, _ek_not_defined)) {
if (field_type == "stress") {
for (UInt m = 0; m < this->materials.size(); ++m) {
const auto & stress_vec = this->materials[m]->getStress(element_type);
const auto & elem_filter =
this->materials[m]->getElementFilter(element_type);
Array<Real> int_stress_vec(elem_filter.size(),
spatial_dimension * spatial_dimension,
"int_of_stress");
fem.integrate(stress_vec, int_stress_vec,
spatial_dimension * spatial_dimension, element_type,
_not_ghost, elem_filter);
for (UInt k = 0; k < elem_filter.size(); ++k)
average += int_stress_vec(k, row_index * spatial_dimension +
col_index); // 3 is the value
// for the yy (in
// 3D, the value is
// 4)
}
} else if (field_type == "strain") {
for (UInt m = 0; m < this->materials.size(); ++m) {
const auto & gradu_vec = this->materials[m]->getGradU(element_type);
const auto & elem_filter =
this->materials[m]->getElementFilter(element_type);
Array<Real> int_gradu_vec(elem_filter.size(),
spatial_dimension * spatial_dimension,
"int_of_gradu");
fem.integrate(gradu_vec, int_gradu_vec,
spatial_dimension * spatial_dimension, element_type,
_not_ghost, elem_filter);
for (UInt k = 0; k < elem_filter.size(); ++k)
/// averaging is done only for normal components, so stress and strain
/// are equal
average +=
0.5 *
(int_gradu_vec(k, row_index * spatial_dimension + col_index) +
int_gradu_vec(k, col_index * spatial_dimension + row_index));
}
} else if (field_type == "eigen_grad_u") {
for (UInt m = 0; m < this->materials.size(); ++m) {
const auto & eigen_gradu_vec =
this->materials[m]->getInternal<Real>("eigen_grad_u")(element_type);
const auto & elem_filter =
this->materials[m]->getElementFilter(element_type);
Array<Real> int_eigen_gradu_vec(elem_filter.size(),
spatial_dimension * spatial_dimension,
"int_of_gradu");
fem.integrate(eigen_gradu_vec, int_eigen_gradu_vec,
spatial_dimension * spatial_dimension, element_type,
_not_ghost, elem_filter);
for (UInt k = 0; k < elem_filter.size(); ++k)
/// averaging is done only for normal components, so stress and strain
/// are equal
average +=
int_eigen_gradu_vec(k, row_index * spatial_dimension + col_index);
}
} else {
AKANTU_ERROR("Averaging not implemented for this field!!!");
}
}
return average / this->volume;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::homogenizeStiffness(Matrix<Real> & C_macro) {
AKANTU_DEBUG_IN();
const UInt dim = 2;
AKANTU_DEBUG_ASSERT(this->spatial_dimension == dim,
"Is only implemented for 2D!!!");
/// apply three independent loading states to determine C
/// 1. eps_el = (1;0;0) 2. eps_el = (0,1,0) 3. eps_el = (0,0,0.5)
/// clear the eigenstrain
Matrix<Real> zero_eigengradu(dim, dim, 0.);
GhostType gt = _not_ghost;
for (auto element_type : mesh.elementTypes(dim, gt, _ek_not_defined)) {
auto & prestrain_vect =
const_cast<Array<Real> &>(this->getMaterial("gel").getInternal<Real>(
"eigen_grad_u")(element_type));
auto prestrain_it =
prestrain_vect.begin(spatial_dimension, spatial_dimension);
auto prestrain_end =
prestrain_vect.end(spatial_dimension, spatial_dimension);
for (; prestrain_it != prestrain_end; ++prestrain_it)
(*prestrain_it) = zero_eigengradu;
}
/// storage for results of 3 different loading states
UInt voigt_size = VoigtHelper<dim>::size;
Matrix<Real> stresses(voigt_size, voigt_size, 0.);
Matrix<Real> strains(voigt_size, voigt_size, 0.);
Matrix<Real> H(dim, dim, 0.);
/// save the damage state before filling up cracks
// ElementTypeMapReal saved_damage("saved_damage");
// saved_damage.initialize(getFEEngine(), _nb_component = 1, _default_value =
// 0);
// this->fillCracks(saved_damage);
/// virtual test 1:
H(0, 0) = 0.01;
this->performVirtualTesting(H, stresses, strains, 0);
/// virtual test 2:
- H.clear();
+ H.zero();
H(1, 1) = 0.01;
this->performVirtualTesting(H, stresses, strains, 1);
/// virtual test 3:
- H.clear();
+ H.zero();
H(0, 1) = 0.01;
this->performVirtualTesting(H, stresses, strains, 2);
/// drain cracks
// this->drainCracks(saved_damage);
/// compute effective stiffness
Matrix<Real> eps_inverse(voigt_size, voigt_size);
eps_inverse.inverse(strains);
C_macro.mul<false, false>(stresses, eps_inverse);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::performVirtualTesting(const Matrix<Real> & H,
Matrix<Real> & eff_stresses,
Matrix<Real> & eff_strains,
const UInt test_no) {
AKANTU_DEBUG_IN();
this->applyBoundaryConditions(H);
auto & solver = this->getNonLinearSolver();
solver.set("max_iterations", 2);
solver.set("threshold", 1e-6);
solver.set("convergence_type", SolveConvergenceCriteria::_solution);
this->solveStep();
/// get average stress and strain
eff_stresses(0, test_no) = this->averageTensorField(0, 0, "stress");
eff_strains(0, test_no) = this->averageTensorField(0, 0, "strain");
eff_stresses(1, test_no) = this->averageTensorField(1, 1, "stress");
eff_strains(1, test_no) = this->averageTensorField(1, 1, "strain");
eff_stresses(2, test_no) = this->averageTensorField(1, 0, "stress");
eff_strains(2, test_no) = 2. * this->averageTensorField(1, 0, "strain");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::homogenizeEigenGradU(
Matrix<Real> & eigen_gradu_macro) {
AKANTU_DEBUG_IN();
eigen_gradu_macro(0, 0) = this->averageTensorField(0, 0, "eigen_grad_u");
eigen_gradu_macro(1, 1) = this->averageTensorField(1, 1, "eigen_grad_u");
eigen_gradu_macro(0, 1) = this->averageTensorField(0, 1, "eigen_grad_u");
eigen_gradu_macro(1, 0) = this->averageTensorField(1, 0, "eigen_grad_u");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::initMaterials() {
AKANTU_DEBUG_IN();
// make sure the material are instantiated
if (!are_materials_instantiated)
instantiateMaterials();
if (use_RVE_mat_selector) {
const Vector<Real> & lowerBounds = mesh.getLowerBounds();
const Vector<Real> & upperBounds = mesh.getUpperBounds();
Real bottom = lowerBounds(1);
Real top = upperBounds(1);
Real box_size = std::abs(top - bottom);
Real eps = box_size * 1e-6;
auto tmp = std::make_shared<GelMaterialSelector>(*this, box_size, "gel",
this->nb_gel_pockets, eps);
tmp->setFallback(material_selector);
material_selector = tmp;
}
this->assignMaterialToElements();
// synchronize the element material arrays
this->synchronize(SynchronizationTag::_material_id);
for (auto & material : materials) {
/// init internals properties
const auto type = material->getID();
if (type.find("material_FE2") != std::string::npos)
continue;
material->initMaterial();
}
this->synchronize(SynchronizationTag::_smm_init_mat);
if (this->non_local_manager) {
this->non_local_manager->initialize();
}
// SolidMechanicsModel::initMaterials();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::fillCracks(ElementTypeMapReal & saved_damage) {
const auto & mat_gel = this->getMaterial("gel");
Real E_gel = mat_gel.get("E");
Real E_homogenized = 0.;
for (auto && mat : materials) {
if (mat->getName() == "gel" || mat->getName() == "FE2_mat")
continue;
Real E = mat->get("E");
auto & damage = mat->getInternal<Real>("damage");
for (auto && type : damage.elementTypes()) {
const auto & elem_filter = mat->getElementFilter(type);
auto nb_integration_point = getFEEngine().getNbIntegrationPoints(type);
auto sav_dam_it =
make_view(saved_damage(type), nb_integration_point).begin();
for (auto && data :
zip(elem_filter, make_view(damage(type), nb_integration_point))) {
auto el = std::get<0>(data);
auto & dam = std::get<1>(data);
Vector<Real> sav_dam = sav_dam_it[el];
sav_dam = dam;
for (auto q : arange(dam.size())) {
E_homogenized = (E_gel - E) * dam(q) + E;
dam(q) = 1. - (E_homogenized / E);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelRVE::drainCracks(
const ElementTypeMapReal & saved_damage) {
for (auto && mat : materials) {
if (mat->getName() == "gel" || mat->getName() == "FE2_mat")
continue;
auto & damage = mat->getInternal<Real>("damage");
for (auto && type : damage.elementTypes()) {
const auto & elem_filter = mat->getElementFilter(type);
auto nb_integration_point = getFEEngine().getNbIntegrationPoints(type);
auto sav_dam_it =
make_view(saved_damage(type), nb_integration_point).begin();
for (auto && data :
zip(elem_filter, make_view(damage(type), nb_integration_point))) {
auto el = std::get<0>(data);
auto & dam = std::get<1>(data);
Vector<Real> sav_dam = sav_dam_it[el];
dam = sav_dam;
}
}
}
}
} // namespace akantu
diff --git a/extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.hh b/extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.hh
index 5a3ca21ce..68c37ee23 100644
--- a/extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.hh
+++ b/extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.hh
@@ -1,232 +1,232 @@
/**
* @file solid_mechanics_model_RVE.hh
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Wed Jan 13 14:54:18 2016
*
* @brief SMM for RVE computations in FE2 simulations
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLID_MECHANICS_MODEL_RVE_HH__
-#define __AKANTU_SOLID_MECHANICS_MODEL_RVE_HH__
+#ifndef AKANTU_SOLID_MECHANICS_MODEL_RVE_HH_
+#define AKANTU_SOLID_MECHANICS_MODEL_RVE_HH_
/* -------------------------------------------------------------------------- */
#include "aka_grid_dynamic.hh"
#include "solid_mechanics_model.hh"
#include <unordered_set>
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelRVE : public SolidMechanicsModel {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SolidMechanicsModelRVE(Mesh & mesh, bool use_RVE_mat_selector = true,
UInt nb_gel_pockets = 400,
UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model",
const MemoryID & memory_id = 0);
virtual ~SolidMechanicsModelRVE();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
void initFullImpl(const ModelOptions & option) override;
/// initialize the materials
void initMaterials() override;
public:
/// apply boundary contions based on macroscopic deformation gradient
virtual void
applyBoundaryConditions(const Matrix<Real> & displacement_gradient);
/// apply homogeneous temperature field from the macroscale level to the RVEs
virtual void applyHomogeneousTemperature(const Real & temperature);
/// advance the reactions -> grow gel and apply homogenized properties
void advanceASR(const Matrix<Real> & prestrain);
/// compute average stress or strain in the model
Real averageTensorField(UInt row_index, UInt col_index,
const ID & field_type);
/// compute effective stiffness of the RVE
void homogenizeStiffness(Matrix<Real> & C_macro);
/// compute average eigenstrain
void homogenizeEigenGradU(Matrix<Real> & eigen_gradu_macro);
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
inline void unpackData(CommunicationBuffer & buffer,
const Array<UInt> & index,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(CornerNodes, corner_nodes, const Array<UInt> &);
AKANTU_GET_MACRO(Volume, volume, Real);
private:
/// find the corner nodes
void findCornerNodes();
/// perform virtual testing
void performVirtualTesting(const Matrix<Real> & H,
Matrix<Real> & eff_stresses,
Matrix<Real> & eff_strains, const UInt test_no);
void fillCracks(ElementTypeMapReal & saved_damage);
void drainCracks(const ElementTypeMapReal & saved_damage);
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
/// volume of the RVE
Real volume;
/// corner nodes 1, 2, 3, 4 (see Leonardo's thesis, page 98)
Array<UInt> corner_nodes;
/// bottom nodes
std::unordered_set<UInt> bottom_nodes;
/// left nodes
std::unordered_set<UInt> left_nodes;
/// standard mat selector or user one
bool use_RVE_mat_selector;
/// the number of gel pockets inside the RVE
UInt nb_gel_pockets;
/// dump counter
UInt nb_dumps;
};
inline void SolidMechanicsModelRVE::unpackData(CommunicationBuffer & buffer,
const Array<UInt> & index,
const SynchronizationTag & tag) {
SolidMechanicsModel::unpackData(buffer, index, tag);
// if (tag == SynchronizationTag::_smm_uv) {
// auto disp_it = displacement->begin(spatial_dimension);
//
// for (auto node : index) {
// Vector<Real> current_disp(disp_it[node]);
//
// // if node is at the bottom, u_bottom = u_top +u_2 -u_3
// if (bottom_nodes.count(node)) {
// current_disp += Vector<Real>(disp_it[corner_nodes(1)]);
// current_disp -= Vector<Real>(disp_it[corner_nodes(2)]);
// }
// // if node is at the left, u_left = u_right +u_4 -u_3
// else if (left_nodes.count(node)) {
// current_disp += Vector<Real>(disp_it[corner_nodes(3)]);
// current_disp -= Vector<Real>(disp_it[corner_nodes(2)]);
// }
// }
// }
}
/* -------------------------------------------------------------------------- */
/* ASR material selector */
/* -------------------------------------------------------------------------- */
class GelMaterialSelector : public MeshDataMaterialSelector<std::string> {
public:
GelMaterialSelector(SolidMechanicsModel & model, const Real box_size,
const std::string & gel_material,
const UInt nb_gel_pockets, Real /*tolerance*/ = 0.)
: MeshDataMaterialSelector<std::string>("physical_names", model),
model(model), gel_material(gel_material),
nb_gel_pockets(nb_gel_pockets), nb_placed_gel_pockets(0),
box_size(box_size) {
Mesh & mesh = this->model.getMesh();
UInt spatial_dimension = model.getSpatialDimension();
Element el{_triangle_3, 0, _not_ghost};
UInt nb_element = mesh.getNbElement(el.type, el.ghost_type);
Array<Real> barycenter(nb_element, spatial_dimension);
for (auto && data : enumerate(make_view(barycenter, spatial_dimension))) {
el.element = std::get<0>(data);
auto & bary = std::get<1>(data);
mesh.getBarycenter(el, bary);
}
/// generate the gel pockets
srand(0.);
Vector<Real> center(spatial_dimension);
UInt placed_gel_pockets = 0;
std::set<int> checked_baries;
while (placed_gel_pockets != nb_gel_pockets) {
/// get a random bary center
UInt bary_id = rand() % nb_element;
if (checked_baries.find(bary_id) != checked_baries.end())
continue;
checked_baries.insert(bary_id);
el.element = bary_id;
if (MeshDataMaterialSelector<std::string>::operator()(el) == 1)
continue; /// element belongs to paste
gel_pockets.push_back(el);
placed_gel_pockets += 1;
}
}
UInt operator()(const Element & elem) {
UInt temp_index = MeshDataMaterialSelector<std::string>::operator()(elem);
if (temp_index == 1)
return temp_index;
std::vector<Element>::const_iterator iit = gel_pockets.begin();
std::vector<Element>::const_iterator eit = gel_pockets.end();
if (std::find(iit, eit, elem) != eit) {
nb_placed_gel_pockets += 1;
std::cout << nb_placed_gel_pockets << " gelpockets placed" << std::endl;
return model.getMaterialIndex(gel_material);
;
}
return 0;
}
protected:
SolidMechanicsModel & model;
std::string gel_material;
std::vector<Element> gel_pockets;
UInt nb_gel_pockets;
UInt nb_placed_gel_pockets;
Real box_size;
};
} // namespace akantu
///#include "material_selector_tmpl.hh"
-#endif /* __AKANTU_SOLID_MECHANICS_MODEL_RVE_HH__ */
+#endif /* AKANTU_SOLID_MECHANICS_MODEL_RVE_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_brittle.hh b/extra_packages/extra-materials/src/material_damage/material_brittle.hh
index 34c7187e7..5466e2c56 100644
--- a/extra_packages/extra-materials/src/material_damage/material_brittle.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_brittle.hh
@@ -1,110 +1,110 @@
/**
* @file material_brittle.hh
*
* @author Aranda Ruiz Josue <josue.arandaruiz@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
*
* @brief Brittle damage law
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_BRITTLE_HH__
-#define __AKANTU_MATERIAL_BRITTLE_HH__
+#ifndef AKANTU_MATERIAL_BRITTLE_HH_
+#define AKANTU_MATERIAL_BRITTLE_HH_
namespace akantu {
/**
* Material brittle
*
* parameters in the material files :
* - S_0 : Critical stress at low strain rate (default: 157e6)
* - E_0 : Low strain rate threshold (default: 27e3)
* - A,B,C,D : Fitting parameters for the critical stress at high strain
* rates
* (default: 1.622e-11, -1.3274e-6, 3.6544e-2, -181.38)
*/
template <UInt spatial_dimension>
class MaterialBrittle : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialBrittle(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
- void initMaterial();
+ void initMaterial() override;
- virtual void updateInternalParameters();
+ void updateInternalParameters() override;
/// constitutive law for all element of a type
- void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
+ void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & grad_v,
Matrix<Real> & sigma, Real & dam,
Real & sigma_equivalent,
Real & fracture_stress);
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma, Real & dam,
Real & sigma_c,
Real & fracture_stress);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// strain rate arrays ordered by element types
InternalField<Real> strain_rate_brittle;
// polynome constants for critical stress value
Real A;
Real B;
Real C;
Real D;
// minimum strain rate
Real E_0;
// Critical stress at low strain rates
Real S_0;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_brittle_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_brittle_HH__ */
+#endif /* AKANTU_MATERIAL_brittle_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_brittle_non_local.hh b/extra_packages/extra-materials/src/material_damage/material_brittle_non_local.hh
index f81367501..e079ed307 100644
--- a/extra_packages/extra-materials/src/material_damage/material_brittle_non_local.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_brittle_non_local.hh
@@ -1,88 +1,88 @@
/**
* @file material_brittle_non_local.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
*
* @brief MaterialBrittleNonLocal header for non-local damage
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_brittle.hh"
#include "material_damage_non_local.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_BRITTLE_NON_LOCAL_HH__
-#define __AKANTU_MATERIAL_BRITTLE_NON_LOCAL_HH__
+#ifndef AKANTU_MATERIAL_BRITTLE_NON_LOCAL_HH_
+#define AKANTU_MATERIAL_BRITTLE_NON_LOCAL_HH_
namespace akantu {
/**
* Material Brittle Non local
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialBrittleNonLocal
: public MaterialDamageNonLocal<spatial_dimension,
MaterialBrittle<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef MaterialDamageNonLocal<spatial_dimension,
MaterialBrittle<spatial_dimension>>
MaterialBrittleNonLocalParent;
MaterialBrittleNonLocal(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialBrittleNonLocal(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
protected:
/// constitutive law
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost);
/// associate the non-local variables of the material to their neighborhoods
virtual void nonLocalVariableToNeighborhood();
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Sigma_max, Sigma_max, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> Sigma_max;
InternalField<Real> Sigma_maxnl;
InternalField<Real> Sigma_fracture;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_brittle_non_local_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_BRITTLE_NON_LOCAL_HH__ */
+#endif /* AKANTU_MATERIAL_BRITTLE_NON_LOCAL_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_damage_iterative.cc b/extra_packages/extra-materials/src/material_damage/material_damage_iterative.cc
index 1f675151c..ec5bb0e5b 100644
--- a/extra_packages/extra-materials/src/material_damage/material_damage_iterative.cc
+++ b/extra_packages/extra-materials/src/material_damage/material_damage_iterative.cc
@@ -1,246 +1,246 @@
/**
* @file material_damage_iterative.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Specialization of the class material damage to damage only one gauss
* point at a time and propagate damage in a linear way. Max principal stress
* criterion is used as a failure criterion.
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage_iterative.hh"
#include "communicator.hh"
#include "data_accessor.hh"
#include "solid_mechanics_model_RVE.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialDamageIterative<spatial_dimension>::MaterialDamageIterative(
SolidMechanicsModel & model, const ID & id)
: MaterialDamage<spatial_dimension>(model, id), Sc("Sc", *this),
reduction_step("damage_step", *this),
equivalent_stress("equivalent_stress", *this), max_reductions(0),
norm_max_equivalent_stress(0) {
AKANTU_DEBUG_IN();
this->registerParam("Sc", Sc, _pat_parsable, "critical stress threshold");
this->registerParam("prescribed_dam", prescribed_dam, 0.1,
_pat_parsable | _pat_modifiable, "prescribed damage");
this->registerParam(
"dam_threshold", dam_threshold, 0.8, _pat_parsable | _pat_modifiable,
"damage threshold at which damage damage will be set to 1");
this->registerParam(
"dam_tolerance", dam_tolerance, 0.01, _pat_parsable | _pat_modifiable,
"damage tolerance to decide if quadrature point will be damageed");
this->registerParam("max_damage", max_damage, 0.99999,
_pat_parsable | _pat_modifiable, "maximum damage value");
this->registerParam("max_reductions", max_reductions, UInt(10),
_pat_parsable | _pat_modifiable, "max reductions");
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->Sc.initialize(1);
this->equivalent_stress.initialize(1);
this->reduction_step.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDamageIterative<spatial_dimension>::
computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// Vector to store eigenvalues of current stress tensor
Vector<Real> eigenvalues(spatial_dimension);
auto Sc_it = Sc(el_type, ghost_type).begin();
auto equivalent_stress_it = equivalent_stress(el_type, ghost_type).begin();
Array<Real>::const_matrix_iterator grad_u_it =
grad_u.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_matrix_iterator grad_u_end =
grad_u.end(spatial_dimension, spatial_dimension);
Real * dam = this->damage(el_type, ghost_type).storage();
Matrix<Real> sigma(spatial_dimension, spatial_dimension);
for (; grad_u_it != grad_u_end; ++grad_u_it) {
- sigma.clear();
+ sigma.zero();
MaterialElastic<spatial_dimension>::computeStressOnQuad(*grad_u_it, sigma,
0.);
computeDamageAndStressOnQuad(sigma, *dam);
/// compute eigenvalues
sigma.eig(eigenvalues);
/// find max eigenvalue and normalize by tensile strength
*equivalent_stress_it =
*(std::max_element(eigenvalues.storage(),
eigenvalues.storage() + spatial_dimension)) /
*(Sc_it);
++Sc_it;
++equivalent_stress_it;
++dam;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDamageIterative<spatial_dimension>::computeAllStresses(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// reset normalized maximum equivalent stress
if (ghost_type == _not_ghost)
norm_max_equivalent_stress = 0;
MaterialDamage<spatial_dimension>::computeAllStresses(ghost_type);
/// find global Gauss point with highest stress
auto rve_model = dynamic_cast<SolidMechanicsModelRVE *>(&this->model);
if (rve_model == NULL) {
/// is no RVE model
const auto & comm = this->model.getMesh().getCommunicator();
comm.allReduce(norm_max_equivalent_stress, SynchronizerOperation::_max);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDamageIterative<spatial_dimension>::
findMaxNormalizedEquivalentStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (ghost_type == _not_ghost) {
// const Array<Real> & e_stress = equivalent_stress(el_type);
// if (e_stress.begin() != e_stress.end() ) {
// auto equivalent_stress_it_max =
// std::max_element(e_stress.begin(),e_stress.end());
// /// check if max equivalent stress for this element type is greater
// than the current norm_max_eq_stress
// if (*equivalent_stress_it_max > norm_max_equivalent_stress)
// norm_max_equivalent_stress = *equivalent_stress_it_max;
// }
const Array<Real> & e_stress = equivalent_stress(el_type);
auto equivalent_stress_it = e_stress.begin();
auto equivalent_stress_end = e_stress.end();
Array<Real> & dam = this->damage(el_type);
auto dam_it = dam.begin();
for (; equivalent_stress_it != equivalent_stress_end;
++equivalent_stress_it, ++dam_it) {
/// check if max equivalent stress for this element type is greater than
/// the current norm_max_eq_stress and if the element is not already fully
/// damaged
if (*equivalent_stress_it > norm_max_equivalent_stress &&
*dam_it < max_damage) {
norm_max_equivalent_stress = *equivalent_stress_it;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDamageIterative<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialDamage<spatial_dimension>::computeStress(el_type, ghost_type);
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeDamageAndStressOnQuad(sigma, *dam);
++dam;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
computeNormalizedEquivalentStress(this->gradu(el_type, ghost_type), el_type,
ghost_type);
norm_max_equivalent_stress = 0;
findMaxNormalizedEquivalentStress(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
UInt MaterialDamageIterative<spatial_dimension>::updateDamage() {
UInt nb_damaged_elements = 0;
AKANTU_DEBUG_ASSERT(prescribed_dam > 0.,
"Your prescribed damage must be greater than zero");
if (norm_max_equivalent_stress >= 1.) {
AKANTU_DEBUG_IN();
/// update the damage only on non-ghosts elements! Doesn't make sense to
/// update on ghost.
GhostType ghost_type = _not_ghost;
for (auto && el_type : this->model.getFEEngine().getMesh().elementTypes(
spatial_dimension, ghost_type)) {
const Array<Real> & e_stress = equivalent_stress(el_type);
auto equivalent_stress_it = e_stress.begin();
auto equivalent_stress_end = e_stress.end();
Array<Real> & dam = this->damage(el_type);
auto dam_it = dam.begin();
auto reduction_it = this->reduction_step(el_type, ghost_type).begin();
for (; equivalent_stress_it != equivalent_stress_end;
++equivalent_stress_it, ++dam_it, ++reduction_it) {
/// check if damage occurs
if (*equivalent_stress_it >=
(1 - dam_tolerance) * norm_max_equivalent_stress) {
/// check if this element can still be damaged
if (*reduction_it == this->max_reductions)
continue;
*reduction_it += 1;
if (*reduction_it == this->max_reductions) {
*dam_it = max_damage;
} else {
*dam_it += prescribed_dam;
}
nb_damaged_elements += 1;
}
}
}
}
auto * rve_model = dynamic_cast<SolidMechanicsModelRVE *>(&this->model);
if (rve_model == NULL) {
const auto & comm = this->model.getMesh().getCommunicator();
comm.allReduce(nb_damaged_elements, SynchronizerOperation::_sum);
}
AKANTU_DEBUG_OUT();
return nb_damaged_elements;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDamageIterative<spatial_dimension>::updateEnergiesAfterDamage(
ElementType el_type) {
MaterialDamage<spatial_dimension>::updateEnergies(el_type);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(damage_iterative, MaterialDamageIterative);
} // namespace akantu
diff --git a/extra_packages/extra-materials/src/material_damage/material_damage_iterative.hh b/extra_packages/extra-materials/src/material_damage/material_damage_iterative.hh
index 02e1a9deb..c844568f1 100644
--- a/extra_packages/extra-materials/src/material_damage/material_damage_iterative.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_damage_iterative.hh
@@ -1,145 +1,145 @@
/**
* @file material_damage_iterative.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Specialization of the class material damage to damage only one gauss
* point at a time and propagate damage in a linear way. Max principal stress
* criterion is used as a failure criterion.
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_DAMAGE_ITERATIVE_HH__
-#define __AKANTU_MATERIAL_DAMAGE_ITERATIVE_HH__
+#ifndef AKANTU_MATERIAL_DAMAGE_ITERATIVE_HH_
+#define AKANTU_MATERIAL_DAMAGE_ITERATIVE_HH_
namespace akantu {
/**
* Material damage iterative
*
* parameters in the material files :
* - Sc
*/
template <UInt spatial_dimension>
class MaterialDamageIterative : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialDamageIterative(SolidMechanicsModel & model, const ID & id = "");
- virtual ~MaterialDamageIterative(){};
+ ~MaterialDamageIterative() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// virtual void updateInternalParameters();
- virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
+ void computeAllStresses(GhostType ghost_type = _not_ghost) override;
/// update internal field damage
virtual UInt updateDamage();
- UInt updateDamage(UInt quad_index, const Real eq_stress,
- const ElementType & el_type, const GhostType & ghost_type);
+ UInt updateDamage(UInt quad_index, Real eq_stress,
+ ElementType el_type, GhostType ghost_type);
/// update energies after damage has been updated
- virtual void updateEnergiesAfterDamage(ElementType el_type);
+ void updateEnergiesAfterDamage(ElementType el_type) override;
/// compute the equivalent stress on each Gauss point (i.e. the max prinicpal
/// stress) and normalize it by the tensile strength
virtual void
computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// find max normalized equivalent stress
void findMaxNormalizedEquivalentStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
protected:
/// constitutive law for all element of a type
- virtual void computeStress(ElementType el_type,
- GhostType ghost_type = _not_ghost);
+ void computeStress(ElementType el_type,
+ GhostType ghost_type = _not_ghost) override;
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma, Real & dam);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get max normalized equivalent stress
AKANTU_GET_MACRO(NormMaxEquivalentStress, norm_max_equivalent_stress, Real);
/// get a non-const reference to the max normalized equivalent stress
AKANTU_GET_MACRO_NOT_CONST(NormMaxEquivalentStress,
norm_max_equivalent_stress, Real &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// resistance to damage
RandomInternalField<Real> Sc;
/// the reduction
InternalField<UInt> reduction_step;
/// internal field to store equivalent stress on each Gauss point
InternalField<Real> equivalent_stress;
/// the number of total reductions steps until complete failure
UInt max_reductions;
/// damage increment
Real prescribed_dam;
/// maximum equivalent stress
Real norm_max_equivalent_stress;
/// deviation from max stress at which Gauss point will still get damaged
Real dam_tolerance;
/// define damage threshold at which damage will be set to 1
Real dam_threshold;
/// maximum damage value
Real max_damage;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_damage_iterative_inline_impl.hh"
-#endif /* __AKANTU_MATERIAL_DAMAGE_ITERATIVE_HH__ */
+#endif /* AKANTU_MATERIAL_DAMAGE_ITERATIVE_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_damage_iterative_inline_impl.hh b/extra_packages/extra-materials/src/material_damage/material_damage_iterative_inline_impl.hh
index f537c3fcc..1e6f9c816 100644
--- a/extra_packages/extra-materials/src/material_damage/material_damage_iterative_inline_impl.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_damage_iterative_inline_impl.hh
@@ -1,91 +1,91 @@
/**
* @file material_damage_iterative_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Implementation of inline functions of the material damage iterative
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage_iterative.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void
MaterialDamageIterative<spatial_dimension>::computeDamageAndStressOnQuad(
Matrix<Real> & sigma, Real & dam) {
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
UInt MaterialDamageIterative<spatial_dimension>::updateDamage(
- UInt quad_index, const Real /*eq_stress*/, const ElementType & el_type,
- const GhostType & ghost_type) {
+ UInt quad_index, const Real /*eq_stress*/, ElementType el_type,
+ GhostType ghost_type) {
AKANTU_DEBUG_ASSERT(prescribed_dam > 0.,
"Your prescribed damage must be greater than zero");
Array<Real> & dam = this->damage(el_type, ghost_type);
Real & dam_on_quad = dam(quad_index);
/// check if damage occurs
if (equivalent_stress(el_type, ghost_type)(quad_index) >=
(1 - dam_tolerance) * norm_max_equivalent_stress) {
if (dam_on_quad < dam_threshold)
dam_on_quad += prescribed_dam;
else
dam_on_quad = max_damage;
return 1;
}
return 0;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline UInt MaterialDamageIterative<spatial_dimension>::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_user_2) {
return sizeof(Real) * this->getModel().getNbIntegrationPoints(elements);
}
return MaterialDamage<spatial_dimension>::getNbData(elements, tag);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialDamageIterative<spatial_dimension>::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_user_2) {
DataAccessor<Element>::packElementalDataHelper(
this->damage, buffer, elements, true, this->damage.getFEEngine());
}
return MaterialDamage<spatial_dimension>::packData(buffer, elements, tag);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialDamageIterative<spatial_dimension>::unpackData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == SynchronizationTag::_user_2) {
DataAccessor<Element>::unpackElementalDataHelper(
this->damage, buffer, elements, true, this->damage.getFEEngine());
}
return MaterialDamage<spatial_dimension>::unpackData(buffer, elements, tag);
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
diff --git a/extra_packages/extra-materials/src/material_damage/material_damage_iterative_non_local.hh b/extra_packages/extra-materials/src/material_damage/material_damage_iterative_non_local.hh
index 8d8b14194..af8b329eb 100644
--- a/extra_packages/extra-materials/src/material_damage/material_damage_iterative_non_local.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_damage_iterative_non_local.hh
@@ -1,80 +1,80 @@
/**
* @file material_damage_iterative_non_local.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief MaterialDamageIterativeNonLocal header for non-local damage
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_iterative.hh"
#include "material_damage_non_local.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_DAMAGE_ITERATIVE_NON_LOCAL_HH__
-#define __AKANTU_MATERIAL_DAMAGE_ITERATIVE_NON_LOCAL_HH__
+#ifndef AKANTU_MATERIAL_DAMAGE_ITERATIVE_NON_LOCAL_HH_
+#define AKANTU_MATERIAL_DAMAGE_ITERATIVE_NON_LOCAL_HH_
namespace akantu {
/**
* Material Damage Iterative Non local
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialDamageIterativeNonLocal
: public MaterialDamageNonLocal<
spatial_dimension, MaterialDamageIterative<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef MaterialDamageNonLocal<spatial_dimension,
MaterialDamageIterative<spatial_dimension>>
MaterialDamageIterativeNonLocalParent;
MaterialDamageIterativeNonLocal(SolidMechanicsModel & model,
const ID & id = "");
virtual ~MaterialDamageIterativeNonLocal(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
virtual void computeNonLocalStresses(GhostType ghost_type);
protected:
void computeStress(ElementType type, GhostType ghost_type);
void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost);
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> grad_u_nl;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_damage_iterative_non_local_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_DAMAGE_ITERATIVE_NON_LOCAL_HH__ */
+#endif /* AKANTU_MATERIAL_DAMAGE_ITERATIVE_NON_LOCAL_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_damage_iterative_non_local_inline_impl.hh b/extra_packages/extra-materials/src/material_damage/material_damage_iterative_non_local_inline_impl.hh
index d69ac493b..906cc0802 100644
--- a/extra_packages/extra-materials/src/material_damage/material_damage_iterative_non_local_inline_impl.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_damage_iterative_non_local_inline_impl.hh
@@ -1,88 +1,88 @@
/**
* @file material_damage_iterative_non_local_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief MaterialDamageIterativeNonLocal inline function implementation
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
} // namespace akantu
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#include <string>
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialDamageIterativeNonLocal<spatial_dimension>::
MaterialDamageIterativeNonLocal(SolidMechanicsModel & model, const ID & id)
- : Material(model, id), MaterialDamageIterativeNonLocalParent(model, id),
+ : MaterialDamageIterativeNonLocalParent(model, id),
grad_u_nl("grad_u non local", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = true;
this->grad_u_nl.initialize(spatial_dimension * spatial_dimension);
this->model.getNonLocalManager().registerNonLocalVariable(
this->gradu.getName(), grad_u_nl.getName(),
spatial_dimension * spatial_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDamageIterativeNonLocal<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialDamageIterativeNonLocalParent::initMaterial();
this->model.getNonLocalManager().nonLocalVariableToNeighborhood(
grad_u_nl.getName(), this->name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDamageIterativeNonLocal<spatial_dimension>::computeStress(
- ElementType type, GhostType ghost_type) {
+ ElementType /*type*/, GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDamageIterativeNonLocal<spatial_dimension>::computeNonLocalStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// compute the stress (based on the elastic law)
MaterialDamage<spatial_dimension>::computeStress(el_type, ghost_type);
/// multiply the stress by (1-d) to get the effective stress
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeDamageAndStressOnQuad(sigma, *dam);
++dam;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
/// compute the normalized equivalent stress
this->computeNormalizedEquivalentStress(this->grad_u_nl(el_type, ghost_type),
el_type, ghost_type);
/// find the maximum
this->norm_max_equivalent_stress = 0;
this->findMaxNormalizedEquivalentStress(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
diff --git a/extra_packages/extra-materials/src/material_damage/material_damage_linear.hh b/extra_packages/extra-materials/src/material_damage/material_damage_linear.hh
index 8999c6f92..7c00c44f3 100644
--- a/extra_packages/extra-materials/src/material_damage/material_damage_linear.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_damage_linear.hh
@@ -1,85 +1,85 @@
/**
* @file material_damage_linear.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
*
*
* @brief Material isotropic elastic + linear softening
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_DAMAGE_LINEAR_HH__
-#define __AKANTU_MATERIAL_DAMAGE_LINEAR_HH__
+#ifndef AKANTU_MATERIAL_DAMAGE_LINEAR_HH_
+#define AKANTU_MATERIAL_DAMAGE_LINEAR_HH_
namespace akantu {
/**
* Material liner damage
*
* parameters in the material files :
* - Sigc : (default: 1e5)
* - Gc : (default: 2)
*/
template <UInt spatial_dimension>
class MaterialDamageLinear : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialDamageLinear(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialDamageLinear(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & F, Matrix<Real> & sigma,
Real & damage, Real & K);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// kind of toughness
Real Gc;
/// critical stress
Real Sigc;
/// damage internal variable
InternalField<Real> K;
Real Epsmin, Epsmax;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_damage_linear_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_DAMAGE_LINEAR_HH__ */
+#endif /* AKANTU_MATERIAL_DAMAGE_LINEAR_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_iterative_stiffness_reduction.cc b/extra_packages/extra-materials/src/material_damage/material_iterative_stiffness_reduction.cc
index 4f3023f7f..2b5046261 100644
--- a/extra_packages/extra-materials/src/material_damage/material_iterative_stiffness_reduction.cc
+++ b/extra_packages/extra-materials/src/material_damage/material_iterative_stiffness_reduction.cc
@@ -1,203 +1,203 @@
/**
* @file material_iterative_stiffness_reduction.cc
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Thu Feb 18 16:03:56 2016
*
* @brief Implementation of material iterative stiffness reduction
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_iterative_stiffness_reduction.hh"
#include "communicator.hh"
#include "solid_mechanics_model_RVE.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialIterativeStiffnessReduction<spatial_dimension>::
MaterialIterativeStiffnessReduction(SolidMechanicsModel & model,
const ID & id)
: MaterialDamageIterative<spatial_dimension>(model, id),
eps_u("ultimate_strain", *this), D("tangent", *this), Gf(0.),
crack_band_width(0.), reduction_constant(0.) {
AKANTU_DEBUG_IN();
this->registerParam("Gf", Gf, _pat_parsable | _pat_modifiable,
"fracture energy");
this->registerParam("crack_band_width", crack_band_width,
_pat_parsable | _pat_modifiable, "crack_band_width");
this->registerParam("reduction_constant", reduction_constant, 2.,
_pat_parsable | _pat_modifiable, "reduction constant");
this->eps_u.initialize(1);
this->D.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIterativeStiffnessReduction<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialDamageIterative<spatial_dimension>::initMaterial();
for (auto ghost_type : ghost_types) {
/// loop over all types in the filter
for (auto & el_type :
this->element_filter.elementTypes(_ghost_type = ghost_type)) {
/// get the stiffness on each quad point
auto Sc_it = this->Sc(el_type, ghost_type).begin();
/// get the tangent of the tensile softening on each quad point
auto D_it = this->D(el_type, ghost_type).begin();
auto D_end = this->D(el_type, ghost_type).end();
/// get the ultimate strain on each quad
auto eps_u_it = this->eps_u(el_type, ghost_type).begin();
// compute the tangent and the ultimate strain for each quad
for (; D_it != D_end; ++Sc_it, ++D_it, ++eps_u_it) {
*eps_u_it = ((2. * this->Gf) / (*Sc_it * this->crack_band_width));
*D_it = *(Sc_it) / ((*eps_u_it) - ((*Sc_it) / this->E));
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIterativeStiffnessReduction<spatial_dimension>::
computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// storage for the current stress
Matrix<Real> sigma(spatial_dimension, spatial_dimension);
/// Vector to store eigenvalues of current stress tensor
Vector<Real> eigenvalues(spatial_dimension);
/// iterators on the needed internal fields
auto Sc_it = this->Sc(el_type, ghost_type).begin();
auto dam_it = this->damage(el_type, ghost_type).begin();
auto equivalent_stress_it =
this->equivalent_stress(el_type, ghost_type).begin();
auto grad_u_it = grad_u.begin(spatial_dimension, spatial_dimension);
auto grad_u_end = grad_u.end(spatial_dimension, spatial_dimension);
/// loop over all the quadrature points and compute the equivalent stress
for (; grad_u_it != grad_u_end; ++grad_u_it) {
/// compute the stress
- sigma.clear();
+ sigma.zero();
MaterialElastic<spatial_dimension>::computeStressOnQuad(*grad_u_it, sigma,
0.);
MaterialDamageIterative<spatial_dimension>::computeDamageAndStressOnQuad(
sigma, *dam_it);
/// compute eigenvalues
sigma.eig(eigenvalues);
/// find max eigenvalue and normalize by tensile strength
*equivalent_stress_it =
*(std::max_element(eigenvalues.storage(),
eigenvalues.storage() + spatial_dimension)) /
(*Sc_it);
++Sc_it;
++equivalent_stress_it;
++dam_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
UInt MaterialIterativeStiffnessReduction<spatial_dimension>::updateDamage() {
UInt nb_damaged_elements = 0;
if (this->norm_max_equivalent_stress >= 1.) {
AKANTU_DEBUG_IN();
/// update the damage only on non-ghosts elements! Doesn't make sense to
/// update on ghost.
GhostType ghost_type = _not_ghost;
/// loop over all the elements
for (auto && el_type : this->model.getFEEngine().getMesh().elementTypes(
spatial_dimension, ghost_type)) {
/// get iterators on the needed internal fields
auto equivalent_stress_it =
this->equivalent_stress(el_type, ghost_type).begin();
auto equivalent_stress_end =
this->equivalent_stress(el_type, ghost_type).end();
auto dam_it = this->damage(el_type, ghost_type).begin();
auto reduction_it = this->reduction_step(el_type, ghost_type).begin();
auto eps_u_it = this->eps_u(el_type, ghost_type).begin();
auto Sc_it = this->Sc(el_type, ghost_type).begin();
auto D_it = this->D(el_type, ghost_type).begin();
/// loop over all the quads of the given element type
for (; equivalent_stress_it != equivalent_stress_end;
++equivalent_stress_it, ++dam_it, ++reduction_it, ++eps_u_it,
++Sc_it, ++D_it) {
/// check if damage occurs
if (*equivalent_stress_it >=
(1 - this->dam_tolerance) * this->norm_max_equivalent_stress) {
/// check if this element can still be damaged
if (*reduction_it == this->max_reductions)
continue;
/// increment the counter of stiffness reduction steps
*reduction_it += 1;
if (*reduction_it == this->max_reductions)
*dam_it = this->max_damage;
else {
/// update the damage on this quad
*dam_it =
1. - (1. / std::pow(this->reduction_constant, *reduction_it));
/// update the stiffness on this quad
*Sc_it = (*eps_u_it) * (1. - (*dam_it)) * this->E * (*D_it) /
((1. - (*dam_it)) * this->E + (*D_it));
}
nb_damaged_elements += 1;
}
}
}
}
auto rve_model = dynamic_cast<SolidMechanicsModelRVE *>(&this->model);
if (rve_model == NULL) {
const auto & comm = this->model.getMesh().getCommunicator();
comm.allReduce(nb_damaged_elements, SynchronizerOperation::_sum);
}
AKANTU_DEBUG_OUT();
return nb_damaged_elements;
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(iterative_stiffness_reduction,
MaterialIterativeStiffnessReduction);
} // namespace akantu
diff --git a/extra_packages/extra-materials/src/material_damage/material_iterative_stiffness_reduction.hh b/extra_packages/extra-materials/src/material_damage/material_iterative_stiffness_reduction.hh
index 0cf24923b..0d8a00349 100644
--- a/extra_packages/extra-materials/src/material_damage/material_iterative_stiffness_reduction.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_iterative_stiffness_reduction.hh
@@ -1,104 +1,104 @@
/**
* @file material_iterative_stiffness_reduction.hh
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Thu Feb 18 15:25:05 2016
*
* @brief Damage material with constant stiffness reduction
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage_iterative.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ITERATIVE_STIFFNESS_REDUCTION_HH__
-#define __AKANTU_MATERIAL_ITERATIVE_STIFFNESS_REDUCTION_HH__
+#ifndef AKANTU_MATERIAL_ITERATIVE_STIFFNESS_REDUCTION_HH_
+#define AKANTU_MATERIAL_ITERATIVE_STIFFNESS_REDUCTION_HH_
namespace akantu {
/**
* Material damage iterative
*
* parameters in the material files :
* - Gfx
* - h
* - Sc
*/
/// Proposed by Rots and Invernizzi, 2004: Regularized sequentially linear
// saw-tooth softening model (section 4.2)
template <UInt spatial_dimension>
class MaterialIterativeStiffnessReduction
: public MaterialDamageIterative<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialIterativeStiffnessReduction(SolidMechanicsModel & model,
const ID & id = "");
virtual ~MaterialIterativeStiffnessReduction(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// init the material
virtual void initMaterial();
/// compute the equivalent stress on each Gauss point (i.e. the max prinicpal
/// stress) and normalize it by the tensile stiffness
virtual void
computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// update internal field damage
virtual UInt updateDamage();
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the ultimate strain
InternalField<Real> eps_u;
/// the tangent of the tensile stress-strain softening
InternalField<Real> D;
/// fracture energy
Real Gf;
/// crack_band_width for normalization of fracture energy
Real crack_band_width;
/// the reduction constant (denoated by a in the paper of rots)
Real reduction_constant;
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_ITERATIVE_STIFFNESS_REDUCTION_HH__ */
+#endif /* AKANTU_MATERIAL_ITERATIVE_STIFFNESS_REDUCTION_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage.hh b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage.hh
index 3d69f5014..6690943d3 100644
--- a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage.hh
@@ -1,146 +1,146 @@
/**
* @file material_orthotropic_damage.hh
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Sun Mar 8 12:49:56 2015
*
* @brief Material for orthotropic damage
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_HH__
-#define __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_HH__
+#ifndef AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_HH_
+#define AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_HH_
namespace akantu {
template <UInt spatial_dimension,
template <UInt> class Parent = MaterialElastic>
class MaterialOrthotropicDamage : public Parent<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialOrthotropicDamage(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialOrthotropicDamage(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
- virtual void initMaterial();
+ void initMaterial() override;
/// compute the tangent stiffness matrix for an element type
- virtual void computeTangentModuli(const ElementType & el_type,
- Array<Real> & tangent_matrix,
- GhostType ghost_type = _not_ghost);
+ void computeTangentModuli(ElementType el_type,
+ Array<Real> & tangent_matrix,
+ GhostType ghost_type = _not_ghost) override;
protected:
/// update the dissipated energy, must be called after the stress have been
/// computed
void updateEnergies(ElementType el_type) override;
/// compute the tangent stiffness matrix for a given quadrature point
inline void computeTangentModuliOnQuad(
Matrix<Real> & tangent, const Matrix<Real> C, const Matrix<Real> & dam,
const Matrix<Real> & dam_directions, Matrix<Real> & O_prime,
Matrix<Real> & S_prime, Matrix<Real> & O, Matrix<Real> & S,
Matrix<Real> & rotation_tmp);
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma,
Matrix<Real> & one_minus_D,
Matrix<Real> & root_one_minus_D,
Matrix<Real> & damage,
Matrix<Real> & first_term,
Matrix<Real> & third_term);
/// rotate a Matrix of size dim*dim into the coordinate system of the FE
/// computation
inline void rotateIntoComputationFrame(const Matrix<Real> & to_rotate,
Matrix<Real> & rotated,
const Matrix<Real> & damage_directions,
Matrix<Real> & rotation_tmp);
/// rotate a Matrix of size dim*dim into the coordinate system of the damage
inline void rotateIntoNewFrame(const Matrix<Real> & to_rotate,
Matrix<Real> & rotated,
const Matrix<Real> & damage_directions,
Matrix<Real> & rotation_tmp);
/// compute (1-D)
inline void computeOneMinusD(Matrix<Real> & one_minus_D,
const Matrix<Real> & damage);
/// compute (1-D)^(1/2)
inline void computeSqrtOneMinusD(const Matrix<Real> & one_minus_D,
Matrix<Real> & sqrt_one_minus_D);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy for the time step
Real getDissipatedEnergy() const;
// virtual Real getEnergy(std::string type);
// virtual Real getEnergy(std::string energy_id, ElementType type, UInt index)
// {
// return Parent<spatial_dimension>::getEnergy(energy_id, type, index);
// };
AKANTU_GET_MACRO_NOT_CONST(Damage, damage, ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Damage, damage, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real)
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage internal variable
InternalField<Real> damage;
/// dissipated energy
InternalField<Real> dissipated_energy;
/// contain the current value of @f$ \int_0^{\epsilon}\sigma(\omega)d\omega
/// @f$ the dissipated energy
InternalField<Real> int_sigma;
/// direction vectors for the damage frame
InternalField<Real> damage_dir_vecs;
Real eta;
/// maximum damage value
Real max_damage;
};
} // namespace akantu
#include "material_orthotropic_damage_tmpl.hh"
-#endif /* __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_HH__ */
+#endif /* AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative.cc b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative.cc
index 744410d2c..c96f40708 100644
--- a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative.cc
+++ b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative.cc
@@ -1,375 +1,375 @@
/**
* @file material_damage_iterative.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date Sun Mar 8 12:54:30 2015
*
* @brief Specialization of the class material damage to damage only one gauss
* point at a time and propagate damage in a linear way. Max principal stress
* criterion is used as a failure criterion.
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material_orthotropic_damage_iterative.hh"
#include "communicator.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialOrthotropicDamageIterative<spatial_dimension>::
MaterialOrthotropicDamageIterative(SolidMechanicsModel & model,
const ID & id)
: MaterialOrthotropicDamage<spatial_dimension>(model, id), Sc("Sc", *this),
equivalent_stress("equivalent_stress", *this),
stress_dir("equiv_stress_dir", *this), norm_max_equivalent_stress(0) {
AKANTU_DEBUG_IN();
this->registerParam("Sc", Sc, _pat_parsable, "critical stress threshold");
this->registerParam("prescribed_dam", prescribed_dam, 0.1,
_pat_parsable | _pat_modifiable,
"increase of damage in every step");
this->registerParam(
"dam_threshold", dam_threshold, 0.8, _pat_parsable | _pat_modifiable,
"damage threshold at which damage damage will be set to 1");
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->Sc.initialize(1);
this->equivalent_stress.initialize(1);
this->stress_dir.initialize(spatial_dimension * spatial_dimension);
/// the Gauss point with the highest stress can only be of type _not_ghost
q_max.ghost_type = _not_ghost;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialOrthotropicDamageIterative<spatial_dimension>::
computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// Vector to store eigenvalues of current stress tensor
Vector<Real> eigenvalues(spatial_dimension);
auto Sc_it = Sc(el_type).begin();
auto equivalent_stress_it = equivalent_stress(el_type).begin();
Array<Real>::const_matrix_iterator grad_u_it =
grad_u.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_matrix_iterator grad_u_end =
grad_u.end(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator stress_dir_it =
this->stress_dir(el_type).begin(spatial_dimension, spatial_dimension);
/// initialize matrix to store the stress for the criterion (only different in
/// non-local)
Matrix<Real> sigma(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator damage_iterator =
this->damage(el_type, ghost_type)
.begin(this->spatial_dimension, this->spatial_dimension);
Array<Real>::matrix_iterator damage_dir_it =
this->damage_dir_vecs(el_type, ghost_type)
.begin(this->spatial_dimension, this->spatial_dimension);
/// for the computation of the Cauchy stress the matrices (1-D) and
/// (1-D)^(1/2) are needed. For the formulation see Engineering
/// Damage Mechanics by Lemaitre and Desmorat.
Matrix<Real> one_minus_D(this->spatial_dimension, this->spatial_dimension);
Matrix<Real> sqrt_one_minus_D(this->spatial_dimension,
this->spatial_dimension);
Matrix<Real> one_minus_D_rotated(this->spatial_dimension,
this->spatial_dimension);
Matrix<Real> sqrt_one_minus_D_rotated(this->spatial_dimension,
this->spatial_dimension);
Matrix<Real> rotation_tmp(this->spatial_dimension, this->spatial_dimension);
/// create matrix to store the first term of the computation of the
/// Cauchy stress
Matrix<Real> first_term(this->spatial_dimension, this->spatial_dimension);
Matrix<Real> third_term(this->spatial_dimension, this->spatial_dimension);
for (; grad_u_it != grad_u_end;
++Sc_it, ++equivalent_stress_it, ++stress_dir_it, ++grad_u_it) {
- sigma.clear();
+ sigma.zero();
MaterialOrthotropicDamage<spatial_dimension>::computeStressOnQuad(
*grad_u_it, sigma, 0.);
/// rotate the tensors from the damage principal coordinate system to the CS
/// of the computation
if (!(Math::are_float_equal((*damage_iterator).trace(), 0))) {
/// compute (1-D) and (1-D)^1/2
this->computeOneMinusD(one_minus_D, *damage_iterator);
this->computeSqrtOneMinusD(one_minus_D, sqrt_one_minus_D);
this->rotateIntoComputationFrame(one_minus_D, one_minus_D_rotated,
*damage_dir_it, rotation_tmp);
this->rotateIntoComputationFrame(sqrt_one_minus_D,
sqrt_one_minus_D_rotated, *damage_dir_it,
rotation_tmp);
} else {
this->computeOneMinusD(one_minus_D_rotated, *damage_iterator);
this->computeSqrtOneMinusD(one_minus_D_rotated, sqrt_one_minus_D_rotated);
}
computeDamageAndStressOnQuad(sigma, one_minus_D_rotated,
sqrt_one_minus_D_rotated, *damage_iterator,
first_term, third_term);
/// compute the maximum principal stresses and their directions
sigma.eig(eigenvalues, *stress_dir_it);
*equivalent_stress_it = eigenvalues(0) / *(Sc_it);
++damage_dir_it;
++damage_iterator;
}
// for(;sigma_it != sigma_end; ++sigma_it,
// ++Sc_it, ++equivalent_stress_it, ++stress_dir_it) {
// /// compute the maximum principal stresses and their directions
// (*sigma_it).eig(eigenvalues, *stress_dir_it);
// *equivalent_stress_it = eigenvalues(0) / *(Sc_it);
// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialOrthotropicDamageIterative<spatial_dimension>::computeAllStresses(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// reset normalized maximum equivalent stress
if (ghost_type == _not_ghost)
norm_max_equivalent_stress = 0;
MaterialOrthotropicDamage<spatial_dimension>::computeAllStresses(ghost_type);
/// find global Gauss point with highest stress
this->model.getMesh().getCommunicator().allReduce(
norm_max_equivalent_stress, SynchronizerOperation::_max);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialOrthotropicDamageIterative<spatial_dimension>::
findMaxNormalizedEquivalentStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (ghost_type == _not_ghost) {
/// initialize the iterators for the equivalent stress and the damage
const Array<Real> & e_stress = equivalent_stress(el_type);
auto equivalent_stress_it = e_stress.begin();
auto equivalent_stress_end = e_stress.end();
Array<Real> & dam = this->damage(el_type);
auto dam_it = dam.begin(this->spatial_dimension, this->spatial_dimension);
auto damage_directions_it =
this->damage_dir_vecs(el_type, _not_ghost)
.begin(this->spatial_dimension, this->spatial_dimension);
auto stress_dir_it = this->stress_dir(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
/// initialize the matrices for damage rotation results
Matrix<Real> tmp(spatial_dimension, spatial_dimension);
Matrix<Real> dam_in_computation_frame(spatial_dimension, spatial_dimension);
Matrix<Real> dam_in_stress_frame(spatial_dimension, spatial_dimension);
for (; equivalent_stress_it != equivalent_stress_end;
++equivalent_stress_it, ++dam_it, ++damage_directions_it,
++stress_dir_it) {
/// check if max equivalent stress for this element type is greater than
/// the current norm_max_eq_stress
if (*equivalent_stress_it > norm_max_equivalent_stress &&
(spatial_dimension * this->max_damage - (*dam_it).trace() >
Math::getTolerance())) {
if (Math::are_float_equal((*dam_it).trace(), 0)) {
/// gauss point has not been damaged yet
norm_max_equivalent_stress = *equivalent_stress_it;
q_max.type = el_type;
q_max.global_num = equivalent_stress_it - e_stress.begin();
}
else {
/// find the damage increment on this Gauss point
/// rotate damage into stress frame
this->rotateIntoComputationFrame(*dam_it, dam_in_computation_frame,
*damage_directions_it, tmp);
this->rotateIntoNewFrame(dam_in_computation_frame,
dam_in_stress_frame, *stress_dir_it, tmp);
/// add damage increment
dam_in_stress_frame(0, 0) += prescribed_dam;
/// find new principal directions of damage
Vector<Real> dam_eigenvalues(spatial_dimension);
dam_in_stress_frame.eig(dam_eigenvalues);
bool limit_reached = false;
for (UInt i = 0; i < spatial_dimension; ++i) {
if (dam_eigenvalues(i) + Math::getTolerance() > this->max_damage)
limit_reached = true;
}
if (!limit_reached) {
norm_max_equivalent_stress = *equivalent_stress_it;
q_max.type = el_type;
q_max.global_num = equivalent_stress_it - e_stress.begin();
}
}
} /// end if equiv_stress > max_equiv_stress
} /// end loop over all gauss points of this element type
} // end if(_not_ghost)
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialOrthotropicDamageIterative<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialOrthotropicDamage<spatial_dimension>::computeStress(el_type,
ghost_type);
auto damage_iterator =
this->damage(el_type, ghost_type)
.begin(this->spatial_dimension, this->spatial_dimension);
auto damage_dir_it =
this->damage_dir_vecs(el_type, ghost_type)
.begin(this->spatial_dimension, this->spatial_dimension);
/// for the computation of the Cauchy stress the matrices (1-D) and
/// (1-D)^(1/2) are needed. For the formulation see Engineering
/// Damage Mechanics by Lemaitre and Desmorat.
Matrix<Real> one_minus_D(this->spatial_dimension, this->spatial_dimension);
Matrix<Real> sqrt_one_minus_D(this->spatial_dimension,
this->spatial_dimension);
Matrix<Real> one_minus_D_rotated(this->spatial_dimension,
this->spatial_dimension);
Matrix<Real> sqrt_one_minus_D_rotated(this->spatial_dimension,
this->spatial_dimension);
Matrix<Real> rotation_tmp(this->spatial_dimension, this->spatial_dimension);
/// create matrix to store the first term of the computation of the
/// Cauchy stress
Matrix<Real> first_term(this->spatial_dimension, this->spatial_dimension);
Matrix<Real> third_term(this->spatial_dimension, this->spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
/// rotate the tensors from the damage principal coordinate system to the CS
/// of the computation
if (!(Math::are_float_equal((*damage_iterator).trace(), 0))) {
/// compute (1-D) and (1-D)^1/2
this->computeOneMinusD(one_minus_D, *damage_iterator);
this->computeSqrtOneMinusD(one_minus_D, sqrt_one_minus_D);
this->rotateIntoComputationFrame(one_minus_D, one_minus_D_rotated,
*damage_dir_it, rotation_tmp);
this->rotateIntoComputationFrame(sqrt_one_minus_D, sqrt_one_minus_D_rotated,
*damage_dir_it, rotation_tmp);
} else {
this->computeOneMinusD(one_minus_D_rotated, *damage_iterator);
this->computeSqrtOneMinusD(one_minus_D_rotated, sqrt_one_minus_D_rotated);
}
computeDamageAndStressOnQuad(sigma, one_minus_D_rotated,
sqrt_one_minus_D_rotated, *damage_iterator,
first_term, third_term);
++damage_dir_it;
++damage_iterator;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
computeNormalizedEquivalentStress(this->gradu(el_type, ghost_type), el_type,
ghost_type);
norm_max_equivalent_stress = 0;
findMaxNormalizedEquivalentStress(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
UInt MaterialOrthotropicDamageIterative<spatial_dimension>::updateDamage() {
UInt nb_damaged_elements = 0;
AKANTU_DEBUG_ASSERT(prescribed_dam > 0.,
"Your prescribed damage must be greater than zero");
if (norm_max_equivalent_stress >= 1.) {
AKANTU_DEBUG_IN();
/// get the arrays and iterators for the element_type of the highest
/// quadrature point
ElementType el_type = q_max.type;
UInt q_global_num = q_max.global_num;
Array<Real> & dam = this->damage(el_type, _not_ghost);
auto dam_it = dam.begin(this->spatial_dimension, this->spatial_dimension);
auto damage_directions_it =
this->damage_dir_vecs(el_type, _not_ghost)
.begin(this->spatial_dimension, this->spatial_dimension);
auto stress_dir_it = this->stress_dir(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
/// initialize the matrices for damage rotation results
Matrix<Real> tmp(spatial_dimension, spatial_dimension);
Matrix<Real> dam_in_computation_frame(spatial_dimension, spatial_dimension);
Matrix<Real> dam_in_stress_frame(spatial_dimension, spatial_dimension);
/// references to damage and directions of highest Gauss point
Matrix<Real> q_dam = dam_it[q_global_num];
Matrix<Real> q_dam_dir = damage_directions_it[q_global_num];
Matrix<Real> q_stress_dir = stress_dir_it[q_global_num];
/// increment damage
/// find the damage increment on this Gauss point
/// rotate damage into stress frame
this->rotateIntoComputationFrame(q_dam, dam_in_computation_frame, q_dam_dir,
tmp);
this->rotateIntoNewFrame(dam_in_computation_frame, dam_in_stress_frame,
q_stress_dir, tmp);
/// add damage increment
dam_in_stress_frame(0, 0) += prescribed_dam;
/// find new principal directions of damage
Vector<Real> dam_eigenvalues(spatial_dimension);
dam_in_stress_frame.eig(dam_eigenvalues, q_dam_dir);
for (UInt i = 0; i < spatial_dimension; ++i) {
q_dam(i, i) = dam_eigenvalues(i);
if (q_dam(i, i) + Math::getTolerance() >= dam_threshold)
q_dam(i, i) = this->max_damage;
}
nb_damaged_elements += 1;
}
this->model.getMesh().getCommunicator().allReduce(
nb_damaged_elements, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return nb_damaged_elements;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialOrthotropicDamageIterative<
spatial_dimension>::updateEnergiesAfterDamage(ElementType el_type) {
MaterialOrthotropicDamage<spatial_dimension>::updateEnergies(el_type);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(orthotropic_damage_iterative,
MaterialOrthotropicDamageIterative);
} // namespace akantu
diff --git a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative.hh b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative.hh
index b54acdc04..8a54d3998 100644
--- a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative.hh
@@ -1,127 +1,127 @@
/**
* @file material_orthtropic_damage_iterative.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date Sun Mar 8 12:54:30 2015
*
* @brief Specialization of the class material orthotropic damage to
* damage only one gauss point at a time and propagate damage in a
* linear way. Max principal stress criterion is used as a failure
* criterion.
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_orthotropic_damage.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_HH__
-#define __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_HH__
+#ifndef AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_HH_
+#define AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_HH_
namespace akantu {
/**
* Material damage iterative
*
* parameters in the material files :
* - Sc
*/
template <UInt spatial_dimension>
class MaterialOrthotropicDamageIterative
: public MaterialOrthotropicDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialOrthotropicDamageIterative(SolidMechanicsModel & model,
const ID & id = "");
virtual ~MaterialOrthotropicDamageIterative(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// virtual void updateInternalParameters();
virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
/// update internal field damage
UInt updateDamage();
/// update energies after damage has been updated
virtual void updateEnergiesAfterDamage(ElementType el_type);
protected:
/// constitutive law for all element of a type
virtual void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// compute the equivalent stress on each Gauss point (i.e. the max prinicpal
/// stress) and normalize it by the tensile strength
void computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// find max normalized equivalent stress
void findMaxNormalizedEquivalentStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma,
Matrix<Real> & one_minus_D,
Matrix<Real> & root_one_minus_D,
Matrix<Real> & damage,
Matrix<Real> & first_term,
Matrix<Real> & third_term);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get max normalized equivalent stress
AKANTU_GET_MACRO(NormMaxEquivalentStress, norm_max_equivalent_stress, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// resistance to damage
RandomInternalField<Real> Sc;
/// internal field to store equivalent stress on each Gauss point
InternalField<Real> equivalent_stress;
/// internal field to store the direction of the current damage frame
InternalField<Real> stress_dir;
/// damage increment
Real prescribed_dam;
/// maximum equivalent stress
Real norm_max_equivalent_stress;
/// define damage threshold at which damage will be set to 1
Real dam_threshold;
/// quadrature point with highest equivalent Stress
IntegrationPoint q_max;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_orthotropic_damage_iterative_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_HH__ */
+#endif /* AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative_non_local.hh b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative_non_local.hh
index 59f738620..0f3cd4585 100644
--- a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative_non_local.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_iterative_non_local.hh
@@ -1,84 +1,84 @@
/**
* @file material_orthotropic_damage_iterative_non_local.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief MaterialOrthotropicDamageIterativeNonLocal header for non-local
* damage
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_non_local.hh"
#include "material_orthotropic_damage_iterative.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_NON_LOCAL_HH__
-#define __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_NON_LOCAL_HH__
+#ifndef AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_NON_LOCAL_HH_
+#define AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_NON_LOCAL_HH_
namespace akantu {
/**
* Material Damage Iterative Non local
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialOrthotropicDamageIterativeNonLocal
: public MaterialDamageNonLocal<
spatial_dimension,
MaterialOrthotropicDamageIterative<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef MaterialDamageNonLocal<
spatial_dimension, MaterialOrthotropicDamageIterative<spatial_dimension>>
MaterialOrthotropicDamageIterativeNonLocalParent;
MaterialOrthotropicDamageIterativeNonLocal(SolidMechanicsModel & model,
const ID & id = "");
virtual ~MaterialOrthotropicDamageIterativeNonLocal(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
protected:
void computeStress(ElementType type, GhostType ghost_type);
void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost);
/// associate the non-local variables of the material to their neighborhoods
virtual void nonLocalVariableToNeighborhood();
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> grad_u_nl;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_orthotropic_damage_iterative_non_local_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_NON_LOCAL_HH__ */
+#endif /* AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_ITERATIVE_NON_LOCAL_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_non_local.hh b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_non_local.hh
index 49e5106de..840c6d582 100644
--- a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_non_local.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_non_local.hh
@@ -1,103 +1,103 @@
/**
* @file material_orthotropic_damage_non_local.hh
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Sun Mar 22 21:10:27 2015
*
* @brief interface for non local orthotropic damage material
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_NON_LOCAL_HH__
-#define __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_NON_LOCAL_HH__
+#ifndef AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_NON_LOCAL_HH_
+#define AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_NON_LOCAL_HH_
namespace akantu {
template <UInt spatial_dimension, class MaterialOrthotropicDamageLocal>
class MaterialOrthotropicDamageNonLocal
: public MaterialOrthotropicDamageLocal,
public MaterialNonLocal<spatial_dimension> {
public:
typedef MaterialNonLocal<spatial_dimension> MaterialNonLocalParent;
typedef MaterialOrthotropicDamageLocal MaterialOrthotropicDamageParent;
MaterialOrthotropicDamageNonLocal(SolidMechanicsModel & model, const ID & id)
: Material(model, id), MaterialOrthotropicDamageParent(model, id),
MaterialNonLocalParent(model, id){};
/* ------------------------------------------------------------------------ */
virtual void initMaterial() {
MaterialOrthotropicDamageParent::initMaterial();
MaterialNonLocalParent::initMaterial();
}
protected:
/* --------------------------------------------------------------------------
*/
virtual void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost) = 0;
/* ------------------------------------------------------------------------ */
void computeNonLocalStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = this->model.getFEEngine().getMesh().firstType(
spatial_dimension, ghost_type);
Mesh::type_iterator last_type =
this->model.getFEEngine().getMesh().lastType(spatial_dimension,
ghost_type);
for (; it != last_type; ++it) {
computeNonLocalStress(*it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
public:
/* ------------------------------------------------------------------------ */
virtual inline UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
return MaterialNonLocalParent::getNbDataForElements(elements, tag) +
MaterialOrthotropicDamageParent::getNbDataForElements(elements, tag);
}
virtual inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
MaterialNonLocalParent::packElementData(buffer, elements, tag);
MaterialOrthotropicDamageParent::packElementData(buffer, elements, tag);
}
virtual inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
MaterialNonLocalParent::unpackElementData(buffer, elements, tag);
MaterialOrthotropicDamageParent::unpackElementData(buffer, elements, tag);
}
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_NON_LOCAL_HH__ */
+#endif /* AKANTU_MATERIAL_ORTHOTROPIC_DAMAGE_NON_LOCAL_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_tmpl.hh b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_tmpl.hh
index 0347f05ad..2da4fcb7f 100644
--- a/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_tmpl.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_orthotropic_damage_tmpl.hh
@@ -1,321 +1,321 @@
/**
* @file material_orthotropic_damage_tmpl.hh
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Sun Mar 8 12:54:30 2015
*
* @brief Specialization of the material class for the orthotropic
* damage material
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_orthotropic_damage.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
MaterialOrthotropicDamage<spatial_dimension, Parent>::MaterialOrthotropicDamage(
SolidMechanicsModel & model, const ID & id)
: Parent<spatial_dimension>(model, id), damage("damage", *this),
dissipated_energy("damage dissipated energy", *this),
int_sigma("integral of sigma", *this),
damage_dir_vecs("damage_principal_directions", *this) {
AKANTU_DEBUG_IN();
this->registerParam("eta", eta, 2., _pat_parsable | _pat_modifiable,
"Damage sensitivity parameter");
this->registerParam("max_damage", max_damage, 0.99999,
_pat_parsable | _pat_modifiable, "maximum damage value");
this->is_non_local = false;
this->use_previous_stress = true;
this->use_previous_gradu = true;
/// use second order tensor for description of damage state
this->damage.initialize(spatial_dimension * spatial_dimension);
this->dissipated_energy.initialize(1);
this->int_sigma.initialize(1);
this->damage_dir_vecs.initialize(spatial_dimension * spatial_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialOrthotropicDamage<spatial_dimension, Parent>::initMaterial() {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the dissipated energy in each element by a trapezoidal approximation
* of
* @f$ Ed = \int_0^{\epsilon}\sigma(\omega)d\omega -
* \frac{1}{2}\sigma:\epsilon@f$
*/
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialOrthotropicDamage<spatial_dimension, Parent>::updateEnergies(
ElementType el_type) {
Parent<spatial_dimension>::updateEnergies(el_type);
this->computePotentialEnergy(el_type);
auto epsilon_p =
this->gradu.previous(el_type).begin(spatial_dimension, spatial_dimension);
auto sigma_p = this->stress.previous(el_type).begin(spatial_dimension,
spatial_dimension);
auto epot = this->potential_energy(el_type).begin();
auto ints = this->int_sigma(el_type).begin();
auto ed = this->dissipated_energy(el_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
Matrix<Real> delta_gradu_it(grad_u);
delta_gradu_it -= *epsilon_p;
Matrix<Real> sigma_h(sigma);
sigma_h += *sigma_p;
Real dint = .5 * sigma_h.doubleDot(delta_gradu_it);
*ints += dint;
*ed = *ints - *epot;
++epsilon_p;
++sigma_p;
++epot;
++ints;
++ed;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialOrthotropicDamage<spatial_dimension, Parent>::computeTangentModuli(
- const ElementType & el_type, Array<Real> & tangent_matrix,
+ ElementType el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::computeTangentModuli(el_type, tangent_matrix,
ghost_type);
/// get the damage array for current element type
Array<Real> & dam = this->damage(el_type);
auto dam_it = dam.begin(this->spatial_dimension, this->spatial_dimension);
/// get the directions of damage for the current element type
Array<Real> & dam_dirs = this->damage_dir_vecs(el_type);
auto damage_directions_it =
dam_dirs.begin(this->spatial_dimension, this->spatial_dimension);
/// for the computation of the Cauchy stress the matrices (1-D) and
/// (1-D)^(1/2) are needed. For the formulation see Engineering
/// Damage Mechanics by Lemaitre and Desmorat.
Matrix<Real> one_minus_D(this->spatial_dimension, this->spatial_dimension);
Matrix<Real> sqrt_one_minus_D(this->spatial_dimension,
this->spatial_dimension);
Matrix<Real> one_minus_D_rot(spatial_dimension, spatial_dimension);
Matrix<Real> sqrt_one_minus_D_rot(spatial_dimension, spatial_dimension);
Matrix<Real> rotation_tmp(spatial_dimension, spatial_dimension);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
if (!(Math::are_float_equal((*dam_it).trace(), 0)))
computeTangentModuliOnQuad(tangent, tangent, *dam_it, *damage_directions_it,
one_minus_D, sqrt_one_minus_D, one_minus_D_rot,
sqrt_one_minus_D_rot, rotation_tmp);
++dam_it;
++damage_directions_it;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialOrthotropicDamage<spatial_dimension, Parent>::
computeTangentModuliOnQuad(Matrix<Real> & tangent, const Matrix<Real> C,
const Matrix<Real> & dam,
const Matrix<Real> & dam_directions,
Matrix<Real> & O_prime, Matrix<Real> & S_prime,
Matrix<Real> & O, Matrix<Real> & S,
Matrix<Real> & rotation_tmp) {
/// effect of damage on stiffness matrix: See Ragueneau et al. 2008, p. 423,
/// ep. 7
Real trace_D = dam.trace();
this->computeOneMinusD(O_prime, dam);
this->computeSqrtOneMinusD(O_prime, S_prime);
this->rotateIntoComputationFrame(O_prime, O, dam_directions, rotation_tmp);
this->rotateIntoComputationFrame(S_prime, S, dam_directions, rotation_tmp);
/// compute new stiffness matrix in damage coordinate system
if (spatial_dimension == 1)
tangent *= (1 - dam(0, 0));
if (spatial_dimension == 2) {
Real min_val =
std::min((this->eta / spatial_dimension * trace_D), this->max_damage);
/// first row
tangent(0, 0) =
(C(0, 0) * S(0, 0) * S(0, 0) + C(1, 0) * S(0, 1) * S(0, 1) -
(min_val / 2. - 1. / 2) * (C(0, 0) + C(1, 0)) +
(O(0, 0) * (C(0, 0) * O(0, 0) + C(1, 0) * O(1, 1))) / (trace_D - 2.));
tangent(0, 1) =
(C(0, 1) * S(0, 0) * S(0, 0) + C(1, 1) * S(0, 1) * S(0, 1) -
(min_val / 2. - 1. / 2) * (C(0, 1) + C(1, 1)) +
(O(0, 0) * (C(0, 1) * O(0, 0) + C(1, 1) * O(1, 1))) / (trace_D - 2.));
tangent(0, 2) = (2. * C(2, 2) * S(0, 0) * S(0, 1) +
(2. * C(2, 2) * O(0, 0) * O(0, 1)) / (trace_D - 2.));
/// second row
tangent(1, 0) =
(C(0, 0) * S(0, 1) * S(0, 1) + C(1, 0) * S(1, 1) * S(1, 1) -
(min_val / 2. - 1. / 2) * (C(0, 0) + C(1, 0)) +
(O(1, 1) * (C(0, 0) * O(0, 0) + C(1, 0) * O(1, 1))) / (trace_D - 2.));
tangent(1, 1) =
(C(0, 1) * S(0, 1) * S(0, 1) + C(1, 1) * S(1, 1) * S(1, 1) -
(min_val / 2. - 1. / 2) * (C(0, 1) + C(1, 1)) +
(O(1, 1) * (C(0, 1) * O(0, 0) + C(1, 1) * O(1, 1))) / (trace_D - 2.));
tangent(1, 2) = (2. * C(2, 2) * S(0, 1) * S(1, 1) +
(2. * C(2, 2) * O(0, 1) * O(1, 1)) / (trace_D - 2.));
/// third row
tangent(2, 0) =
((O(0, 1) * (C(0, 0) * O(0, 0) + C(1, 0) * O(1, 1))) / (trace_D - 2.) +
C(0, 0) * S(0, 0) * S(0, 1) + C(1, 0) * S(0, 1) * S(1, 1));
tangent(2, 1) =
((O(0, 1) * (C(0, 1) * O(0, 0) + C(1, 1) * O(1, 1))) / (trace_D - 2.) +
C(0, 1) * S(0, 0) * S(0, 1) + C(1, 1) * S(0, 1) * S(1, 1));
tangent(2, 2) = ((2. * C(2, 2) * O(0, 1) * O(0, 1)) / (trace_D - 2.) +
C(2, 2) * S(0, 1) * S(0, 1) + C(2, 2) * S(0, 0) * S(1, 1));
}
if (spatial_dimension == 3) {
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
inline void MaterialOrthotropicDamage<spatial_dimension, Parent>::
computeDamageAndStressOnQuad(Matrix<Real> & sigma,
Matrix<Real> & one_minus_D,
Matrix<Real> & sqrt_one_minus_D,
Matrix<Real> & damage,
Matrix<Real> & first_term,
Matrix<Real> & third_term) {
/// Definition of Cauchy stress based on second order damage tensor:
/// "Anisotropic damage modelling of biaxial behaviour and rupture
/// of concrete strucutres", Ragueneau et al., 2008, Eq. 7
first_term.mul<false, false>(sqrt_one_minus_D, sigma);
first_term *= sqrt_one_minus_D;
Real second_term = 0;
for (UInt i = 0; i < this->spatial_dimension; ++i) {
for (UInt j = 0; j < this->spatial_dimension; ++j)
second_term += sigma(i, j) * one_minus_D(i, j);
}
second_term /= (this->spatial_dimension - damage.trace());
one_minus_D *= second_term;
third_term.eye(1. / this->spatial_dimension * sigma.trace() *
(1 - eta / (this->spatial_dimension) * damage.trace()));
sigma.copy(first_term);
sigma -= one_minus_D;
sigma += third_term;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
inline void MaterialOrthotropicDamage<spatial_dimension, Parent>::
rotateIntoComputationFrame(const Matrix<Real> & to_rotate,
Matrix<Real> & rotated,
const Matrix<Real> & damage_directions,
Matrix<Real> & rotation_tmp) {
rotation_tmp.mul<false, true>(to_rotate, damage_directions);
rotated.mul<false, false>(damage_directions, rotation_tmp);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
inline void
MaterialOrthotropicDamage<spatial_dimension, Parent>::rotateIntoNewFrame(
const Matrix<Real> & to_rotate, Matrix<Real> & rotated,
const Matrix<Real> & damage_directions, Matrix<Real> & rotation_tmp) {
rotation_tmp.mul<false, false>(to_rotate, damage_directions);
rotated.mul<true, false>(damage_directions, rotation_tmp);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
inline void
MaterialOrthotropicDamage<spatial_dimension, Parent>::computeOneMinusD(
Matrix<Real> & one_minus_D, const Matrix<Real> & damage) {
/// compute one minus
one_minus_D.eye();
one_minus_D -= damage;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
inline void
MaterialOrthotropicDamage<spatial_dimension, Parent>::computeSqrtOneMinusD(
const Matrix<Real> & one_minus_D, Matrix<Real> & sqrt_one_minus_D) {
/// To compute (1-D)^1/2 we need to check that we are in the
/// principal coordinate system of the damage
#ifndef AKANTU_NDEBUG
for (UInt i = 0; i < this->spatial_dimension; ++i) {
for (UInt j = 0; j < this->spatial_dimension; ++j) {
if (i != j)
AKANTU_DEBUG_ASSERT(Math::are_float_equal(one_minus_D(i, j), 0),
"The damage tensor has off-diagonal parts");
}
}
#endif // AKANTU_NDEBUG
/// compute (1-D)^1/2
sqrt_one_minus_D.copy(one_minus_D);
for (UInt i = 0; i < this->spatial_dimension; ++i)
sqrt_one_minus_D(i, i) = std::sqrt(sqrt_one_minus_D(i, i));
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/extra_packages/extra-materials/src/material_damage/material_vreepeerlings.hh b/extra_packages/extra-materials/src/material_damage/material_vreepeerlings.hh
index 1fc80a6a1..54bcafe6b 100644
--- a/extra_packages/extra-materials/src/material_damage/material_vreepeerlings.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_vreepeerlings.hh
@@ -1,141 +1,141 @@
/**
* @file material_vreepeerlings.hh
*
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
*
* @brief Specialization of the material class for the VreePeerlings material
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_VREEPEERLINGS_HH__
-#define __AKANTU_MATERIAL_VREEPEERLINGS_HH__
+#ifndef AKANTU_MATERIAL_VREEPEERLINGS_HH_
+#define AKANTU_MATERIAL_VREEPEERLINGS_HH_
namespace akantu {
/**
* Material vreepeerlings
*
* parameters in the material files :
* - Kapaoi : (default: 0.0001) Initial threshold (of the equivalent strain)
* >= Crate
* - Kapac : (default: 0.0002) Final threshold (of the equivalent strain)
* - Arate : (default: 1.) Fitting parameter (must be close to 1 to do tend
* to 0 the stress in the damaged element)
* - Brate : (default: 1.) This parameter determines the rate at which the
* damage grows
* - Crate : (default: 0.0001) This parameter determines the rate at which
* the damage grows
* - Kct : (default: 1.) Ratio between compressive and tensile strength
*/
template <UInt spatial_dimension,
template <UInt> class MatParent = MaterialElastic>
class MaterialVreePeerlings
: public MaterialDamage<spatial_dimension, MatParent> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef MaterialDamage<spatial_dimension, MatParent>
MaterialVreePeerlingsParent;
MaterialVreePeerlings(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialVreePeerlings(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & F, Matrix<Real> & sigma,
Real & dam, Real & Equistrain_rate,
Real & Equistrain, Real & Kapaq, Real dt,
Matrix<Real> & strain_rate_vrpgls,
Real & FullDam_ValStrain,
Real & FullDam_ValStrain_rate,
Real & Nb_damage);
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma, Real & dam,
Real & Equistrain_rate,
Real & Equistrain, Real & Kapaq,
Real dt, Real & FullDam_Valstrain,
Real & FullDam_Valstrain_rate,
Real & Nb_damage);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Initial threshold (of the equivalent strain) (used in the initial step)
Real Kapaoi;
/// Final threshold (of the equivalent strain) (used in the initial step)
Real Kapac;
/// This parameter determines the rate at which the damage grows
Real Arate;
/// This parameter determines the rate at which the damage grows
Real Brate;
/// This parameter determines the rate at which the damage grows
Real Crate;
/// Ratio between compressive and tensile strength
Real Kct;
/// Randomness on Kapaoi
Real Kapao_randomness;
/// Kapa vector which contains the initial damage threshold
RandomInternalField<Real> Kapa;
/// Strain rate tensor to compute the rate dependent damage law
InternalField<Real> strain_rate_vreepeerlings;
/// Value of the equivalent strain when damage = 1
InternalField<Real> Full_dam_value_strain;
/// Value of the equivalent strain rate when damage = 1
InternalField<Real> Full_dam_value_strain_rate;
/// Count the number of times that the material is damaged to damage = 0 until
/// damage = 1
InternalField<Real> Number_damage;
/// Equivalent strain used to compute the damage evolution
InternalField<Real> equi_strain;
/// Equivalent strain rate used to compute the damage evolution
InternalField<Real> equi_strain_rate;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_vreepeerlings_inline_impl.hh"
#include "material_vreepeerlings_tmpl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_VREEPEERLINGS_HH__ */
+#endif /* AKANTU_MATERIAL_VREEPEERLINGS_HH_ */
diff --git a/extra_packages/extra-materials/src/material_damage/material_vreepeerlings_non_local.hh b/extra_packages/extra-materials/src/material_damage/material_vreepeerlings_non_local.hh
index 5e71d0c73..1d0b1db19 100644
--- a/extra_packages/extra-materials/src/material_damage/material_vreepeerlings_non_local.hh
+++ b/extra_packages/extra-materials/src/material_damage/material_vreepeerlings_non_local.hh
@@ -1,89 +1,89 @@
/**
* @file material_vreepeerlings_non_local.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
*
* @brief MaterialVreePeerlings header for non-local damage
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_non_local.hh"
#include "material_vreepeerlings.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_VREEPEERLINGS_NON_LOCAL_HH__
-#define __AKANTU_MATERIAL_VREEPEERLINGS_NON_LOCAL_HH__
+#ifndef AKANTU_MATERIAL_VREEPEERLINGS_NON_LOCAL_HH_
+#define AKANTU_MATERIAL_VREEPEERLINGS_NON_LOCAL_HH_
namespace akantu {
/**
* Material VreePeerlings Non local
*
* parameters in the material files :
*/
template <UInt spatial_dimension,
template <UInt> class MatParent = MaterialElastic>
class MaterialVreePeerlingsNonLocal
: public MaterialDamageNonLocal<
spatial_dimension,
MaterialVreePeerlings<spatial_dimension, MatParent>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef MaterialVreePeerlings<spatial_dimension, MatParent> Parent;
typedef MaterialDamageNonLocal<spatial_dimension, Parent>
MaterialVreePeerlingsNonLocalParent;
MaterialVreePeerlingsNonLocal(SolidMechanicsModel & model,
const ID & id = "");
virtual ~MaterialVreePeerlingsNonLocal(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
/// constitutive law for all element of a type
// void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
/// constitutive law
virtual void computeNonLocalStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// non local version of equivalent strain
InternalField<Real> equi_strain_non_local;
/// non local version of equivalent strain rate
InternalField<Real> equi_strain_rate_non_local;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_vreepeerlings_non_local_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_VREEPEERLINGS_NON_LOCAL_HH__ */
+#endif /* AKANTU_MATERIAL_VREEPEERLINGS_NON_LOCAL_HH_ */
diff --git a/extra_packages/extra-materials/src/material_extra_includes.hh b/extra_packages/extra-materials/src/material_extra_includes.hh
index 94351a841..e54cc75af 100644
--- a/extra_packages/extra-materials/src/material_extra_includes.hh
+++ b/extra_packages/extra-materials/src/material_extra_includes.hh
@@ -1,69 +1,69 @@
/**
* @file material_extra_includes.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
*
* @brief Extra list of materials
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_EXTRA_INCLUDES_HH__
-#define __AKANTU_MATERIAL_EXTRA_INCLUDES_HH__
+#ifndef AKANTU_MATERIAL_EXTRA_INCLUDES_HH_
+#define AKANTU_MATERIAL_EXTRA_INCLUDES_HH_
#ifndef AKANTU_CMAKE_LIST_MATERIALS
// visco-elastic materials
#include "material_stiffness_proportional.hh"
// damage materials
#include "material_brittle.hh"
#include "material_damage_iterative.hh"
#include "material_damage_linear.hh"
#include "material_iterative_stiffness_reduction.hh"
#include "material_orthotropic_damage_iterative.hh"
#include "material_vreepeerlings.hh"
// plasticity
#include "material_viscoplastic.hh"
// multi-scale simulations
#include "material_FE2.hh"
#endif
#if defined(AKANTU_DAMAGE_NON_LOCAL)
#ifndef AKANTU_CMAKE_LIST_MATERIALS
#include "material_brittle_non_local.hh"
#include "material_damage_iterative_non_local.hh"
#include "material_orthotropic_damage_iterative_non_local.hh"
#include "material_orthotropic_damage_non_local.hh"
#include "material_vreepeerlings_non_local.hh"
#endif
#define AKANTU_DAMAGE_NON_LOCAL_MATERIAL_EXTRA_LIST \
((2, (brittle_non_local, MaterialBrittleNonLocal)))( \
(2, (damage_iterative_non_local, MaterialDamageIterativeNonLocal)))( \
(2, (damage_orthotropic_iterative_non_local, \
MaterialOrthotropicDamageIterativeNonLocal)))
#else
#define AKANTU_DAMAGE_NON_LOCAL_MATERIAL_EXTRA_LIST
#endif
#define AKANTU_EXTRA_MATERIAL_LIST \
((2, (damage_linear, MaterialDamageLinear)))( \
(2, (brittle, MaterialBrittle)))((2, (material_FE2, MaterialFE2)))( \
(2, (damage_iterative, MaterialDamageIterative)))( \
(2, \
(iterative_stiffness_reduction, MaterialIterativeStiffnessReduction)))( \
(2, (vreepeerlings, MaterialVreePeerlings)))( \
(2, (ve_stiffness_prop, MaterialStiffnessProportional)))( \
(2, (visco_plastic, MaterialViscoPlastic)))( \
(2, (orthotropic_damage_iterative, MaterialOrthotropicDamageIterative)))
-#endif /* __AKANTU_MATERIAL_EXTRA_INCLUDES_HH__ */
+#endif /* AKANTU_MATERIAL_EXTRA_INCLUDES_HH_ */
diff --git a/extra_packages/extra-materials/src/material_plastic/material_viscoplastic.cc b/extra_packages/extra-materials/src/material_plastic/material_viscoplastic.cc
index 870827fee..1068fa7a4 100644
--- a/extra_packages/extra-materials/src/material_plastic/material_viscoplastic.cc
+++ b/extra_packages/extra-materials/src/material_plastic/material_viscoplastic.cc
@@ -1,107 +1,107 @@
/**
* @file material_viscoplastic.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
*
*
* @brief Specialization of the material class for isotropic viscoplastic
* (small deformation)
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material_viscoplastic.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialViscoPlastic<dim>::MaterialViscoPlastic(SolidMechanicsModel & model,
const ID & id)
: MaterialPlastic<dim>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("rate", rate, 0., _pat_parsable | _pat_modifiable,
"Rate sensitivity component");
this->registerParam("edot0", edot0, 0., _pat_parsable | _pat_modifiable,
"Reference strain rate");
this->registerParam("ts", ts, 0., _pat_parsable | _pat_modifiable,
"Time Step");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialViscoPlastic<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * iso_hardening = this->iso_hardening(el_type, ghost_type).storage();
auto previous_grad_u_it =
this->gradu.previous(el_type, ghost_type).begin(dim, dim);
auto previous_sigma_it =
this->stress.previous(el_type, ghost_type).begin(dim, dim);
auto inelastic_strain_it =
this->inelastic_strain(el_type, ghost_type).begin(dim, dim);
auto previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type, ghost_type).begin(dim, dim);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, *previous_grad_u_it, sigma, *previous_sigma_it,
*inelastic_strain_it, *previous_inelastic_strain_it,
*iso_hardening);
++inelastic_strain_it;
++iso_hardening;
++previous_grad_u_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialViscoPlastic<dim>::computeTangentModuli(
- __attribute__((unused)) const ElementType & el_type,
+ __attribute__((unused)) ElementType el_type,
Array<Real> & tangent_matrix,
__attribute__((unused)) GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto previous_sigma_it =
this->stress.previous(el_type, ghost_type).begin(dim, dim);
auto previous_strain_it =
this->gradu.previous(el_type, ghost_type).begin(dim, dim);
Real * iso_hardening = this->iso_hardening(el_type, ghost_type).storage();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
Matrix<Real> & previous_grad_u = *previous_strain_it;
Matrix<Real> & previous_sigma_tensor = *previous_sigma_it;
computeTangentModuliOnQuad(tangent, grad_u, previous_grad_u, sigma,
previous_sigma_tensor, *iso_hardening);
++previous_sigma_it;
++previous_strain_it;
++iso_hardening;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(visco_plastic, MaterialViscoPlastic);
} // namespace akantu
diff --git a/extra_packages/extra-materials/src/material_plastic/material_viscoplastic.hh b/extra_packages/extra-materials/src/material_plastic/material_viscoplastic.hh
index 240fe5926..eabfd8768 100644
--- a/extra_packages/extra-materials/src/material_plastic/material_viscoplastic.hh
+++ b/extra_packages/extra-materials/src/material_plastic/material_viscoplastic.hh
@@ -1,99 +1,99 @@
/**
* @file material_viscoplastic.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
*
*
* @brief Specialization of the material class for
* MaterialLinearIsotropicHardening to include viscous effects (small
* deformation)
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_VISCOPLASTIC_HH__
-#define __AKANTU_MATERIAL_VISCOPLASTIC_HH__
+#ifndef AKANTU_MATERIAL_VISCOPLASTIC_HH_
+#define AKANTU_MATERIAL_VISCOPLASTIC_HH_
namespace akantu {
/**
* Material plastic isotropic
*
* parameters in the material files :
* - h : Hardening parameter (default: 0)
* - sigmay : Yield stress
* - rate : Rate sensitivity
* - edot0 : Reference strain rate
*
* - ts: Time step
*/
template <UInt spatial_dimension>
class MaterialViscoPlastic : public MaterialPlastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialViscoPlastic(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
virtual void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// compute the tangent stiffness matrix for an element type
- void computeTangentModuli(const ElementType & el_type,
+ void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
protected:
inline void
computeStressOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain,
Real & iso_hardening) const;
inline void computeTangentModuliOnQuad(
Matrix<Real> & tangent, const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u, const Matrix<Real> & sigma_tensor,
const Matrix<Real> & previous_sigma_tensor,
const Real & iso_hardening) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Rate sensitivity component (rate)
Real rate;
/// Reference strain rate (edot0)
Real edot0;
/// Time step (ts)
Real ts;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_viscoplastic_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_VISCOPLASTIC_HH__ */
+#endif /* AKANTU_MATERIAL_VISCOPLASTIC_HH_ */
diff --git a/extra_packages/extra-materials/src/material_viscoelastic/material_stiffness_proportional.cc b/extra_packages/extra-materials/src/material_viscoelastic/material_stiffness_proportional.cc
index 87e8457e2..2bdf201b2 100644
--- a/extra_packages/extra-materials/src/material_viscoelastic/material_stiffness_proportional.cc
+++ b/extra_packages/extra-materials/src/material_viscoelastic/material_stiffness_proportional.cc
@@ -1,124 +1,121 @@
/**
* @file material_stiffness_proportional.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
*
* @brief Special. of the material class for the caughey viscoelastic material
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material_stiffness_proportional.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialStiffnessProportional<spatial_dimension>::MaterialStiffnessProportional(
SolidMechanicsModel & model, const ID & id)
: MaterialElastic<spatial_dimension>(model, id),
stress_viscosity("stress_viscosity", *this),
stress_elastic("stress_elastic", *this) {
AKANTU_DEBUG_IN();
this->registerParam("Alpha", alpha, 0., _pat_parsable | _pat_modifiable,
"Artificial viscous ratio");
this->stress_viscosity.initialize(spatial_dimension * spatial_dimension);
this->stress_elastic.initialize(spatial_dimension * spatial_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialStiffnessProportional<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialElastic<spatial_dimension>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialStiffnessProportional<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> & elem_filter = this->element_filter(el_type, ghost_type);
Array<Real> & stress_visc = stress_viscosity(el_type, ghost_type);
Array<Real> & stress_el = stress_elastic(el_type, ghost_type);
MaterialElastic<spatial_dimension>::computeStress(el_type, ghost_type);
Array<Real> & velocity = this->model.getVelocity();
Array<Real> strain_rate(0, spatial_dimension * spatial_dimension,
"strain_rate");
this->model.getFEEngine().gradientOnIntegrationPoints(
velocity, strain_rate, spatial_dimension, el_type, ghost_type,
elem_filter);
Array<Real>::matrix_iterator strain_rate_it =
strain_rate.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator stress_visc_it =
stress_visc.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator stress_el_it =
stress_el.begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & grad_v = *strain_rate_it;
Matrix<Real> & sigma_visc = *stress_visc_it;
Matrix<Real> & sigma_el = *stress_el_it;
MaterialElastic<spatial_dimension>::computeStressOnQuad(grad_v, sigma_visc);
sigma_visc *= alpha;
sigma_el.copy(sigma);
sigma += sigma_visc;
++strain_rate_it;
++stress_visc_it;
++stress_el_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialStiffnessProportional<spatial_dimension>::computePotentialEnergy(
- ElementType el_type, GhostType ghost_type) {
+ ElementType el_type) {
AKANTU_DEBUG_IN();
- if (ghost_type != _not_ghost)
- return;
-
- Array<Real> & stress_el = stress_elastic(el_type, ghost_type);
+ Array<Real> & stress_el = stress_elastic(el_type);
Array<Real>::matrix_iterator stress_el_it =
stress_el.begin(spatial_dimension, spatial_dimension);
- Real * epot = this->potential_energy(el_type, ghost_type).storage();
+ Real * epot = this->potential_energy(el_type).storage();
- MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
+ MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
Matrix<Real> & sigma_el = *stress_el_it;
MaterialElastic<spatial_dimension>::computePotentialEnergyOnQuad(
grad_u, sigma_el, *epot);
epot++;
++stress_el_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(ve_stiffness_prop, MaterialStiffnessProportional);
} // namespace akantu
diff --git a/extra_packages/extra-materials/src/material_viscoelastic/material_stiffness_proportional.hh b/extra_packages/extra-materials/src/material_viscoelastic/material_stiffness_proportional.hh
index 8dc4ed748..dbb3bac45 100644
--- a/extra_packages/extra-materials/src/material_viscoelastic/material_stiffness_proportional.hh
+++ b/extra_packages/extra-materials/src/material_viscoelastic/material_stiffness_proportional.hh
@@ -1,99 +1,98 @@
/**
* @file material_stiffness_proportional.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
*
* @brief Material isotropic visco-elastic with viscosity proportional to the
* stiffness
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_STIFFNESS_PROPORTIONAL_HH__
-#define __AKANTU_MATERIAL_STIFFNESS_PROPORTIONAL_HH__
+#ifndef AKANTU_MATERIAL_STIFFNESS_PROPORTIONAL_HH_
+#define AKANTU_MATERIAL_STIFFNESS_PROPORTIONAL_HH_
namespace akantu {
/**
* Material visco-elastic @f[\sigma = E\epsilon + \alpha E*
* \frac{d\epsilon}{dt}@f]
* it can be seen as a Kelvin-Voigt solid with @f[\eta = \alpha E @f]
*
* The material satisfies the Caughey condition, the visco-elastic solid has the
* same eigen-modes as the elastic one. (T.K. Caughey 1960 - Journal of Applied
* Mechanics 27, 269-271. Classical normal modes in damped linear systems.)
*
* parameters in the material files :
* - rho : density (default: 0)
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - Plane_Stress : if 0: plane strain, else: plane stress (default: 0)
* - alpha : viscous ratio
*/
template <UInt spatial_dimension>
class MaterialStiffnessProportional
: public MaterialElastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialStiffnessProportional(SolidMechanicsModel & model,
const ID & id = "");
virtual ~MaterialStiffnessProportional(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
- void initMaterial();
+ void initMaterial() override;
/// constitutive law for all element of a type
- void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
+ void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost) override;
/// compute the potential energy for all elements
- virtual void computePotentialEnergy(ElementType el_type,
- GhostType ghost_type = _not_ghost);
+ void computePotentialEnergy(ElementType el_type) override;
protected:
/// constitutive law for a given quadrature point
// inline void computeStress(Real * F, Real * sigma);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// stress due to viscosity
InternalField<Real> stress_viscosity;
/// stress due to elasticity
InternalField<Real> stress_elastic;
/// viscous ratio
Real alpha;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "material_elastic_caughey_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_STIFFNESS_PROPORTIONAL_HH__ */
+#endif /* AKANTU_MATERIAL_STIFFNESS_PROPORTIONAL_HH_ */
diff --git a/extra_packages/extra-materials/test/test_material_damage/test_material_damage_iterative_non_local_serial.cc b/extra_packages/extra-materials/test/test_material_damage/test_material_damage_iterative_non_local_serial.cc
index cb198daf4..2995a6616 100644
--- a/extra_packages/extra-materials/test/test_material_damage/test_material_damage_iterative_non_local_serial.cc
+++ b/extra_packages/extra-materials/test/test_material_damage/test_material_damage_iterative_non_local_serial.cc
@@ -1,235 +1,235 @@
/**
* @file test_material_damage_iterative_non_local_serial.cc
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Thu Nov 26 12:20:15 2015
*
* @brief test the material damage iterative non local in serial
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage_iterative_non_local.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
Math::setTolerance(1e-13);
debug::setDebugLevel(dblWarning);
initialize("material_non_local.dat", argc, argv);
const UInt spatial_dimension = 2;
ElementType element_type = _triangle_3;
/// read the mesh and partion it
Mesh mesh(spatial_dimension);
mesh.read("plate.msh");
/// model creation
SolidMechanicsModel model(mesh);
/// initialization of the model
model.initFull(SolidMechanicsModelOptions(_static));
/// boundary conditions
/// Dirichlet BC
mesh.createGroupsFromMeshData<std::string>(
"physical_names"); // creates groups from mesh names
model.applyBC(BC::Dirichlet::FixedValue(0, _x), "left");
model.applyBC(BC::Dirichlet::FixedValue(0, _y), "bottom");
model.applyBC(BC::Dirichlet::FixedValue(2., _y), "top");
/// add fields that should be dumped
model.setBaseName("material_damage_iterative_test");
model.addDumpFieldVector("displacement");
;
model.addDumpField("stress");
model.addDumpField("blocked_dofs");
model.addDumpField("residual");
model.addDumpField("grad_u");
model.addDumpField("grad_u non local");
model.addDumpField("damage");
model.addDumpField("partitions");
model.addDumpField("material_index");
model.addDumpField("Sc");
model.addDumpField("force");
model.addDumpField("equivalent_stress");
model.dump();
MaterialDamageIterativeNonLocal<spatial_dimension> & material =
dynamic_cast<MaterialDamageIterativeNonLocal<spatial_dimension> &>(
model.getMaterial(0));
Real error;
bool converged = false;
Real max_eq_stress = 0;
/// solve the system
converged =
model.solveStep<_scm_newton_raphson_tangent_modified,
SolveConvergenceCriteria::_increment>(1e-4, error, 2);
if (converged == false) {
std::cout << "The error is: " << error << std::endl;
AKANTU_DEBUG_ASSERT(converged, "Did not converge");
}
model.dump();
/// check the non-local grad_u: since grad_u is constant everywhere
/// also the grad_u non-local has to be constant
Array<Real> & grad_u_nl =
material.getInternal<Real>("grad_u non local")(element_type, _not_ghost);
Array<Real>::const_matrix_iterator grad_u_nl_it =
grad_u_nl.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_matrix_iterator grad_u_nl_end =
grad_u_nl.end(spatial_dimension, spatial_dimension);
Real diff = 0.;
Matrix<Real> diff_matrix(spatial_dimension, spatial_dimension);
Matrix<Real> const_grad_u(spatial_dimension, spatial_dimension, 0.);
const_grad_u(1, 1) = 1.;
for (; grad_u_nl_it != grad_u_nl_end; ++grad_u_nl_it) {
diff_matrix = (*grad_u_nl_it) - const_grad_u;
diff += diff_matrix.norm<L_2>();
}
if (diff > 10.e-13) {
std::cout << "Error in the non-local grad_u computation" << std::endl;
return EXIT_FAILURE;
}
/// change the displacement in one node to modify grad_u
Array<Real> & displ = model.getDisplacement();
displ(0, 1) = 2.6;
/// compute stresses: this will average grad_u and compute the max. eq. stress
model.updateResidual();
model.dump();
/// due to the change in the displacement element 33 and 37 will
/// have a grad_u different then one
const Array<Real> & grad_u =
material.getInternal<Real>("grad_u")(element_type, _not_ghost);
Array<Real>::const_matrix_iterator grad_u_it =
grad_u.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_matrix_iterator grad_u_end =
grad_u.end(spatial_dimension, spatial_dimension);
diff = 0.;
- diff_matrix.clear();
+ diff_matrix.zero();
UInt counter = 0;
for (; grad_u_it != grad_u_end; ++grad_u_it) {
diff_matrix = (*grad_u_it) - const_grad_u;
if (counter == 34 || counter == 38) {
if ((diff_matrix.norm<L_2>()) < 0.1) {
std::cout << "Error in the grad_u computation" << std::endl;
return EXIT_FAILURE;
}
} else
diff += diff_matrix.norm<L_2>();
++counter;
}
if (diff > 10.e-13) {
std::cout << "Error in the grad_u computation" << std::endl;
return EXIT_FAILURE;
}
/// check that the non-local grad_u
diff = 0.;
- diff_matrix.clear();
+ diff_matrix.zero();
Real nl_radius = 1.0; /// same values as in material file
grad_u_nl_it = grad_u_nl.begin(spatial_dimension, spatial_dimension);
ElementTypeMapReal quad_coords("quad_coords");
mesh.initElementTypeMapArray(quad_coords, spatial_dimension,
spatial_dimension, false, _ek_regular, true);
model.getFEEngine().computeIntegrationPointsCoordinates(quad_coords);
UInt nb_elements = mesh.getNbElement(element_type, _not_ghost);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(element_type);
Array<Real> & coords = quad_coords(element_type, _not_ghost);
auto coord_it = coords.begin(spatial_dimension);
Vector<Real> q1(spatial_dimension);
Vector<Real> q2(spatial_dimension);
q1 = coord_it[34];
q2 = coord_it[38];
for (UInt e = 0; e < nb_elements; ++e) {
for (UInt q = 0; q < nb_quads; ++q, ++coord_it, ++grad_u_nl_it) {
diff_matrix = (*grad_u_nl_it) - const_grad_u;
if ((q1.distance(*coord_it) <= (nl_radius + Math::getTolerance())) ||
(q2.distance(*coord_it) <= (nl_radius + Math::getTolerance()))) {
if ((diff_matrix.norm<L_2>()) < 1.e-6) {
std::cout << (diff_matrix.norm<L_2>()) << std::endl;
std::cout << "Error in the non-local grad_u computation" << std::endl;
return EXIT_FAILURE;
}
} else
diff += diff_matrix.norm<L_2>();
}
}
if (diff > 10.e-13) {
std::cout << "Error in the non-local grad_u computation" << std::endl;
return EXIT_FAILURE;
}
/// make sure that the normalized equivalent stress is based on the
/// non-local grad_u for this test check the elements that have the
/// constant stress of 1 but different non-local gradu because they
/// are in the neighborhood of the modified elements
coord_it = coords.begin(spatial_dimension);
const Array<Real> & eq_stress =
material.getInternal<Real>("equivalent_stress")(element_type, _not_ghost);
Array<Real>::const_scalar_iterator eq_stress_it = eq_stress.begin();
counter = 0;
for (UInt e = 0; e < nb_elements; ++e) {
for (UInt q = 0; q < nb_quads;
++q, ++coord_it, ++grad_u_nl_it, ++eq_stress_it) {
if (counter == 34 || counter == 38)
continue;
if (((q1.distance(*coord_it) <= (nl_radius + Math::getTolerance())) ||
(q2.distance(*coord_it) <= (nl_radius + Math::getTolerance()))) &&
Math::are_float_equal(*eq_stress_it, 0.1)) {
std::cout << "the normalized equivalent stress is most likely based on "
"the local, not the non-local grad_u!!!!"
<< std::endl;
finalize();
return EXIT_FAILURE;
}
++counter;
}
}
max_eq_stress = material.getNormMaxEquivalentStress();
if (!Math::are_float_equal(max_eq_stress, 0.1311267235941873)) {
std::cout << "the maximum equivalent stress is wrong" << std::endl;
finalize();
return EXIT_FAILURE;
}
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/extra_packages/igfem/src/dumper_igfem_connectivity.hh b/extra_packages/igfem/src/dumper_igfem_connectivity.hh
index ede071068..42191d61b 100644
--- a/extra_packages/igfem/src/dumper_igfem_connectivity.hh
+++ b/extra_packages/igfem/src/dumper_igfem_connectivity.hh
@@ -1,116 +1,116 @@
/**
* @file dumper_igfem_connectivity.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Iterator for the IGFEM connectivity
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
-#ifndef __AKANTU_DUMPER_IGFEM_CONNECTIVITY_HH__
-#define __AKANTU_DUMPER_IGFEM_CONNECTIVITY_HH__
+#ifndef AKANTU_DUMPER_IGFEM_CONNECTIVITY_HH_
+#define AKANTU_DUMPER_IGFEM_CONNECTIVITY_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_igfem_element_iterator.hh"
#include "dumper_igfem_generic_elemental_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <class types>
class igfem_connectivity_field_iterator
: public igfem_element_iterator<types, igfem_connectivity_field_iterator> {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
typedef igfem_element_iterator<types,
dumpers::igfem_connectivity_field_iterator>
parent;
typedef typename types::return_type return_type;
typedef typename types::field_type field_type;
typedef typename types::array_iterator array_iterator;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
igfem_connectivity_field_iterator(
const field_type & field, const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it, const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost, UInt sub_element = 0)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type,
sub_element) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
return_type operator*() {
const Vector<UInt> & element_connect = *this->array_it;
/// get the local sub_element connectivity and the nodes per sub-element
UInt * sub_connec_ptr =
IGFEMHelper::getSubElementConnectivity(*this->tit, this->sub_element);
UInt nb_nodes_sub_el =
IGFEMHelper::getNbNodesPerSubElement(*this->tit, this->sub_element);
/// get the global sub element connectivity
Vector<UInt> sub_element_connect(nb_nodes_sub_el);
for (UInt i = 0; i < nb_nodes_sub_el; ++i) {
UInt lc = sub_connec_ptr[i];
sub_element_connect(i) = element_connect(lc);
}
return sub_element_connect;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
class IGFEMConnectivityField
: public IGFEMGenericElementalField<SingleType<UInt, Vector, false>,
igfem_connectivity_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef SingleType<UInt, Vector, false> types;
typedef igfem_connectivity_field_iterator<types> iterator;
typedef types::field_type field_type;
typedef IGFEMGenericElementalField<types, igfem_connectivity_field_iterator>
parent;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
IGFEMConnectivityField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost)
: parent(field, spatial_dimension, ghost_type) {}
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
-#endif /*__AKANTU_DUMPER_IGFEM_CONNECTIVITY_HH__ */
+#endif /*AKANTU_DUMPER_IGFEM_CONNECTIVITY_HH_ */
diff --git a/extra_packages/igfem/src/dumper_igfem_element_iterator.hh b/extra_packages/igfem/src/dumper_igfem_element_iterator.hh
index e7c0958fd..09a320438 100644
--- a/extra_packages/igfem/src/dumper_igfem_element_iterator.hh
+++ b/extra_packages/igfem/src/dumper_igfem_element_iterator.hh
@@ -1,181 +1,181 @@
/**
* @file dumper_igfem_element_iterator.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Iterators for IGFEM elemental fields
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
-#ifndef __AKANTU_DUMPER_IGFEM_ELEMENT_ITERATOR_HH__
-#define __AKANTU_DUMPER_IGFEM_ELEMENT_ITERATOR_HH__
+#ifndef AKANTU_DUMPER_IGFEM_ELEMENT_ITERATOR_HH_
+#define AKANTU_DUMPER_IGFEM_ELEMENT_ITERATOR_HH_
/* -------------------------------------------------------------------------- */
#include "element.hh"
#include "igfem_helper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <class types, template <class> class final_iterator>
class igfem_element_iterator {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef typename types::it_type it_type;
typedef typename types::field_type field_type;
typedef typename types::array_type array_type;
typedef typename types::array_iterator array_iterator;
typedef final_iterator<types> iterator;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
igfem_element_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost,
UInt sub_element = 0)
: field(field), tit(t_it), tit_end(t_it_end), array_it(array_it),
array_it_end(array_it_end), ghost_type(ghost_type),
sub_element(sub_element) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
bool operator!=(const iterator & it) const {
return (ghost_type != it.ghost_type) ||
(tit != it.tit ||
((array_it != it.array_it) || sub_element != it.sub_element));
}
iterator & operator++() {
if (!this->sub_element)
this->sub_element += 1;
else {
++array_it;
this->sub_element = 0;
while (array_it == array_it_end && tit != tit_end) {
++tit;
if (tit != tit_end) {
const array_type & vect = field(*tit, ghost_type);
UInt _nb_data_per_elem = getNbDataPerElem(*tit);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.getSize() * nb_component) / _nb_data_per_elem;
array_it = vect.begin_reinterpret(_nb_data_per_elem, size);
array_it_end = vect.end_reinterpret(_nb_data_per_elem, size);
}
}
}
return *(static_cast<iterator *>(this));
}
ElementType getType() {
ElementType sub_type = IGFEMHelper::getSubElementType(*tit, sub_element);
return sub_type;
}
/// get IOHelperType for sub-element
UInt element_type() { return getIOHelperType(this->getType()); }
/// get current parent element????
Element getCurrentElement() {
return Element(*tit, array_it.getCurrentIndex());
}
- UInt getNbDataPerElem(const ElementType & type) const {
+ UInt getNbDataPerElem(ElementType type) const {
/// nb of data per parent element!
if (!nb_data_per_elem.exists(type, ghost_type))
return field(type, ghost_type).getNbComponent();
return nb_data_per_elem(type, ghost_type);
}
void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data) {
/// nb of data per parent element!
this->nb_data_per_elem = nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the field to iterate on
const field_type & field;
/// field iterator
typename field_type::type_iterator tit;
/// field iterator end
typename field_type::type_iterator tit_end;
/// array iterator
array_iterator array_it;
/// internal iterator end
array_iterator array_it_end;
/// ghost type identification
const GhostType ghost_type;
/// number of data per element
ElementTypeMap<UInt> nb_data_per_elem;
/// index of sub-element
UInt sub_element;
/// sub_element end
UInt sub_element_end;
};
/* -------------------------------------------------------------------------- */
template <typename types>
class igfem_elemental_field_iterator
: public igfem_element_iterator<types, igfem_elemental_field_iterator> {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
typedef igfem_element_iterator<
types, ::akantu::dumpers::igfem_elemental_field_iterator>
parent;
typedef typename types::it_type it_type;
typedef typename types::return_type return_type;
typedef typename types::field_type field_type;
typedef typename types::array_iterator array_iterator;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
igfem_elemental_field_iterator(
const field_type & field, const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it, const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost, UInt sub_element = 0)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type,
sub_element) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
return_type operator*() { return *this->array_it; }
private:
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_DUMPER_IGFEM_ELEMENT_ITERATOR_HH__ */
+#endif /* AKANTU_DUMPER_IGFEM_ELEMENT_ITERATOR_HH_ */
diff --git a/extra_packages/igfem/src/dumper_igfem_elemental_field.hh b/extra_packages/igfem/src/dumper_igfem_elemental_field.hh
index 9f2fafdaa..323c2dc7e 100644
--- a/extra_packages/igfem/src/dumper_igfem_elemental_field.hh
+++ b/extra_packages/igfem/src/dumper_igfem_elemental_field.hh
@@ -1,56 +1,56 @@
/**
* @file dumper_igfem_elemental_field.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief description of IGFEM elemental fields
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
-#ifndef __AKANTU_DUMPER_IGFEM_ELEMENTAL_FIELD_HH__
-#define __AKANTU_DUMPER_IGFEM_ELEMENTAL_FIELD_HH__
+#ifndef AKANTU_DUMPER_IGFEM_ELEMENTAL_FIELD_HH_
+#define AKANTU_DUMPER_IGFEM_ELEMENTAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_field.hh"
#include "dumper_igfem_generic_elemental_field.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename T, template <class> class ret = Vector,
bool filtered = false>
class IGFEMElementalField
: public IGFEMGenericElementalField<SingleType<T, ret, filtered>,
igfem_elemental_field_iterator> {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
typedef SingleType<T, ret, filtered> types;
typedef typename types::field_type field_type;
typedef elemental_field_iterator<types> iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
IGFEMElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_igfem)
: IGFEMGenericElementalField<types, igfem_elemental_field_iterator>(
field, spatial_dimension, ghost_type, element_kind) {}
};
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_IGFEM_ELEMENTAL_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_IGFEM_ELEMENTAL_FIELD_HH_ */
diff --git a/extra_packages/igfem/src/dumper_igfem_generic_elemental_field.hh b/extra_packages/igfem/src/dumper_igfem_generic_elemental_field.hh
index 48408e983..66bb3bf07 100644
--- a/extra_packages/igfem/src/dumper_igfem_generic_elemental_field.hh
+++ b/extra_packages/igfem/src/dumper_igfem_generic_elemental_field.hh
@@ -1,143 +1,143 @@
/**
* @file dumper_igfem_generic_elemental_field.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief generic interface IGFEM elemental fields
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DUMPER_IGFEM_GENERIC_ELEMENTAL_FIELD_HH__
-#define __AKANTU_DUMPER_IGFEM_GENERIC_ELEMENTAL_FIELD_HH__
+#ifndef AKANTU_DUMPER_IGFEM_GENERIC_ELEMENTAL_FIELD_HH_
+#define AKANTU_DUMPER_IGFEM_GENERIC_ELEMENTAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_generic_elemental_field.hh"
#include "dumper_igfem_element_iterator.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <class _types, template <class> class iterator_type>
class IGFEMGenericElementalField
: public GenericElementalField<_types, iterator_type> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef _types types;
typedef typename types::data_type data_type;
typedef typename types::it_type it_type;
typedef typename types::field_type field_type;
typedef typename types::array_type array_type;
typedef typename types::array_iterator array_iterator;
typedef typename field_type::type_iterator field_type_iterator;
typedef iterator_type<types> iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IGFEMGenericElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_igfem)
:
GenericElementalField<types, iterator_type>(field, spatial_dimension,
ghost_type, kind) {
this->checkHomogeneity();
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// return the size of the contained data: i.e. the number of elements ?
virtual UInt size() {
this->checkHomogeneity();
return ((this->nb_total_element) * 2);
}
virtual iterator begin() {
field_type_iterator tit;
field_type_iterator end;
UInt sub_element = 0;
/// type iterators on the elemental field
tit = this->field.firstType(this->spatial_dimension, this->ghost_type,
this->element_kind);
end = this->field.lastType(this->spatial_dimension, this->ghost_type,
this->element_kind);
/// skip all types without data
ElementType type = *tit;
for (; tit != end && this->field(*tit, this->ghost_type).getSize() == 0;
++tit) {
}
type = *tit;
if (tit == end)
return this->end();
/// getting information for the field of the given type
const array_type & vect = this->field(type, this->ghost_type);
UInt nb_data_per_elem = this->getNbDataPerElem(type);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.getSize() * nb_component) / nb_data_per_elem;
/// define element-wise iterator
array_iterator it = vect.begin_reinterpret(nb_data_per_elem, size);
array_iterator it_end = vect.end_reinterpret(nb_data_per_elem, size);
/// define data iterator
iterator rit = iterator(this->field, tit, end, it, it_end, this->ghost_type,
sub_element);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
virtual iterator end() {
field_type_iterator tit;
field_type_iterator end;
UInt sub_element = 0;
tit = this->field.firstType(this->spatial_dimension, this->ghost_type,
this->element_kind);
end = this->field.lastType(this->spatial_dimension, this->ghost_type,
this->element_kind);
ElementType type = *tit;
for (; tit != end; ++tit)
type = *tit;
const array_type & vect = this->field(type, this->ghost_type);
UInt nb_data = this->getNbDataPerElem(type);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.getSize() * nb_component) / nb_data;
array_iterator it = vect.end_reinterpret(nb_data, size);
iterator rit =
iterator(this->field, end, end, it, it, this->ghost_type, sub_element);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
};
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_IGFEM_GENERIC_ELEMENTAL_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_IGFEM_GENERIC_ELEMENTAL_FIELD_HH_ */
diff --git a/extra_packages/igfem/src/dumper_igfem_material_internal_field.hh b/extra_packages/igfem/src/dumper_igfem_material_internal_field.hh
index 2196f5a92..80c602966 100644
--- a/extra_packages/igfem/src/dumper_igfem_material_internal_field.hh
+++ b/extra_packages/igfem/src/dumper_igfem_material_internal_field.hh
@@ -1,53 +1,53 @@
/**
* @file dumper_igfem_material_internal_field.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief description of IGFEM material internal field
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
-#ifndef __AKANTU_DUMPER_IGFEM_MATERIAL_INTERNAL_FIELD_HH__
-#define __AKANTU_DUMPER_IGFEM_MATERIAL_INTERNAL_FIELD_HH__
+#ifndef AKANTU_DUMPER_IGFEM_MATERIAL_INTERNAL_FIELD_HH_
+#define AKANTU_DUMPER_IGFEM_MATERIAL_INTERNAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_igfem_quadrature_points_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename T, bool filtered = false>
class IGFEMInternalMaterialField
: public IGFEMGenericElementalField<SingleType<T, Vector, filtered>,
igfem_quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef SingleType<T, Vector, filtered> types;
typedef IGFEMGenericElementalField<types, igfem_quadrature_point_iterator>
parent;
typedef typename types::field_type field_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
IGFEMInternalMaterialField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_igfem)
: parent(field, spatial_dimension, ghost_type, kind) {}
};
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_IGFEM_MATERIAL_INTERNAL_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_IGFEM_MATERIAL_INTERNAL_FIELD_HH_ */
diff --git a/extra_packages/igfem/src/dumper_igfem_quadrature_points_field.hh b/extra_packages/igfem/src/dumper_igfem_quadrature_points_field.hh
index c6d702e2c..38b060bba 100644
--- a/extra_packages/igfem/src/dumper_igfem_quadrature_points_field.hh
+++ b/extra_packages/igfem/src/dumper_igfem_quadrature_points_field.hh
@@ -1,140 +1,140 @@
/**
* @file dumper_igfem_quadrature_points_field.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief description of IGFEM quadrature points field
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
-#ifndef __AKANTU_DUMPER_IGFEM_QUADRATURE_POINTS_FIELD_HH__
-#define __AKANTU_DUMPER_IGFEM_QUADRATURE_POINTS_FIELD_HH__
+#ifndef AKANTU_DUMPER_IGFEM_QUADRATURE_POINTS_FIELD_HH_
+#define AKANTU_DUMPER_IGFEM_QUADRATURE_POINTS_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_igfem_elemental_field.hh"
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename types>
class igfem_quadrature_point_iterator
: public igfem_element_iterator<types, igfem_quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef igfem_element_iterator<types, dumpers::igfem_quadrature_point_iterator>
parent;
typedef typename types::data_type data_type;
typedef typename types::return_type return_type;
typedef typename types::field_type field_type;
typedef typename types::array_iterator array_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
igfem_quadrature_point_iterator(
const field_type & field, const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it, const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost, UInt sub_element = 0)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type,
sub_element) {}
return_type operator*() {
const Vector<data_type> & mat_internal_field = *this->array_it;
/// get nb data per sub element
UInt nb_sub_1_internal_points =
IGFEMHelper::getNbQuadraturePoints(*this->tit, 0);
UInt nb_sub_2_internal_points =
IGFEMHelper::getNbQuadraturePoints(*this->tit, 1);
UInt nb_data = this->getNbDataPerElem(*(this->tit)) /
(nb_sub_1_internal_points + nb_sub_2_internal_points);
UInt nb_sub_components = 0;
if (!(this->sub_element))
nb_sub_components = nb_data * nb_sub_1_internal_points;
else
nb_sub_components = nb_data * nb_sub_2_internal_points;
Vector<data_type> sub_mat_internal_field(nb_sub_components);
if (!(this->sub_element)) {
for (UInt i = 0; i < nb_sub_components; ++i)
sub_mat_internal_field(i) = mat_internal_field(i);
} else {
for (UInt i = 0; i < nb_sub_components; ++i)
sub_mat_internal_field(i) =
mat_internal_field(nb_data * nb_sub_1_internal_points + i);
}
return sub_mat_internal_field;
}
};
// /* --------------------------------------------------------------------------
// */
// /* Fields type description */
// /* --------------------------------------------------------------------------
// */
// template<class types, template <class> class iterator_type>
// class GenericQuadraturePointsField :
// public GenericElementalField<types,iterator_type> {
// public:
// /* ------------------------------------------------------------------------
// */
// /* Typedefs */
// /* ------------------------------------------------------------------------
// */
// typedef iterator_type<types> iterator;
// typedef typename types::field_type field_type;
// typedef typename iterator::it_type T;
// typedef GenericElementalField<types,iterator_type> parent;
// /* ------------------------------------------------------------------------
// */
// /* Constructors/Destructors */
// /* ------------------------------------------------------------------------
// */
// GenericQuadraturePointsField(const field_type & field,
// UInt spatial_dimension = _all_dimensions,
// GhostType ghost_type = _not_ghost,
// ElementKind element_kind = _ek_not_defined) :
// parent(field, spatial_dimension, ghost_type, element_kind) { }
// /* ------------------------------------------------------------------------
// */
// /* Methods */
// /* ------------------------------------------------------------------------
// */
// virtual iterator begin() {
// iterator it = parent::begin();
// return it;
// }
// virtual iterator end () {
// iterator it = parent::end();
// return it;
// }
// };
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_IGFEM_QUADRATURE_POINTS_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_IGFEM_QUADRATURE_POINTS_FIELD_HH_ */
diff --git a/extra_packages/igfem/src/element_class_igfem.hh b/extra_packages/igfem/src/element_class_igfem.hh
index 86c85eeda..69b7ca250 100644
--- a/extra_packages/igfem/src/element_class_igfem.hh
+++ b/extra_packages/igfem/src/element_class_igfem.hh
@@ -1,297 +1,297 @@
/**
* @file element_class_igfem.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
*
* @brief Specialization for interface-enriched finite elements
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_CLASS_IGFEM_HH__
-#define __AKANTU_ELEMENT_CLASS_IGFEM_HH__
+#ifndef AKANTU_ELEMENT_CLASS_IGFEM_HH_
+#define AKANTU_ELEMENT_CLASS_IGFEM_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type>
class InterpolationElement<interpolation_type, _itk_igfem> {
public:
using interpolation_property = InterpolationProperty<interpolation_type>;
/* ------------------------------------------------------------------------ */
/* Member functions */
/* ------------------------------------------------------------------------ */
public:
static void assembleShapes(const Vector<Real> & parent_interpolation,
const Vector<Real> & sub_interpolation,
Vector<Real> & interpolation,
UInt sub_element = 0) {
/// N1, N2, N3 of parent triangle
UInt nb_nodes_parent = InterpolationElement<
interpolation_property::parent_interpolation_type>::getShapeSize();
for (UInt i = 0; i < nb_nodes_parent; ++i) {
interpolation(i) = parent_interpolation(i);
}
/// add the enrichment
UInt * enriched_node = enrichments[sub_element];
for (UInt e = 0; e < nb_enrichments; ++e) {
interpolation(nb_nodes_parent + e) = sub_interpolation(enriched_node[e]);
}
}
static void
assembleShapeDerivatives(const Matrix<Real> & parent_interpolation,
const Matrix<Real> & sub_interpolation,
Matrix<Real> & interpolation, UInt sub_element = 0) {
/// N1, N2, N3 of parent triangle
UInt nb_nodes_parent = InterpolationElement<
interpolation_property::parent_interpolation_type>::getShapeSize();
for (UInt i = 0; i < nb_nodes_parent; ++i) {
Vector<Real> ip(interpolation(i));
ip = parent_interpolation(i);
}
/// add the enrichment
UInt * enriched_node = enrichments[sub_element];
for (UInt e = 0; e < nb_enrichments; ++e) {
Vector<Real> ip(interpolation(nb_nodes_parent + e));
ip = sub_interpolation(enriched_node[e]);
}
}
static void interpolate(const Matrix<Real> & nodal_values,
const Vector<Real> & shapes,
Vector<Real> & interpolated) {
Matrix<Real> interpm(interpolated.storage(), nodal_values.rows(), 1);
Matrix<Real> shapesm(shapes.storage(),
interpolation_property::nb_nodes_per_element, 1);
interpm.mul<false, false>(nodal_values, shapesm);
}
public:
static AKANTU_GET_MACRO_NOT_CONST(
ShapeSize, interpolation_property::nb_nodes_per_element, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
ShapeDerivativesSize,
(interpolation_property::nb_nodes_per_element *
interpolation_property::natural_space_dimension),
UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NaturalSpaceDimension, interpolation_property::natural_space_dimension,
UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NbNodesPerInterpolationElement,
interpolation_property::nb_nodes_per_element, UInt);
static AKANTU_GET_MACRO_NOT_CONST(NbSubElements, interpolation_property::nb_sub_elements, UInt);
static UInt * getSubElementConnectivity(UInt t = 0) {
return &(interpolation_property::sub_element_connectivity[t]);
};
static UInt getNbEnrichments() { return interpolation_property::nb_enrichments; };
static UInt * getSubElementEnrichments(UInt t = 0) { return &(interpolation_property::enrichments[t]); };
protected:
/// storage of the subelement local connectivity
static UInt sub_element_connectivity_vect[];
/// local connectivity of subelements
static UInt * sub_element_connectivity[];
/// nb of subelements
static UInt nb_sub_elements;
/// storage of enrichments
static UInt enrichment_vect[];
static UInt * enrichments[];
static UInt nb_enrichments;
};
} // namespace akantu
#include "interpolation_element_igfem_tmpl.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
#define AKANTU_DEFINE_IGFEM_ELEMENT_CLASS_PROPERTY( \
elem_type, geom_type, interp_type, parent_el_type, sub_el_type_1, \
sub_el_type_2, elem_kind, sp, min_int_order) \
template <> struct ElementClassProperty<elem_type> { \
static const GeometricalType geometrical_type{geom_type}; \
static const InterpolationType interpolation_type{interp_type}; \
static const ElementType parent_element_type{parent_el_type}; \
static const ElementType sub_element_type_1{sub_el_type_1}; \
static const ElementType sub_element_type_2{sub_el_type_2}; \
static const ElementKind element_kind{elem_kind}; \
static const UInt spatial_dimension{sp}; \
static const UInt minimal_integration_order{min_int_order}; \
}
/* -------------------------------------------------------------------------- */
template <ElementType element_type>
class ElementClass<element_type, _ek_igfem>
: public GeometricalElement<
ElementClassProperty<element_type>::geometrical_type>,
public InterpolationElement<
ElementClassProperty<element_type>::interpolation_type> {
protected:
using geometrical_element =
GeometricalElement<ElementClassProperty<element_type>::geometrical_type>;
using interpolation_element = InterpolationElement<
ElementClassProperty<element_type>::interpolation_type>;
using parent_element =
ElementClass<ElementClassProperty<element_type>::parent_element_type>;
using element_property = ElementClassProperty<element_type>;
using interpolation_property =
typename interpolation_element::interpolation_property;
/* ------------------------------------------------------------------------ */
/* Member functions */
/* ------------------------------------------------------------------------ */
public:
static void getSubElementCoords(const Matrix<Real> & element_coords,
Matrix<Real> & sub_coords,
const UInt sub_element) {
/// get the sub_element_type
/// constexrp ElementType sub_el_type = getSubElementType(sub_element);
UInt nb_nodes_sub_el = 0;
switch (sub_element) {
case 0:
nb_nodes_sub_el =
ElementClass<ElementClassProperty<element_type>::sub_element_type_1>::
getNbNodesPerInterpolationElement();
break;
case 1:
nb_nodes_sub_el =
ElementClass<ElementClassProperty<element_type>::sub_element_type_2>::
getNbNodesPerInterpolationElement();
break;
}
for (UInt i = 0; i < nb_nodes_sub_el; ++i) {
UInt lc = InterpolationElement<
ElementClassProperty<element_type>::interpolation_type>::
sub_element_connectivity[sub_element][i];
Vector<Real> sub_c(sub_coords(i));
sub_c = element_coords(lc);
}
}
static void getParentCoords(const Matrix<Real> & element_coords,
Matrix<Real> & parent_coords) {
const ElementType parent_type =
ElementClassProperty<element_type>::parent_element_type;
UInt nb_nodes_parent_el =
ElementClass<parent_type>::getNbNodesPerInterpolationElement();
for (UInt i = 0; i < nb_nodes_parent_el; ++i) {
Vector<Real> parent_c(parent_coords(i));
parent_c = element_coords(i);
}
}
/// map the points from the reference domain of the subelement to the physical
/// domain
static void mapToPhysicalDomain(const Matrix<Real> & element_coords,
Matrix<Real> & sub_coords,
Matrix<Real> & sub_shapes,
Matrix<Real> & physical_points,
UInt sub_element = 0) {
/// get the sub_element_type
getSubElementCoords(element_coords, sub_coords, sub_element);
/// map the points of the subelements in the physical domain
switch (sub_element) {
case 0:
ElementClass<ElementClassProperty<element_type>::sub_element_type_1>::
interpolate(sub_coords, sub_shapes, physical_points);
break;
case 1:
ElementClass<ElementClassProperty<element_type>::sub_element_type_2>::
interpolate(sub_coords, sub_shapes, physical_points);
break;
}
}
/// map the points from the physical domain to the parent reference domain
static void mapToParentRefDomain(const Matrix<Real> & element_coords,
Matrix<Real> & parent_coords,
Matrix<Real> & physical_points,
Matrix<Real> & natural_coords) {
const ElementType parent_type =
ElementClassProperty<element_type>::parent_element_type;
getParentCoords(element_coords, parent_coords);
/// map the points from the physical domain into the parent reference domain
ElementClass<parent_type>::inverseMap(physical_points, parent_coords,
natural_coords);
}
/// map the points from the subelement reference domain to the parent
/// reference domain
static void mapFromSubRefToParentRef(const Matrix<Real> & element_coords,
Matrix<Real> & parent_coords,
Matrix<Real> & sub_coords,
Matrix<Real> & sub_shapes,
Matrix<Real> & physical_points,
Matrix<Real> & natural_points,
UInt /*nb_points*/, UInt sub_element) {
mapToPhysicalDomain(element_coords, sub_coords, sub_shapes, physical_points,
sub_element);
mapToParentRefDomain(element_coords, parent_coords, physical_points,
natural_points);
}
static void mapFromSubRefToParentRef(const Matrix<Real> & element_coords,
Matrix<Real> & sub_coords,
Matrix<Real> & parent_coords,
Matrix<Real> & sub_shapes,
Matrix<Real> & physical_points,
Matrix<Real> & parent_el_natural_coords,
UInt sub_element) {
mapToPhysicalDomain(element_coords, sub_coords, sub_shapes, physical_points,
sub_element);
mapToParentRefDomain(element_coords, parent_coords, physical_points,
parent_el_natural_coords);
}
/// compute the normal of a surface defined by the function f
static inline void
computeNormalsOnNaturalCoordinates(const Matrix<Real> & /*coord*/,
Matrix<Real> & /*f*/,
Matrix<Real> & /*normals*/) {
AKANTU_TO_IMPLEMENT();
}
/// determine orientation of the element with respect to the interface
static inline UInt getOrientation(const Vector<bool> & is_inside);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
static AKANTU_GET_MACRO_NOT_CONST(Kind, _ek_igfem, ElementKind);
static ElementType getP1ElementType() { AKANTU_TO_IMPLEMENT(); };
static AKANTU_GET_MACRO_NOT_CONST(
SpatialDimension, ElementClassProperty<element_type>::spatial_dimension,
UInt);
static ElementType & getFacetType(UInt /*t*/ = 0) { AKANTU_TO_IMPLEMENT(); }
static ElementType * getFacetTypeInternal() { AKANTU_TO_IMPLEMENT(); }
private:
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "geometrical_element_igfem.hh"
/* -------------------------------------------------------------------------- */
#include "element_class_igfem_segment_3_inline_impl.hh"
#include "element_class_igfem_triangle_4_inline_impl.hh"
#include "element_class_igfem_triangle_5_inline_impl.hh"
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_ELEMENT_CLASS_IGFEM_HH__ */
+#endif /* AKANTU_ELEMENT_CLASS_IGFEM_HH_ */
diff --git a/extra_packages/igfem/src/fe_engine_template_tmpl_igfem.hh b/extra_packages/igfem/src/fe_engine_template_tmpl_igfem.hh
index 0e6b39aed..3fe2d31a8 100644
--- a/extra_packages/igfem/src/fe_engine_template_tmpl_igfem.hh
+++ b/extra_packages/igfem/src/fe_engine_template_tmpl_igfem.hh
@@ -1,117 +1,117 @@
/**
* @file shape_igfem_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @brief ShapeIGFEM inline implementation
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss_igfem.hh"
#include "shape_igfem.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_FE_ENGINE_TEMPLATE_TMPL_IGFEM_HH__
-#define __AKANTU_FE_ENGINE_TEMPLATE_TMPL_IGFEM_HH__
+#ifndef AKANTU_FE_ENGINE_TEMPLATE_TMPL_IGFEM_HH_
+#define AKANTU_FE_ENGINE_TEMPLATE_TMPL_IGFEM_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* compatibility functions */
/* -------------------------------------------------------------------------- */
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_igfem,
DefaultIntegrationOrderFunctor>::
initShapeFunctions(const Array<Real> & nodes,
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh::type_iterator it =
mesh.firstType(element_dimension, ghost_type, _ek_igfem);
Mesh::type_iterator end =
mesh.lastType(element_dimension, ghost_type, _ek_igfem);
for (; it != end; ++it) {
ElementType type = *it;
integrator.initIntegrator(nodes, type, ghost_type);
#define INIT(_type) \
do { \
const Matrix<Real> & all_quads = \
integrator.getIntegrationPoints<_type>(ghost_type); \
const Matrix<Real> & quads_1 = integrator.getIntegrationPoints< \
ElementClassProperty<_type>::sub_element_type_1>(ghost_type); \
const Matrix<Real> & quads_2 = integrator.getIntegrationPoints< \
ElementClassProperty<_type>::sub_element_type_2>(ghost_type); \
shape_functions.initShapeFunctions(nodes, all_quads, quads_1, quads_2, \
_type, ghost_type); \
} while (0)
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(INIT);
#undef INIT
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_igfem,
DefaultIntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
- Array<Real> & quadrature_points_coordinates, const ElementType & type,
- const GhostType & ghost_type,
+ Array<Real> & quadrature_points_coordinates, ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
/// create an array with the nodal coordinates that need to be
/// interpolated. The nodal coordinates of the enriched nodes need
/// to be set to zero, because they represent the enrichment of the
/// position field, and the enrichments for this field are all zero!
/// There is no gap in the mesh!
Array<Real> igfem_nodes(nodes_coordinates.getSize(), spatial_dimension);
shape_functions.extractValuesAtStandardNodes(nodes_coordinates, igfem_nodes,
ghost_type);
interpolateOnIntegrationPoints(igfem_nodes, quadrature_points_coordinates,
spatial_dimension, type, ghost_type,
filter_elements);
}
/* -------------------------------------------------------------------------- */
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_igfem,
DefaultIntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
/// create an array with the nodal coordinates that need to be
/// interpolated. The nodal coordinates of the enriched nodes need
/// to be set to zero, because they represent the enrichment of the
/// position field, and the enrichments for this field are all zero!
/// There is no gap in the mesh!
Array<Real> igfem_nodes(nodes_coordinates.getSize(), spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
shape_functions.extractValuesAtStandardNodes(nodes_coordinates, igfem_nodes,
ghost_type);
}
interpolateOnIntegrationPoints(igfem_nodes, quadrature_points_coordinates,
filter_elements);
}
} // namespace akantu
-#endif /* __AKANTU_FE_ENGINE_TEMPLATE_TMPL_IGFEM_HH__ */
+#endif /* AKANTU_FE_ENGINE_TEMPLATE_TMPL_IGFEM_HH_ */
diff --git a/extra_packages/igfem/src/igfem_enrichment.cc b/extra_packages/igfem/src/igfem_enrichment.cc
index b2824769d..b45ca325d 100644
--- a/extra_packages/igfem/src/igfem_enrichment.cc
+++ b/extra_packages/igfem/src/igfem_enrichment.cc
@@ -1,100 +1,100 @@
/**
* @file igfem_enrichment.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Implementation of IGFEM enrichment
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "igfem_enrichment.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
IGFEMEnrichment::IGFEMEnrichment(Mesh & mesh) : intersector_sphere(mesh) {}
/* -------------------------------------------------------------------------- */
void IGFEMEnrichment::initialize() { intersector_sphere.init(); }
/* -------------------------------------------------------------------------- */
void IGFEMEnrichment::update(ID domain) {
if (domain == "")
domain = default_geometry;
Geometry & geometry = getGeometry(domain);
intersector_sphere.buildIGFEMMeshFromSpheres(geometry);
}
/* -------------------------------------------------------------------------- */
void IGFEMEnrichment::unRegisterGeometryObject(const ID & domain) {
GeometryMap::iterator it = geometries.find(domain);
AKANTU_DEBUG_ASSERT(it != geometries.end(), "Geometry object with domain "
<< domain
<< " was not found");
geometries.erase(it);
if (!geometries.empty())
default_geometry = (*geometries.begin()).first;
}
/* -------------------------------------------------------------------------- */
void IGFEMEnrichment::registerGeometryObject(Geometry & geometry,
const ID & domain) {
if (geometries.size() == 0)
default_geometry = domain;
#ifndef AKANTU_NDEBUG
GeometryMap::iterator it = geometries.find(domain);
AKANTU_DEBUG_ASSERT(it == geometries.end(), "Geometry object with domain "
<< domain
<< " was already created");
#endif
std::stringstream sstr;
sstr << "geometry:" << domain;
geometries[domain] = &geometry;
}
/* -------------------------------------------------------------------------- */
IGFEMEnrichment::Geometry & IGFEMEnrichment::getGeometry(ID & domain) const {
AKANTU_DEBUG_IN();
if (domain == "")
domain = default_geometry;
GeometryMap::const_iterator it = geometries.find(domain);
AKANTU_DEBUG_ASSERT(it != geometries.end(),
"The geometry " << domain << " is not registered");
AKANTU_DEBUG_OUT();
return *(it->second);
}
/* -------------------------------------------------------------------------- */
void IGFEMEnrichment::moveInterface(Real new_position, ID domain) {
if (domain == "")
domain = default_geometry;
Geometry & geometry = getGeometry(domain);
/// for this type of IGFEM enrichment the geometry consists of a list of
/// spheres
/// -> need to loop over spheres and change their radius,
/// which specifies the position of interfaces
Geometry::const_iterator query_it = geometry.begin();
Geometry sphere_list;
for (; query_it != geometry.end(); ++query_it) {
SK::Sphere_3 sphere(query_it->center(), new_position * new_position);
sphere_list.push_back(sphere);
}
- geometry.clear();
+ geometry.zero();
geometry = sphere_list;
this->update(domain);
}
} // namespace akantu
diff --git a/extra_packages/igfem/src/igfem_enrichment.hh b/extra_packages/igfem/src/igfem_enrichment.hh
index 1aaf87f7d..de1bbc360 100644
--- a/extra_packages/igfem/src/igfem_enrichment.hh
+++ b/extra_packages/igfem/src/igfem_enrichment.hh
@@ -1,101 +1,101 @@
/**
* @file igfem_enrichment.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief IGFEM enrichment: handles geometries of interfaces and advancement
* with time
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_IGFEM_ENRICHMENT_HH__
-#define __AKANTU_IGFEM_ENRICHMENT_HH__
+#ifndef AKANTU_IGFEM_ENRICHMENT_HH_
+#define AKANTU_IGFEM_ENRICHMENT_HH_
#include "mesh_igfem_spherical_growing_gel.hh"
#include "mesh_sphere_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class IGFEMEnrichment {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IGFEMEnrichment(Mesh & mesh);
virtual ~IGFEMEnrichment(){};
private:
typedef std::list<Spherical::Sphere_3> Geometry;
typedef std::map<std::string, Geometry *> GeometryMap;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create the mesh primitives
void initialize();
/// get a geometry from the geometry map
virtual Geometry & getGeometry(ID & domain) const;
/// detect the interface
virtual void update(ID domain = "");
/// remove geometry
virtual void unRegisterGeometryObject(const ID & domain = "");
/// insert new geometry
virtual void registerGeometryObject(Geometry & geometry,
const ID & domain = "");
/// check if a point is in a given domain
inline bool isInside(const Vector<Real> & point, ID domain = "") const;
/// move the interface, in this case grow the gel pockets
virtual void moveInterface(Real new_position, ID domain = "");
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
UInt getNbStandardNodes() {
return this->intersector_sphere.getNbStandardNodes();
}
UInt getNbEnrichedNodes() {
return this->intersector_sphere.getNbEnrichedNodes();
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
MeshIgfemSphericalGrowingGel<2> intersector_sphere;
GeometryMap geometries;
/// default geometry object
std::string default_geometry;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "igfem_enrichment_inline_impl.hh"
} // namespace akantu
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_IGFEM_ENRICHMENT_HH__ */
+#endif /* AKANTU_IGFEM_ENRICHMENT_HH_ */
diff --git a/extra_packages/igfem/src/igfem_helper.hh b/extra_packages/igfem/src/igfem_helper.hh
index 703bd4fab..687e9653b 100644
--- a/extra_packages/igfem/src/igfem_helper.hh
+++ b/extra_packages/igfem/src/igfem_helper.hh
@@ -1,148 +1,148 @@
/**
* @file dumper_igfem_element_iterator.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Helper class to return sub element information
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
-#ifndef __AKANTU_IGFEM_HELPER_HH__
-#define __AKANTU_IGFEM_HELPER_HH__
+#ifndef AKANTU_IGFEM_HELPER_HH_
+#define AKANTU_IGFEM_HELPER_HH_
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class FEEngine;
template <ElementType type> struct ElementTypeIGFEMData {
static ElementType igfem_element_types[];
static UInt nb_igfem_types;
};
struct IGFEMHelper {
template <ElementType type>
static VectorProxy<ElementType> getIGFEMElementTypes() {
return VectorProxy<ElementType>(
ElementTypeIGFEMData<type>::igfem_element_types,
ElementTypeIGFEMData<type>::nb_igfem_types);
}
/// get the number of nodes for a given sub-element
- static UInt getNbNodesPerSubElement(const ElementType & type,
+ static UInt getNbNodesPerSubElement(ElementType type,
const UInt sub_element) {
UInt nb_nodes_per_sub_element = 0;
#define GET_NB_NODES_PER_SUB_ELEMENT(type) \
switch (sub_element) { \
case 0: \
nb_nodes_per_sub_element = \
ElementClass<ElementClassProperty<type>::sub_element_type_1>:: \
getNbNodesPerInterpolationElement(); \
break; \
case 1: \
nb_nodes_per_sub_element = \
ElementClass<ElementClassProperty<type>::sub_element_type_2>:: \
getNbNodesPerInterpolationElement(); \
break; \
}
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(GET_NB_NODES_PER_SUB_ELEMENT);
#undef GET_NB_NODES_PER_SUB_ELEMENT
return nb_nodes_per_sub_element;
}
/// get the connectivity for a given sub-element
- static UInt * getSubElementConnectivity(const ElementType & type,
+ static UInt * getSubElementConnectivity(ElementType type,
const UInt sub_element) {
UInt * sub_element_connectivity = NULL;
#define GET_SUB_ELEMENT_CONNECTIVITY(type) \
sub_element_connectivity = \
ElementClass<type>::getSubElementConnectivity(sub_element);
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(GET_SUB_ELEMENT_CONNECTIVITY);
#undef GET_SUB_ELEMENT_CONNECTIVITY
return sub_element_connectivity;
}
/// get the sub-element type
- static ElementType getSubElementType(const ElementType & type,
+ static ElementType getSubElementType(ElementType type,
const UInt sub_element) {
ElementType sub_type = _not_defined;
#define GET_SUB_ELEMENT_TYPE(type) \
switch (sub_element) { \
case 0: \
sub_type = ElementClassProperty<type>::sub_element_type_1; \
break; \
case 1: \
sub_type = ElementClassProperty<type>::sub_element_type_2; \
break; \
}
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(GET_SUB_ELEMENT_TYPE);
#undef GET_SUB_ELEMENT_TYPE
return sub_type;
}
/// get the nb of quads for one sub element type
- static UInt getNbQuadraturePoints(const ElementType & type,
+ static UInt getNbQuadraturePoints(ElementType type,
const UInt sub_element) {
UInt nb_quad_points = 0;
#define GET_NB_QUADS(type) \
switch (sub_element) { \
case 0: \
nb_quad_points = GaussIntegrationElement<ElementClassProperty< \
type>::sub_element_type_1>::getNbQuadraturePoints(); \
break; \
case 1: \
nb_quad_points = GaussIntegrationElement<ElementClassProperty< \
type>::sub_element_type_2>::getNbQuadraturePoints(); \
break; \
}
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(GET_NB_QUADS);
#undef GET_NB_QUADS
return nb_quad_points;
}
/// get the nb of parent nodes of a given igfem element type
- static UInt getNbParentNodes(const ElementType & type) {
+ static UInt getNbParentNodes(ElementType type) {
UInt nb_parent_nodes = 0;
#define GET_NB_PARENT_NODES(type) \
nb_parent_nodes = \
ElementClass<ElementClassProperty<type>::parent_element_type>:: \
getNbNodesPerInterpolationElement();
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(GET_NB_PARENT_NODES);
#undef GET_NB_PARENT_NODES
return nb_parent_nodes;
}
/// get the nb of parent nodes of a given igfem element type
- static UInt getNbEnrichedNodes(const ElementType & type) {
+ static UInt getNbEnrichedNodes(ElementType type) {
UInt nb_enriched_nodes = 0;
#define GET_NB_ENRICHED_NODES(type) \
nb_enriched_nodes = ElementClass<type>::getNbEnrichments();
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(GET_NB_ENRICHED_NODES);
#undef GET_NB_ENRICHED_NODES
return nb_enriched_nodes;
}
/// get the nb of quads for one sub element type
- static UInt getElementOrientation(const ElementType & type,
+ static UInt getElementOrientation(ElementType type,
const Vector<bool> & is_inside) {
UInt orientation = 0;
#define GET_ORIENTATION(type) \
orientation = ElementClass<type>::getOrientation(is_inside);
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(GET_ORIENTATION);
#undef GET_ORIENTATION
return orientation;
}
};
} // namespace akantu
-#endif /* __AKANTU_IGFEM_HELPER_HH__ */
+#endif /* AKANTU_IGFEM_HELPER_HH_ */
diff --git a/extra_packages/igfem/src/integrator_gauss_igfem.hh b/extra_packages/igfem/src/integrator_gauss_igfem.hh
index ca310d34c..bee55b2f7 100644
--- a/extra_packages/igfem/src/integrator_gauss_igfem.hh
+++ b/extra_packages/igfem/src/integrator_gauss_igfem.hh
@@ -1,124 +1,124 @@
/**
* @file integrator_gauss_igfem.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Gauss integration facilities for IGFEM
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_INTEGRATOR_IGFEM_HH__
-#define __AKANTU_INTEGRATOR_IGFEM_HH__
+#ifndef AKANTU_INTEGRATOR_IGFEM_HH_
+#define AKANTU_INTEGRATOR_IGFEM_HH_
/* -------------------------------------------------------------------------- */
#include "integrator.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <class IOF> class IntegratorGauss<_ek_igfem, IOF> : public Integrator {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegratorGauss(const Mesh & mesh, const ID & id = "integrator_gauss",
const MemoryID & memory_id = 0);
virtual ~IntegratorGauss(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline void initIntegrator(const Array<Real> & nodes,
- const ElementType & type,
- const GhostType & ghost_type);
+ ElementType type,
+ GhostType ghost_type);
/// precompute jacobians on elements of type "type"
template <ElementType type>
void precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
- const GhostType & ghost_type);
+ GhostType ghost_type);
/// integrate f on the element "elem" of type "type"
template <ElementType type>
inline void integrateOnElement(const Array<Real> & f, Real * intf,
UInt nb_degree_of_freedom, const UInt elem,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// integrate f for all elements of type "type"
template <ElementType type>
void integrate(const Array<Real> & in_f, Array<Real> & intf,
- UInt nb_degree_of_freedom, const GhostType & ghost_type,
+ UInt nb_degree_of_freedom, GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate one element scalar value on all elements of type "type"
template <ElementType type>
Real integrate(const Vector<Real> & in_f, UInt index,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// integrate scalar field in_f
template <ElementType type>
- Real integrate(const Array<Real> & in_f, const GhostType & ghost_type,
+ Real integrate(const Array<Real> & in_f, GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate partially around a quadrature point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
template <ElementType type>
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
- const GhostType & ghost_type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// return a vector with quadrature points natural coordinates
template <ElementType type>
- const Matrix<Real> & getIntegrationPoints(const GhostType & ghost_type) const;
+ const Matrix<Real> & getIntegrationPoints(GhostType ghost_type) const;
/// return the number of quadrature points for a given element type
template <ElementType type>
inline UInt
- getNbIntegrationPoints(const GhostType & ghost_type = _not_ghost) const;
+ getNbIntegrationPoints(GhostType ghost_type = _not_ghost) const;
/// compute the vector of quadrature points natural coordinates
template <ElementType type>
- void computeQuadraturePoints(const GhostType & ghost_type);
+ void computeQuadraturePoints(GhostType ghost_type);
/// check that the jacobians are not negative
template <ElementType type>
- void checkJacobians(const GhostType & ghost_type) const;
+ void checkJacobians(GhostType ghost_type) const;
public:
/// compute the jacobians on quad points for a given element
template <ElementType type>
void computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
Vector<Real> & jacobians);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
inline void integrate(Real * f, Real * jac, Real * inte,
UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const;
private:
ElementTypeMap<Matrix<Real>> quadrature_points;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "integrator_gauss_igfem_inline_impl.hh"
} // namespace akantu
-#endif /*__AKANTU_INTEGRATOR_IGFEM_HH__ */
+#endif /*AKANTU_INTEGRATOR_IGFEM_HH_ */
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
diff --git a/extra_packages/igfem/src/integrator_gauss_igfem_inline_impl.hh b/extra_packages/igfem/src/integrator_gauss_igfem_inline_impl.hh
index e58250fb4..9b92acc8e 100644
--- a/extra_packages/igfem/src/integrator_gauss_igfem_inline_impl.hh
+++ b/extra_packages/igfem/src/integrator_gauss_igfem_inline_impl.hh
@@ -1,451 +1,451 @@
/**
* @file integrator_gauss_igfem.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Inline functions of gauss integrator for the case of IGFEM
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "fe_engine.hh"
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
#define INIT_INTEGRATOR(type) \
computeQuadraturePoints<type>(ghost_type); \
precomputeJacobiansOnQuadraturePoints<type>(nodes, ghost_type); \
checkJacobians<type>(ghost_type);
template <class IOF>
inline void
IntegratorGauss<_ek_igfem, IOF>::initIntegrator(const Array<Real> & nodes,
- const ElementType & type,
- const GhostType & ghost_type) {
+ ElementType type,
+ GhostType ghost_type) {
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(INIT_INTEGRATOR);
}
#undef INIT_INTEGRATOR
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline UInt IntegratorGauss<_ek_igfem, IOF>::getNbIntegrationPoints(
- const GhostType &) const {
+ GhostType) const {
const ElementType sub_type_1 = ElementClassProperty<type>::sub_element_type_1;
const ElementType sub_type_2 = ElementClassProperty<type>::sub_element_type_2;
UInt nb_quad_points_sub_1 =
GaussIntegrationElement<sub_type_1>::getNbQuadraturePoints();
UInt nb_quad_points_sub_2 =
GaussIntegrationElement<sub_type_2>::getNbQuadraturePoints();
return (nb_quad_points_sub_1 + nb_quad_points_sub_2);
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline void IntegratorGauss<_ek_igfem, IOF>::integrateOnElement(
const Array<Real> & f, Real * intf, UInt nb_degree_of_freedom,
- const UInt elem, const GhostType & ghost_type) const {
+ const UInt elem, GhostType ghost_type) const {
Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points = getNbIntegrationPoints<type>();
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f do not have the good number of component.");
Real * f_val = f.storage() + elem * f.getNbComponent();
Real * jac_val = jac_loc.storage() + elem * nb_quadrature_points;
integrate(f_val, jac_val, intf, nb_degree_of_freedom, nb_quadrature_points);
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline Real IntegratorGauss<_ek_igfem, IOF>::integrate(
- const Vector<Real> & in_f, UInt index, const GhostType & ghost_type) const {
+ const Vector<Real> & in_f, UInt index, GhostType ghost_type) const {
const Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points = getNbIntegrationPoints<type>();
AKANTU_DEBUG_ASSERT(in_f.size() == nb_quadrature_points,
"The vector f do not have nb_quadrature_points entries.");
Real * jac_val = jac_loc.storage() + index * nb_quadrature_points;
Real intf;
integrate(in_f.storage(), jac_val, &intf, 1, nb_quadrature_points);
return intf;
return 0.;
}
/* -------------------------------------------------------------------------- */
template <class IOF>
inline void
IntegratorGauss<_ek_igfem, IOF>::integrate(Real * f, Real * jac, Real * inte,
UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const {
memset(inte, 0, nb_degree_of_freedom * sizeof(Real));
Real * cjac = jac;
for (UInt q = 0; q < nb_quadrature_points; ++q) {
for (UInt dof = 0; dof < nb_degree_of_freedom; ++dof) {
inte[dof] += *f * *cjac;
++f;
}
++cjac;
}
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline const Matrix<Real> &
IntegratorGauss<_ek_igfem, IOF>::getIntegrationPoints(
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_ASSERT(
quadrature_points.exists(type, ghost_type),
"Quadrature points for type "
<< quadrature_points.printType(type, ghost_type)
<< " have not been initialized."
<< " Did you use 'computeQuadraturePoints' function ?");
return quadrature_points(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline void IntegratorGauss<_ek_igfem, IOF>::computeQuadraturePoints(
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
/// typedef for the two subelement_types and the parent element type
const ElementType sub_type_1 = ElementClassProperty<type>::sub_element_type_1;
const ElementType sub_type_2 = ElementClassProperty<type>::sub_element_type_2;
/// store the quadrature points on the two subelements
Matrix<Real> & quads_sub_1 = quadrature_points(sub_type_1, ghost_type);
Matrix<Real> & quads_sub_2 = quadrature_points(sub_type_2, ghost_type);
quads_sub_1 = GaussIntegrationElement<sub_type_1>::getQuadraturePoints();
quads_sub_2 = GaussIntegrationElement<sub_type_2>::getQuadraturePoints();
/// store all quad points for the current type
UInt nb_quad_points_sub_1 =
GaussIntegrationElement<sub_type_1>::getNbQuadraturePoints();
UInt nb_quad_points_sub_2 =
GaussIntegrationElement<sub_type_2>::getNbQuadraturePoints();
UInt spatial_dimension = mesh.getSpatialDimension();
Matrix<Real> & quads = quadrature_points(type, ghost_type);
quads = Matrix<Real>(spatial_dimension,
nb_quad_points_sub_1 + nb_quad_points_sub_2);
Matrix<Real> quads_1(quads.storage(), quads.rows(), nb_quad_points_sub_1);
quads_1 = quads_sub_1;
Matrix<Real> quads_2(quads.storage() + quads.rows() * nb_quad_points_sub_1,
quads.rows(), nb_quad_points_sub_2);
quads_2 = quads_sub_2;
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline void
IntegratorGauss<_ek_igfem, IOF>::computeJacobianOnQuadPointsByElement(
const Matrix<Real> & node_coords, Vector<Real> & jacobians) {
/// optimize: get the matrix from the ElementTypeMap
Matrix<Real> quad = GaussIntegrationElement<type>::getQuadraturePoints();
// jacobian
ElementClass<type>::computeJacobian(quad, node_coords, jacobians);
}
/* -------------------------------------------------------------------------- */
template <class IOF>
inline IntegratorGauss<_ek_igfem, IOF>::IntegratorGauss(
const Mesh & mesh, const ID & id, const MemoryID & memory_id)
: Integrator(mesh, id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline void IntegratorGauss<_ek_igfem, IOF>::checkJacobians(
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
/// typedef for the two subelement_types and the parent element type
const ElementType sub_type_1 = ElementClassProperty<type>::sub_element_type_1;
const ElementType sub_type_2 = ElementClassProperty<type>::sub_element_type_2;
UInt nb_quad_points_sub_1 =
GaussIntegrationElement<sub_type_1>::getNbQuadraturePoints();
UInt nb_quad_points_sub_2 =
GaussIntegrationElement<sub_type_2>::getNbQuadraturePoints();
UInt nb_quadrature_points = nb_quad_points_sub_1 + nb_quad_points_sub_2;
UInt nb_element;
nb_element = mesh.getConnectivity(type, ghost_type).getSize();
Real * jacobians_val = jacobians(type, ghost_type).storage();
for (UInt i = 0; i < nb_element * nb_quadrature_points;
++i, ++jacobians_val) {
if (*jacobians_val < 0)
AKANTU_ERROR(
"Negative jacobian computed,"
<< " possible problem in the element node ordering (Quadrature Point "
<< i % nb_quadrature_points << ":" << i / nb_quadrature_points << ":"
<< type << ":" << ghost_type << ")");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline void
IntegratorGauss<_ek_igfem, IOF>::precomputeJacobiansOnQuadraturePoints(
- const Array<Real> & nodes, const GhostType & ghost_type) {
+ const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// typedef for the two subelement_types and the parent element type
const ElementType sub_type_1 = ElementClassProperty<type>::sub_element_type_1;
const ElementType sub_type_2 = ElementClassProperty<type>::sub_element_type_2;
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
/// get the number of nodes for the subelements and the parent element
UInt nb_nodes_sub_1 =
ElementClass<sub_type_1>::getNbNodesPerInterpolationElement();
UInt nb_nodes_sub_2 =
ElementClass<sub_type_2>::getNbNodesPerInterpolationElement();
UInt nb_quadrature_points_sub_1 =
GaussIntegrationElement<sub_type_1>::getNbQuadraturePoints();
UInt nb_quadrature_points_sub_2 =
GaussIntegrationElement<sub_type_2>::getNbQuadraturePoints();
UInt nb_quadrature_points =
nb_quadrature_points_sub_1 + nb_quadrature_points_sub_2;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<Real> * jacobians_tmp;
if (!jacobians.exists(type, ghost_type))
jacobians_tmp = &jacobians.alloc(nb_element * nb_quadrature_points, 1, type,
ghost_type);
else {
jacobians_tmp = &jacobians(type, ghost_type);
jacobians_tmp->resize(nb_element * nb_quadrature_points);
}
Array<Real>::vector_iterator jacobians_it =
jacobians_tmp->begin_reinterpret(nb_quadrature_points, nb_element);
Vector<Real> weights_sub_1 =
GaussIntegrationElement<sub_type_1>::getWeights();
Vector<Real> weights_sub_2 =
GaussIntegrationElement<sub_type_2>::getWeights();
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
Array<Real>::const_matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
// Matrix<Real> local_coord(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++jacobians_it, ++x_it) {
const Matrix<Real> & X = *x_it;
Matrix<Real> sub_1_coords(spatial_dimension, nb_nodes_sub_1);
Matrix<Real> sub_2_coords(spatial_dimension, nb_nodes_sub_2);
ElementClass<type>::getSubElementCoords(X, sub_1_coords, 0);
ElementClass<type>::getSubElementCoords(X, sub_2_coords, 1);
Vector<Real> & J = *jacobians_it;
/// initialize vectors to store the jacobians for each subelement
Vector<Real> J_sub_1(nb_quadrature_points_sub_1);
Vector<Real> J_sub_2(nb_quadrature_points_sub_2);
computeJacobianOnQuadPointsByElement<sub_type_1>(sub_1_coords, J_sub_1);
computeJacobianOnQuadPointsByElement<sub_type_2>(sub_2_coords, J_sub_2);
J_sub_1 *= weights_sub_1;
J_sub_2 *= weights_sub_2;
/// copy results into the jacobian vector for this element
for (UInt i = 0; i < nb_quadrature_points_sub_1; ++i) {
J(i) = J_sub_1(i);
}
for (UInt i = 0; i < nb_quadrature_points_sub_2; ++i) {
J(i + nb_quadrature_points_sub_1) = J_sub_2(i);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline void IntegratorGauss<_ek_igfem, IOF>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
const Matrix<Real> & quads = quadrature_points(type, ghost_type);
UInt nb_points = quads.cols();
const Array<Real> & jac_loc = jacobians(type, ghost_type);
Array<Real>::const_matrix_iterator J_it;
Array<Real>::matrix_iterator inte_it;
Array<Real>::const_matrix_iterator f_it;
UInt nb_element;
Array<Real> * filtered_J = NULL;
if (filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
const Array<Real> & cfiltered_J = *filtered_J; // \todo temporary patch
J_it = cfiltered_J.begin_reinterpret(nb_points, 1, nb_element);
} else {
nb_element = mesh.getNbElement(type, ghost_type);
J_it = jac_loc.begin_reinterpret(nb_points, 1, nb_element);
}
intf.resize(nb_element);
f_it = in_f.begin_reinterpret(nb_degree_of_freedom, nb_points, nb_element);
inte_it = intf.begin_reinterpret(nb_degree_of_freedom, 1, nb_element);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Matrix<Real> & f = *f_it;
const Matrix<Real> & J = *J_it;
Matrix<Real> & inte_f = *inte_it;
inte_f.mul<false, false>(f, J);
}
delete filtered_J;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline Real IntegratorGauss<_ek_igfem, IOF>::integrate(
- const Array<Real> & in_f, const GhostType & ghost_type,
+ const Array<Real> & in_f, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
Array<Real> intfv(0, 1);
integrate<type>(in_f, intfv, 1, ghost_type, filter_elements);
UInt nb_values = intfv.getSize();
if (nb_values == 0)
return 0.;
UInt nb_values_to_sum = nb_values >> 1;
std::sort(intfv.begin(), intfv.end());
// as long as the half is not empty
while (nb_values_to_sum) {
UInt remaining = (nb_values - 2 * nb_values_to_sum);
if (remaining)
intfv(nb_values - 2) += intfv(nb_values - 1);
// sum to consecutive values and store the sum in the first half
for (UInt i = 0; i < nb_values_to_sum; ++i) {
intfv(i) = intfv(2 * i) + intfv(2 * i + 1);
}
nb_values = nb_values_to_sum;
nb_values_to_sum >>= 1;
}
AKANTU_DEBUG_OUT();
return intfv(0);
}
/* -------------------------------------------------------------------------- */
template <class IOF>
template <ElementType type>
inline void IntegratorGauss<_ek_igfem, IOF>::integrateOnIntegrationPoints(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
UInt nb_element;
const Matrix<Real> & quads = quadrature_points(type, ghost_type);
UInt nb_points = quads.cols();
const Array<Real> & jac_loc = jacobians(type, ghost_type);
Array<Real>::const_scalar_iterator J_it;
Array<Real>::vector_iterator inte_it;
Array<Real>::const_vector_iterator f_it;
Array<Real> * filtered_J = NULL;
if (filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
J_it = filtered_J->begin();
} else {
nb_element = mesh.getNbElement(type, ghost_type);
J_it = jac_loc.begin();
}
intf.resize(nb_element * nb_points);
f_it = in_f.begin(nb_degree_of_freedom);
inte_it = intf.begin(nb_degree_of_freedom);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Real & J = *J_it;
const Vector<Real> & f = *f_it;
Vector<Real> & inte_f = *inte_it;
inte_f = f;
inte_f *= J;
}
delete filtered_J;
AKANTU_DEBUG_OUT();
}
diff --git a/extra_packages/igfem/src/material_igfem/igfem_internal_field.hh b/extra_packages/igfem/src/material_igfem/igfem_internal_field.hh
index 8ce41db84..67fb6fe09 100644
--- a/extra_packages/igfem/src/material_igfem/igfem_internal_field.hh
+++ b/extra_packages/igfem/src/material_igfem/igfem_internal_field.hh
@@ -1,30 +1,30 @@
/**
* @file igfem_internal_field.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief IGFEM internal field
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
#include "internal_field.hh"
-#ifndef __AKANTU_IGFEM_INTERNAL_FIELD_HH__
-#define __AKANTU_IGFEM_INTERNAL_FIELD_HH__
+#ifndef AKANTU_IGFEM_INTERNAL_FIELD_HH_
+#define AKANTU_IGFEM_INTERNAL_FIELD_HH_
namespace akantu {
template <typename T> class IGFEMInternalField : public InternalField<T> {
public:
IGFEMInternalField(const ID & id, Material & material);
virtual ~IGFEMInternalField();
};
} // namespace akantu
-#endif /* __AKANTU_IGFEM_INTERNAL_FIELD_HH__ */
+#endif /* AKANTU_IGFEM_INTERNAL_FIELD_HH_ */
diff --git a/extra_packages/igfem/src/material_igfem/igfem_internal_field_tmpl.hh b/extra_packages/igfem/src/material_igfem/igfem_internal_field_tmpl.hh
index f110de5d7..7dee951ee 100644
--- a/extra_packages/igfem/src/material_igfem/igfem_internal_field_tmpl.hh
+++ b/extra_packages/igfem/src/material_igfem/igfem_internal_field_tmpl.hh
@@ -1,33 +1,33 @@
/**
* @file igfem_internal_field_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Implementation of IGFEM internal field
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
-#ifndef __AKANTU_IGFEM_INTERNAL_FIELD_TMPL_HH__
-#define __AKANTU_IGFEM_INTERNAL_FIELD_TMPL_HH__
+#ifndef AKANTU_IGFEM_INTERNAL_FIELD_TMPL_HH_
+#define AKANTU_IGFEM_INTERNAL_FIELD_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T>
IGFEMInternalField<T>::IGFEMInternalField(const ID & id, Material & material)
: InternalField<T>(
id, material, material.getModel().getFEEngine("IGFEMFEEngine"),
dynamic_cast<MaterialIGFEM &>(material).getElementFilter()) {
this->element_kind = _ek_igfem;
}
/* -------------------------------------------------------------------------- */
template <typename T> IGFEMInternalField<T>::~IGFEMInternalField(){};
} // namespace akantu
-#endif /* __AKANTU_IGFEM_INTERNAL_FIELD_TMPL_HH__ */
+#endif /* AKANTU_IGFEM_INTERNAL_FIELD_TMPL_HH_ */
diff --git a/extra_packages/igfem/src/material_igfem/material_igfem.cc b/extra_packages/igfem/src/material_igfem/material_igfem.cc
index e686b7d34..dceb3322f 100644
--- a/extra_packages/igfem/src/material_igfem/material_igfem.cc
+++ b/extra_packages/igfem/src/material_igfem/material_igfem.cc
@@ -1,367 +1,367 @@
/**
* @file element_class_igfem.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
*
* @brief Implementation parent material for IGFEM
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
#include "material_igfem.hh"
#include "aka_math.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
MaterialIGFEM::MaterialIGFEM(SolidMechanicsModel & model, const ID & id)
: Material(model, id), nb_sub_materials(2),
sub_material("sub_material", *this), name_sub_mat_1(""),
name_sub_mat_2("") {
AKANTU_DEBUG_IN();
this->model = dynamic_cast<SolidMechanicsModelIGFEM *>(&model);
this->fem = &(model.getFEEngineClass<MyFEEngineIGFEMType>("IGFEMFEEngine"));
this->model->getMesh().initElementTypeMapArray(
element_filter, 1, spatial_dimension, false, _ek_igfem);
this->initialize();
AKANTU_DEBUG_OUT();
};
/* -------------------------------------------------------------------------- */
MaterialIGFEM::~MaterialIGFEM() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialIGFEM::initialize() {
this->gradu.setElementKind(_ek_igfem);
this->stress.setElementKind(_ek_igfem);
this->eigengradu.setElementKind(_ek_igfem);
this->gradu.setFEEngine(*fem);
this->stress.setFEEngine(*fem);
this->eigengradu.setFEEngine(*fem);
registerParam("name_sub_mat_1", name_sub_mat_1, std::string(),
_pat_parsable | _pat_readable);
registerParam("name_sub_mat_2", name_sub_mat_2, std::string(),
_pat_parsable | _pat_readable);
this->sub_material.initialize(1);
}
/* -------------------------------------------------------------------------- */
void MaterialIGFEM::computeQuadraturePointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
/// compute quadrature points position in undeformed configuration
Array<Real> & nodes_coordinates = this->fem->getMesh().getNodes();
Mesh::type_iterator it =
this->element_filter.firstType(spatial_dimension, ghost_type, _ek_igfem);
Mesh::type_iterator last_type =
this->element_filter.lastType(spatial_dimension, ghost_type, _ek_igfem);
for (; it != last_type; ++it) {
const Array<UInt> & elem_filter = this->element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (nb_element) {
UInt nb_tot_quad =
this->fem->getNbIntegrationPoints(*it, ghost_type) * nb_element;
Array<Real> & quads = quadrature_points_coordinates(*it, ghost_type);
quads.resize(nb_tot_quad);
this->model->getFEEngine("IGFEMFEEngine")
.interpolateOnIntegrationPoints(nodes_coordinates, quads,
spatial_dimension, *it, ghost_type,
elem_filter);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stress from the gradu
*
* @param[in] current_position nodes postition + displacements
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void MaterialIGFEM::computeAllStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model->getSpatialDimension();
Mesh::type_iterator it =
this->fem->getMesh().firstType(spatial_dimension, ghost_type, _ek_igfem);
Mesh::type_iterator last_type =
this->fem->getMesh().lastType(spatial_dimension, ghost_type, _ek_igfem);
for (; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
if (elem_filter.getSize()) {
Array<Real> & gradu_vect = gradu(*it, ghost_type);
/// compute @f$\nabla u@f$
this->fem->gradientOnIntegrationPoints(model->getDisplacement(),
gradu_vect, spatial_dimension, *it,
ghost_type, elem_filter);
gradu_vect -= eigengradu(*it, ghost_type);
/// compute @f$\mathbf{\sigma}_q@f$ from @f$\nabla u@f$
computeStress(*it, ghost_type);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// extrapolate internal values
void MaterialIGFEM::extrapolateInternal(const ID & id, const Element & element,
const Matrix<Real> & point,
Matrix<Real> & extrapolated) {
if (this->isInternal<Real>(id, element.kind)) {
UInt nb_element =
this->element_filter(element.type, element.ghost_type).getSize();
const ID name = this->getID() + ":" + id;
UInt nb_quads =
this->internal_vectors_real[name]->getFEEngine().getNbIntegrationPoints(
element.type, element.ghost_type);
const Array<Real> & internal =
this->getArray<Real>(id, element.type, element.ghost_type);
UInt nb_component = internal.getNbComponent();
Array<Real>::const_matrix_iterator internal_it =
internal.begin_reinterpret(nb_component, nb_quads, nb_element);
Element local_element = this->convertToLocalElement(element);
/// instead of really extrapolating, here the value of the first GP
/// is copied into the result vector. This works only for linear
/// elements
/// @todo extrapolate!!!!
AKANTU_DEBUG_WARNING("This is a fix, values are not truly extrapolated");
const Matrix<Real> & values = internal_it[local_element.element];
UInt index = 0;
Vector<Real> tmp(nb_component);
for (UInt j = 0; j < values.cols(); ++j) {
tmp = values(j);
if (tmp.norm() > Math::getTolerance()) {
index = j;
break;
}
}
for (UInt i = 0; i < extrapolated.size(); ++i) {
extrapolated(i) = values(index);
}
} else {
Matrix<Real> default_values(extrapolated.rows(), extrapolated.cols(), 0.);
extrapolated = default_values;
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void MaterialIGFEM::setSubMaterial(const Array<Element> & element_list,
GhostType ghost_type) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialIGFEM::setSubMaterial<_igfem_triangle_5>(
const Array<Element> & element_list, GhostType ghost_type) {
SolidMechanicsModelIGFEM * igfem_model =
static_cast<SolidMechanicsModelIGFEM *>(this->model);
Vector<UInt> sub_material_index(this->nb_sub_materials);
Array<Element>::const_iterator<Element> el_begin = element_list.begin();
Array<Element>::const_iterator<Element> el_end = element_list.end();
const Mesh & mesh = this->model->getMesh();
Array<Real> nodes_coordinates(mesh.getNodes(), true);
Array<Real>::const_vector_iterator nodes_it =
nodes_coordinates.begin(spatial_dimension);
Element el;
el.kind = _ek_igfem;
el.type = _igfem_triangle_5;
el.ghost_type = ghost_type;
UInt nb_nodes_per_el = mesh.getNbNodesPerElement(el.type);
UInt nb_parent_nodes = IGFEMHelper::getNbParentNodes(el.type);
Vector<bool> is_inside(nb_parent_nodes);
const Array<UInt> & connectivity = mesh.getConnectivity(el.type, ghost_type);
Array<UInt>::const_vector_iterator connec_it =
connectivity.begin(nb_nodes_per_el);
/// get the number of quadrature points for the two sub-elements
UInt quads_1 = IGFEMHelper::getNbQuadraturePoints(el.type, 0);
UInt quads_2 = IGFEMHelper::getNbQuadraturePoints(el.type, 1);
UInt nb_total_quads = quads_1 + quads_2;
UInt * sub_mat_ptr = this->sub_material(el.type, ghost_type).storage();
/// loop all elements for the given type
const Array<UInt> & filter = this->element_filter(el.type, ghost_type);
UInt nb_elements = filter.getSize();
for (UInt e = 0; e < nb_elements; ++e, ++connec_it) {
el.element = filter(e);
if (std::find(el_begin, el_end, el) == el_end) {
sub_mat_ptr += nb_total_quads;
continue;
}
for (UInt i = 0; i < nb_parent_nodes; ++i) {
Vector<Real> node = nodes_it[(*connec_it)(i)];
is_inside(i) = igfem_model->isInside(node, this->name_sub_mat_1);
}
UInt orientation = IGFEMHelper::getElementOrientation(el.type, is_inside);
switch (orientation) {
case 0: {
sub_material_index(0) = 0;
sub_material_index(1) = 1;
break;
}
case 1: {
sub_material_index(0) = 1;
sub_material_index(1) = 0;
break;
}
case 2: {
sub_material_index(0) = 0;
sub_material_index(1) = 0;
break;
}
case 3: {
sub_material_index(0) = 1;
sub_material_index(0) = 1;
break;
}
}
for (UInt q = 0; q < quads_1; ++q, ++sub_mat_ptr) {
UInt index = sub_material_index(0);
*sub_mat_ptr = index;
}
for (UInt q = 0; q < quads_2; ++q, ++sub_mat_ptr) {
UInt index = sub_material_index(1);
*sub_mat_ptr = index;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialIGFEM::setSubMaterial<_igfem_triangle_4>(
const Array<Element> & element_list, GhostType ghost_type) {
SolidMechanicsModelIGFEM * igfem_model =
static_cast<SolidMechanicsModelIGFEM *>(this->model);
Vector<UInt> sub_material_index(this->nb_sub_materials);
Array<Element>::const_iterator<Element> el_begin = element_list.begin();
Array<Element>::const_iterator<Element> el_end = element_list.end();
const Mesh & mesh = this->model->getMesh();
Element el;
el.kind = _ek_igfem;
el.ghost_type = ghost_type;
el.type = _igfem_triangle_4;
UInt nb_nodes_per_el = mesh.getNbNodesPerElement(el.type);
Vector<Real> barycenter(spatial_dimension);
const Array<UInt> & connectivity = mesh.getConnectivity(el.type, ghost_type);
Array<UInt>::const_vector_iterator connec_it =
connectivity.begin(nb_nodes_per_el);
/// get the number of quadrature points for the two sub-elements
UInt quads_1 = IGFEMHelper::getNbQuadraturePoints(el.type, 0);
UInt quads_2 = IGFEMHelper::getNbQuadraturePoints(el.type, 1);
UInt nb_total_quads = quads_1 + quads_2;
UInt * sub_mat_ptr = this->sub_material(el.type, ghost_type).storage();
/// loop all elements for the given type
const Array<UInt> & filter = this->element_filter(el.type, ghost_type);
UInt nb_elements = filter.getSize();
for (UInt e = 0; e < nb_elements; ++e, ++connec_it) {
el.element = filter(e);
if (std::find(el_begin, el_end, el) == el_end) {
sub_mat_ptr += nb_total_quads;
continue;
}
for (UInt s = 0; s < this->nb_sub_materials; ++s) {
igfem_model->getSubElementBarycenter(el.element, s, el.type, barycenter,
ghost_type);
sub_material_index(s) =
1 - igfem_model->isInside(barycenter, this->name_sub_mat_1);
}
for (UInt q = 0; q < quads_1; ++q, ++sub_mat_ptr) {
UInt index = sub_material_index(0);
*sub_mat_ptr = index;
}
for (UInt q = 0; q < quads_2; ++q, ++sub_mat_ptr) {
UInt index = sub_material_index(1);
*sub_mat_ptr = index;
}
}
}
/* -------------------------------------------------------------------------- */
void MaterialIGFEM::applyEigenGradU(
const Matrix<Real> & prescribed_eigen_grad_u, const ID & id,
const GhostType ghost_type) {
std::map<UInt, ID>::const_iterator sub_mat_it =
this->sub_material_names.begin();
for (; sub_mat_it != sub_material_names.end(); ++sub_mat_it) {
if (sub_mat_it->second == id) {
UInt sub_element_index = sub_mat_it->first;
ElementTypeMapArray<UInt>::type_iterator it =
this->element_filter.firstType(_all_dimensions, ghost_type,
_ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end =
element_filter.lastType(_all_dimensions, ghost_type, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
if (!element_filter(type, ghost_type).getSize())
continue;
Array<Real>::matrix_iterator eigen_it =
this->eigengradu(type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator eigen_end =
this->eigengradu(type, ghost_type)
.end(spatial_dimension, spatial_dimension);
UInt * sub_mat_ptr = this->sub_material(type, ghost_type).storage();
for (; eigen_it != eigen_end; ++eigen_it, ++sub_mat_ptr) {
if (*sub_mat_ptr == sub_element_index) {
Matrix<Real> & current_eigengradu = *eigen_it;
current_eigengradu = prescribed_eigen_grad_u;
}
}
}
}
}
}
} // namespace akantu
diff --git a/extra_packages/igfem/src/material_igfem/material_igfem.hh b/extra_packages/igfem/src/material_igfem/material_igfem.hh
index 943faa2c4..1d708d2ec 100644
--- a/extra_packages/igfem/src/material_igfem/material_igfem.hh
+++ b/extra_packages/igfem/src/material_igfem/material_igfem.hh
@@ -1,134 +1,134 @@
/**
* @file element_class_igfem.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
*
* @brief Parent material for IGFEM
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "igfem_internal_field.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_IGFEM_HH__
-#define __AKANTU_MATERIAL_IGFEM_HH__
+#ifndef AKANTU_MATERIAL_IGFEM_HH_
+#define AKANTU_MATERIAL_IGFEM_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelIGFEM;
}
namespace akantu {
class MaterialIGFEM : public virtual Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_igfem>
MyFEEngineIGFEMType;
MaterialIGFEM(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialIGFEM();
protected:
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
virtual void extrapolateInternal(const ID & id, const Element & element,
const Matrix<Real> & point,
Matrix<Real> & extrapolated);
/// apply a constant eigengrad_u everywhere in the material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const ID & sub_mat_name,
const GhostType = _not_ghost);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
virtual void computeQuadraturePointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
// virtual void onElementsAdded(const Array<Element> & element_list,
// const NewElementsEvent & event) {};
// virtual void onElementsRemoved(const Array<Element> & element_list,
// const ElementTypeMapArray<UInt> &
// new_numbering,
// const RemovedElementsEvent & event) {};
protected:
/// constitutive law
virtual void computeStress(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost) {}
void initialize();
template <ElementType type>
void setSubMaterial(const Array<Element> & element_list,
GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual inline UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
const UInt nb_sub_materials;
/// pointer to the solid mechanics model for igfem elements
SolidMechanicsModelIGFEM * model;
/// internal field of bool to know to which sub-material a quad point belongs
IGFEMInternalField<UInt> sub_material;
/// material name of first sub-material
std::string name_sub_mat_1;
/// material name of first sub-material
std::string name_sub_mat_2;
/// map the index of the sub-materials to the names
std::map<UInt, ID> sub_material_names;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_igfem_inline_impl.hh"
} // namespace akantu
#include "igfem_internal_field_tmpl.hh"
-#endif /* __AKANTU_MATERIAL_IGFEM_HH__ */
+#endif /* AKANTU_MATERIAL_IGFEM_HH_ */
diff --git a/extra_packages/igfem/src/material_igfem/material_igfem_elastic.cc b/extra_packages/igfem/src/material_igfem/material_igfem_elastic.cc
index 3a4e8ca23..33435cecb 100644
--- a/extra_packages/igfem/src/material_igfem/material_igfem_elastic.cc
+++ b/extra_packages/igfem/src/material_igfem/material_igfem_elastic.cc
@@ -1,241 +1,241 @@
/**
* @file material_igfem_elastic.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Specializaton of material class for the igfem elastic material
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material_igfem_elastic.hh"
#include "material_elastic.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialIGFEMElastic<dim>::MaterialIGFEMElastic(SolidMechanicsModel & model,
const ID & id)
: Material(model, id), Parent(model, id), lambda("lambda", *this),
mu("mu", *this), kpa("kappa", *this) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialIGFEMElastic<dim>::initialize() {
this->lambda.initialize(1);
this->mu.initialize(1);
this->kpa.initialize(1);
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialIGFEMElastic<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Parent::initMaterial();
/// insert the sub_material names into the map
this->sub_material_names[0] = this->name_sub_mat_1;
this->sub_material_names[1] = this->name_sub_mat_2;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMElastic<spatial_dimension>::updateElasticInternals(
const Array<Element> & element_list) {
/// compute the Lamé constants for both sub-materials
Vector<Real> lambda_per_sub_mat(this->nb_sub_materials);
Vector<Real> mu_per_sub_mat(this->nb_sub_materials);
Vector<Real> kpa_per_sub_mat(this->nb_sub_materials);
for (UInt i = 0; i < this->nb_sub_materials; ++i) {
ID mat_name = this->sub_material_names[i];
const MaterialElastic<spatial_dimension> & mat =
dynamic_cast<MaterialElastic<spatial_dimension> &>(
this->model->getMaterial(mat_name));
lambda_per_sub_mat(i) = mat.getLambda();
mu_per_sub_mat(i) = mat.getMu();
kpa_per_sub_mat(i) = mat.getKappa();
}
for (ghost_type_t::iterator g = ghost_type_t::begin();
g != ghost_type_t::end(); ++g) {
GhostType ghost_type = *g;
/// loop over all types in the material
typedef ElementTypeMapArray<UInt>::type_iterator iterator;
iterator it = this->element_filter.firstType(spatial_dimension, ghost_type,
_ek_igfem);
iterator last_type =
this->element_filter.lastType(spatial_dimension, ghost_type, _ek_igfem);
/// loop over all types in the filter
for (; it != last_type; ++it) {
ElementType el_type = *it;
if (el_type == _igfem_triangle_4)
this->template setSubMaterial<_igfem_triangle_4>(element_list,
ghost_type);
else if (el_type == _igfem_triangle_5)
this->template setSubMaterial<_igfem_triangle_5>(element_list,
ghost_type);
else
AKANTU_ERROR("There is currently no other IGFEM type implemented");
UInt nb_element = this->element_filter(el_type, ghost_type).getSize();
UInt nb_quads = this->fem->getNbIntegrationPoints(el_type);
/// get pointer to internals for given type
Real * lambda_ptr = this->lambda(el_type, ghost_type).storage();
Real * mu_ptr = this->mu(el_type, ghost_type).storage();
Real * kpa_ptr = this->kpa(el_type, ghost_type).storage();
UInt * sub_mat_ptr = this->sub_material(el_type, ghost_type).storage();
for (UInt q = 0; q < nb_element * nb_quads;
++q, ++lambda_ptr, ++mu_ptr, ++kpa_ptr, ++sub_mat_ptr) {
UInt index = *sub_mat_ptr;
*lambda_ptr = lambda_per_sub_mat(index);
*mu_ptr = mu_per_sub_mat(index);
*kpa_ptr = kpa_per_sub_mat(index);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMElastic<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent::computeStress(el_type, ghost_type);
if (!this->finite_deformation) {
/// get pointer to internals
Real * lambda_ptr = this->lambda(el_type, ghost_type).storage();
Real * mu_ptr = this->mu(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeStressOnQuad(grad_u, sigma, *lambda_ptr, *mu_ptr);
++lambda_ptr;
++mu_ptr;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
AKANTU_DEBUG_TO_IMPLEMENT();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMElastic<spatial_dimension>::computeTangentModuli(
- __attribute__((unused)) const ElementType & el_type,
+ __attribute__((unused)) ElementType el_type,
Array<Real> & tangent_matrix,
__attribute__((unused)) GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// get pointer to internals
Real * lambda_ptr = this->lambda(el_type, ghost_type).storage();
Real * mu_ptr = this->mu(el_type, ghost_type).storage();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent, *lambda_ptr, *mu_ptr);
++lambda_ptr;
++mu_ptr;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMElastic<spatial_dimension>::computePotentialEnergy(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
// MaterialThermal<spatial_dimension>::computePotentialEnergy(el_type,
// ghost_type);
// if(ghost_type != _not_ghost) return;
// Array<Real>::scalar_iterator epot = this->potential_energy(el_type,
// ghost_type).begin();
// if (!this->finite_deformation) {
// MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
// this->computePotentialEnergyOnQuad(grad_u, sigma, *epot);
// ++epot;
// MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
// } else {
// Matrix<Real> E(spatial_dimension, spatial_dimension);
// MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
// this->template gradUToGreenStrain<spatial_dimension>(grad_u, E);
// this->computePotentialEnergyOnQuad(E, sigma, *epot);
// ++epot;
// MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
// }
AKANTU_DEBUG_TO_IMPLEMENT();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMElastic<spatial_dimension>::computePotentialEnergyByElement(
ElementType type, UInt index, Vector<Real> & epot_on_quad_points) {
// Array<Real>::matrix_iterator gradu_it =
// this->gradu(type).begin(spatial_dimension,
// spatial_dimension);
// Array<Real>::matrix_iterator gradu_end =
// this->gradu(type).begin(spatial_dimension,
// spatial_dimension);
// Array<Real>::matrix_iterator stress_it =
// this->stress(type).begin(spatial_dimension,
// spatial_dimension);
// if (this->finite_deformation)
// stress_it = this->piola_kirchhoff_2(type).begin(spatial_dimension,
// spatial_dimension);
// UInt nb_quadrature_points =
// this->model->getFEEngine().getNbQuadraturePoints(type);
// gradu_it += index*nb_quadrature_points;
// gradu_end += (index+1)*nb_quadrature_points;
// stress_it += index*nb_quadrature_points;
// Real * epot_quad = epot_on_quad_points.storage();
// Matrix<Real> grad_u(spatial_dimension, spatial_dimension);
// for(;gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
// if (this->finite_deformation)
// this->template gradUToGreenStrain<spatial_dimension>(*gradu_it,
// grad_u);
// else
// grad_u.copy(*gradu_it);
// this->computePotentialEnergyOnQuad(grad_u, *stress_it, *epot_quad);
// }
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMElastic<spatial_dimension>::onElementsAdded(
const Array<Element> & element_list, const NewElementsEvent & event) {
Parent::onElementsAdded(element_list, event);
updateElasticInternals(element_list);
};
INSTANTIATE_MATERIAL(MaterialIGFEMElastic);
} // namespace akantu
diff --git a/extra_packages/igfem/src/material_igfem/material_igfem_elastic.hh b/extra_packages/igfem/src/material_igfem/material_igfem_elastic.hh
index 9c8e84150..2e1497b32 100644
--- a/extra_packages/igfem/src/material_igfem/material_igfem_elastic.hh
+++ b/extra_packages/igfem/src/material_igfem/material_igfem_elastic.hh
@@ -1,129 +1,129 @@
/**
* @file element_class_igfem.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
*
* @brief Material isotropic elastic for IGFEM
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_igfem.hh"
#include "plane_stress_toolbox.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_IGFEM_ELASTIC_HH__
-#define __AKANTU_MATERIAL_IGFEM_ELASTIC_HH__
+#ifndef AKANTU_MATERIAL_IGFEM_ELASTIC_HH_
+#define AKANTU_MATERIAL_IGFEM_ELASTIC_HH_
namespace akantu {
/**
* Material elastic isotropic
*
* parameters in the material files :
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - Plane_Stress : if 0: plane strain, else: plane stress (default: 0)
*/
template <UInt spatial_dimension>
class MaterialIGFEMElastic
: public PlaneStressToolbox<spatial_dimension, MaterialIGFEM> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
typedef PlaneStressToolbox<spatial_dimension, MaterialIGFEM> Parent;
public:
MaterialIGFEMElastic(SolidMechanicsModel & model, const ID & id = "");
MaterialIGFEMElastic(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
virtual ~MaterialIGFEMElastic() {}
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void initMaterial();
/// constitutive law for all element of a type
virtual void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// compute the tangent stiffness matrix for an element type
- virtual void computeTangentModuli(const ElementType & el_type,
+ virtual void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
/// compute the elastic potential energy
virtual void computePotentialEnergy(ElementType el_type,
GhostType ghost_type = _not_ghost);
virtual void
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points);
void updateElasticInternals(const Array<Element> & element_list);
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
__attribute__((unused)) const Real lambda,
const Real mu) const;
/// compute the tangent stiffness matrix for an element
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent,
__attribute__((unused))
const Real lambda,
const Real mu) const;
static inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
virtual void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// First Lamé coefficient
IGFEMInternalField<Real> lambda;
/// Second Lamé coefficient (shear modulus)
IGFEMInternalField<Real> mu;
/// Bulk modulus
IGFEMInternalField<Real> kpa;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_igfem_elastic_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_IGFEM_ELASTIC_HH__ */
+#endif /* AKANTU_MATERIAL_IGFEM_ELASTIC_HH_ */
diff --git a/extra_packages/igfem/src/material_igfem/material_igfem_iterative_stiffness_reduction.cc b/extra_packages/igfem/src/material_igfem/material_igfem_iterative_stiffness_reduction.cc
index 82545f896..fbec0e9f9 100644
--- a/extra_packages/igfem/src/material_igfem/material_igfem_iterative_stiffness_reduction.cc
+++ b/extra_packages/igfem/src/material_igfem/material_igfem_iterative_stiffness_reduction.cc
@@ -1,288 +1,288 @@
/**
* @file material_igfem_iterative_stiffness_reduction.cc
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Thu Mar 10 08:37:43 2016
*
* @brief Implementation of igfem material iterative stiffness reduction
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_igfem_iterative_stiffness_reduction.hh"
#include <math.h>
namespace akantu {
template <UInt spatial_dimension>
/* -------------------------------------------------------------------------- */
MaterialIGFEMIterativeStiffnessReduction<spatial_dimension>::
MaterialIGFEMIterativeStiffnessReduction(SolidMechanicsModel & model,
const ID & id)
: Material(model, id), MaterialIGFEMSawToothDamage<spatial_dimension>(model,
id),
eps_u("ultimate_strain", *this), reduction_step("damage_step", *this),
D("tangent", *this), Gf(0.), crack_band_width(0.), max_reductions(0),
reduction_constant(0.) {
AKANTU_DEBUG_IN();
this->eps_u.initialize(1);
this->D.initialize(1);
this->reduction_step.initialize(1);
this->internals_to_transfer.push_back("ultimate_strain");
this->internals_to_transfer.push_back("tangent");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialIGFEMIterativeStiffnessReduction<dim>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialIGFEMSawToothDamage<dim>::initMaterial();
/// get the parameters for the sub-material that can be damaged
ID mat_name = this->sub_material_names[1];
const Material & mat = this->model->getMaterial(mat_name);
this->crack_band_width = mat.getParam<Real>("crack_band_width");
this->max_reductions = mat.getParam<UInt>("max_reductions");
this->reduction_constant = mat.getParam<Real>("reduction_constant");
this->Gf = mat.getParam<Real>("Gf");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMIterativeStiffnessReduction<spatial_dimension>::
computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// storage for the current stress
Matrix<Real> sigma(spatial_dimension, spatial_dimension);
/// Vector to store eigenvalues of current stress tensor
Vector<Real> eigenvalues(spatial_dimension);
/// iterators on the needed internal fields
Array<Real>::const_scalar_iterator Sc_it =
this->Sc(el_type, ghost_type).begin();
Array<Real>::scalar_iterator dam_it =
this->damage(el_type, ghost_type).begin();
Array<Real>::scalar_iterator equivalent_stress_it =
this->equivalent_stress(el_type, ghost_type).begin();
Array<Real>::const_matrix_iterator grad_u_it =
grad_u.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_matrix_iterator grad_u_end =
grad_u.end(spatial_dimension, spatial_dimension);
Real * mu_ptr = this->mu(el_type, ghost_type).storage();
Real * lambda_ptr = this->lambda(el_type, ghost_type).storage();
/// loop over all the quadrature points and compute the equivalent stress
for (; grad_u_it != grad_u_end; ++grad_u_it) {
/// compute the stress
- sigma.clear();
+ sigma.zero();
MaterialIGFEMElastic<spatial_dimension>::computeStressOnQuad(
*grad_u_it, sigma, *lambda_ptr, *mu_ptr);
MaterialIGFEMSawToothDamage<
spatial_dimension>::computeDamageAndStressOnQuad(sigma, *dam_it);
/// compute eigenvalues
sigma.eig(eigenvalues);
/// find max eigenvalue and normalize by tensile strength
*equivalent_stress_it =
*(std::max_element(eigenvalues.storage(),
eigenvalues.storage() + spatial_dimension)) /
(*Sc_it);
++Sc_it;
++equivalent_stress_it;
++dam_it;
++lambda_ptr;
++mu_ptr;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
UInt MaterialIGFEMIterativeStiffnessReduction<
spatial_dimension>::updateDamage() {
UInt nb_damaged_elements = 0;
if (this->norm_max_equivalent_stress >= 1.) {
AKANTU_DEBUG_IN();
/// update the damage only on non-ghosts elements! Doesn't make sense to
/// update on ghost.
GhostType ghost_type = _not_ghost;
;
Mesh::type_iterator it = this->model->getFEEngine().getMesh().firstType(
spatial_dimension, ghost_type, _ek_igfem);
Mesh::type_iterator last_type =
this->model->getFEEngine().getMesh().lastType(spatial_dimension,
ghost_type, _ek_igfem);
/// get the Young's modulus of the damageable sub-material
ID mat_name = this->sub_material_names[1];
Real E = this->model->getMaterial(mat_name).template getParam<Real>("E");
/// loop over all the elements
for (; it != last_type; ++it) {
ElementType el_type = *it;
/// get iterators on the needed internal fields
const Array<UInt> & sub_mat = this->sub_material(el_type, ghost_type);
Array<UInt>::const_scalar_iterator sub_mat_it = sub_mat.begin();
Array<Real>::const_scalar_iterator equivalent_stress_it =
this->equivalent_stress(el_type, ghost_type).begin();
Array<Real>::const_scalar_iterator equivalent_stress_end =
this->equivalent_stress(el_type, ghost_type).end();
Array<Real>::scalar_iterator dam_it =
this->damage(el_type, ghost_type).begin();
Array<UInt>::scalar_iterator reduction_it =
this->reduction_step(el_type, ghost_type).begin();
Array<Real>::const_scalar_iterator eps_u_it =
this->eps_u(el_type, ghost_type).begin();
Array<Real>::scalar_iterator Sc_it =
this->Sc(el_type, ghost_type).begin();
Array<Real>::const_scalar_iterator D_it =
this->D(el_type, ghost_type).begin();
/// loop over all the elements of the given type
UInt nb_element = this->element_filter(el_type, ghost_type).getSize();
UInt nb_quads = this->fem->getNbIntegrationPoints(el_type, ghost_type);
bool damage_element = false;
for (UInt e = 0; e < nb_element; ++e) {
damage_element = false;
/// check if damage occurs in the element
for (UInt q = 0; q < nb_quads;
++q, ++reduction_it, ++sub_mat_it, ++equivalent_stress_it) {
if (*equivalent_stress_it >= (1 - this->dam_tolerance) *
this->norm_max_equivalent_stress &&
*sub_mat_it != 0) {
/// check if this element can still be damaged
if (*reduction_it == this->max_reductions)
continue;
damage_element = true;
}
}
if (damage_element) {
/// damage the element
nb_damaged_elements += 1;
sub_mat_it -= nb_quads;
reduction_it -= nb_quads;
for (UInt q = 0; q < nb_quads; ++q) {
if (*sub_mat_it) {
/// increment the counter of stiffness reduction steps
*reduction_it += 1;
if (*reduction_it == this->max_reductions)
*dam_it = this->max_damage;
else {
/// update the damage on this quad
*dam_it = 1. - (1. / std::pow(this->reduction_constant,
*reduction_it));
/// update the stiffness on this quad
*Sc_it = (*eps_u_it) * (1. - (*dam_it)) * E * (*D_it) /
((1. - (*dam_it)) * E + (*D_it));
}
}
++sub_mat_it;
++dam_it;
++reduction_it;
++eps_u_it;
++Sc_it;
++D_it;
}
} else {
dam_it += nb_quads;
eps_u_it += nb_quads;
Sc_it += nb_quads;
D_it += nb_quads;
}
}
}
}
StaticCommunicator & comm =
akantu::StaticCommunicator::getStaticCommunicator();
comm.allReduce(&nb_damaged_elements, 1, _so_sum);
AKANTU_DEBUG_OUT();
return nb_damaged_elements;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMIterativeStiffnessReduction<
spatial_dimension>::onElementsAdded(__attribute__((unused))
const Array<Element> & element_list,
__attribute__((unused))
const NewElementsEvent & event) {
MaterialIGFEMSawToothDamage<spatial_dimension>::onElementsAdded(element_list,
event);
/// set the correct damage iteration step (is UInt->cannot be interpolated)
Real val = 0.;
for (ghost_type_t::iterator g = ghost_type_t::begin();
g != ghost_type_t::end(); ++g) {
GhostType ghost_type = *g;
/// loop over all types in the material
typedef ElementTypeMapArray<UInt>::type_iterator iterator;
iterator it = this->element_filter.firstType(spatial_dimension, ghost_type,
_ek_igfem);
iterator last_type =
this->element_filter.lastType(spatial_dimension, ghost_type, _ek_igfem);
/// loop over all types in the filter
for (; it != last_type; ++it) {
const ElementType el_type = *it;
Array<Real>::scalar_iterator dam_it =
this->damage(el_type, ghost_type).begin();
Array<UInt>::scalar_iterator reduction_it =
this->reduction_step(el_type, ghost_type).begin();
UInt nb_element = this->element_filter(el_type, ghost_type).getSize();
UInt nb_quads = this->fem->getNbIntegrationPoints(el_type);
UInt * sub_mat_ptr = this->sub_material(el_type, ghost_type).storage();
for (UInt q = 0; q < nb_element * nb_quads;
++q, ++sub_mat_ptr, ++dam_it, ++reduction_it) {
if (*sub_mat_ptr) {
if (Math::are_float_equal(*dam_it, this->max_damage))
*reduction_it = this->max_reductions;
else {
for (UInt i = 0; i < this->max_reductions; ++i) {
val = 1 - (1. / std::pow(this->reduction_constant, i));
if (Math::are_float_equal(val, *dam_it))
*reduction_it = i;
}
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialIGFEMIterativeStiffnessReduction);
} // namespace akantu
diff --git a/extra_packages/igfem/src/material_igfem/material_igfem_iterative_stiffness_reduction.hh b/extra_packages/igfem/src/material_igfem/material_igfem_iterative_stiffness_reduction.hh
index 1a81ec4ae..a72e4a6a4 100644
--- a/extra_packages/igfem/src/material_igfem/material_igfem_iterative_stiffness_reduction.hh
+++ b/extra_packages/igfem/src/material_igfem/material_igfem_iterative_stiffness_reduction.hh
@@ -1,113 +1,113 @@
/**
* @file material_igfem_iterative_stiffness_reduction.hh
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Wed Mar 9 19:44:22 2016
*
* @brief Material for iterative stiffness reduction by contant factor
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_igfem_saw_tooth_damage.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_IGFEM_ITERATIVE_STIFFNESS_REDUCTION_HH__
-#define __AKANTU_MATERIAL_IGFEM_ITERATIVE_STIFFNESS_REDUCTION_HH__
+#ifndef AKANTU_MATERIAL_IGFEM_ITERATIVE_STIFFNESS_REDUCTION_HH_
+#define AKANTU_MATERIAL_IGFEM_ITERATIVE_STIFFNESS_REDUCTION_HH_
namespace akantu {
/**
* Material damage iterative
*
* parameters in the material files :
* - Gfx
* - h
* - Sc
*/
/// Proposed by Rots and Invernizzi, 2004: Regularized sequentially linear
// saw-tooth softening model (section 4.2)
template <UInt spatial_dimension>
class MaterialIGFEMIterativeStiffnessReduction
: public MaterialIGFEMSawToothDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialIGFEMIterativeStiffnessReduction(SolidMechanicsModel & model,
const ID & id = "");
virtual ~MaterialIGFEMIterativeStiffnessReduction(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set the material parameters
virtual void initMaterial();
/// compute the equivalent stress on each Gauss point (i.e. the max prinicpal
/// stress) and normalize it by the tensile stiffness
virtual void
computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// update internal field damage
virtual UInt updateDamage();
virtual void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the ultimate strain
IGFEMInternalField<Real> eps_u;
/// the reduction
IGFEMInternalField<UInt> reduction_step;
/// the tangent of the tensile stress-strain softening
IGFEMInternalField<Real> D;
/// fracture energy
Real Gf;
/// crack band width for normalization of fracture energy
Real crack_band_width;
/// the number of total reductions steps until complete failure
UInt max_reductions;
/// the reduction constant (denoated by a in the paper of rots)
Real reduction_constant;
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_IGFEM_ITERATIVE_STIFFNESS_REDUCTION_HH__ */
+#endif /* AKANTU_MATERIAL_IGFEM_ITERATIVE_STIFFNESS_REDUCTION_HH_ */
diff --git a/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage.cc b/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage.cc
index bbe53b30d..e95cd3dd5 100644
--- a/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage.cc
+++ b/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage.cc
@@ -1,467 +1,466 @@
/**
* @file material_igfem_saw_tooth_damage.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Implementation of the squentially linear saw-tooth damage model for
* IGFEM elements
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material_igfem_saw_tooth_damage.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialIGFEMSawToothDamage<dim>::MaterialIGFEMSawToothDamage(
SolidMechanicsModel & model, const ID & id)
: Material(model, id), Parent(model, id), Sc("Sc", *this),
equivalent_stress("equivalent_stress", *this),
norm_max_equivalent_stress(0) {
AKANTU_DEBUG_IN();
this->Sc.initialize(1);
this->equivalent_stress.initialize(1);
this->damage.setElementKind(_ek_igfem);
this->damage.setFEEngine(*(this->fem));
this->internals_to_transfer.push_back("damage");
this->internals_to_transfer.push_back("Sc");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialIGFEMSawToothDamage<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Parent::initMaterial();
/// get the parameters for the sub-material that can be damaged
ID mat_name = this->sub_material_names[1];
const Material & mat = this->model->getMaterial(mat_name);
this->prescribed_dam = mat.getParam<Real>("prescribed_dam");
this->dam_threshold = mat.getParam<Real>("dam_threshold");
this->dam_tolerance = mat.getParam<Real>("dam_tolerance");
this->max_damage = mat.getParam<Real>("max_damage");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMSawToothDamage<spatial_dimension>::
computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// Vector to store eigenvalues of current stress tensor
Vector<Real> eigenvalues(spatial_dimension);
Array<Real>::const_iterator<Real> Sc_it = Sc(el_type, ghost_type).begin();
Array<Real>::iterator<Real> equivalent_stress_it =
equivalent_stress(el_type, ghost_type).begin();
Array<Real>::const_matrix_iterator grad_u_it =
grad_u.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_matrix_iterator grad_u_end =
grad_u.end(spatial_dimension, spatial_dimension);
/// get pointer to internals
Real * lambda_ptr = this->lambda(el_type, ghost_type).storage();
Real * mu_ptr = this->mu(el_type, ghost_type).storage();
Real * dam = this->damage(el_type, ghost_type).storage();
Matrix<Real> sigma(spatial_dimension, spatial_dimension);
for (; grad_u_it != grad_u_end; ++grad_u_it) {
- sigma.clear();
MaterialIGFEMElastic<spatial_dimension>::computeStressOnQuad(
*grad_u_it, sigma, *lambda_ptr, *mu_ptr);
computeDamageAndStressOnQuad(sigma, *dam);
/// compute eigenvalues
sigma.eig(eigenvalues);
/// find max eigenvalue and normalize by tensile strength
*equivalent_stress_it =
*(std::max_element(eigenvalues.storage(),
eigenvalues.storage() + spatial_dimension)) /
*(Sc_it);
++Sc_it;
++equivalent_stress_it;
++dam;
++lambda_ptr;
++mu_ptr;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMSawToothDamage<spatial_dimension>::computeAllStresses(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// reset normalized maximum equivalent stress
if (ghost_type == _not_ghost)
norm_max_equivalent_stress = 0;
Parent::computeAllStresses(ghost_type);
/// find global Gauss point with highest stress
StaticCommunicator & comm =
akantu::StaticCommunicator::getStaticCommunicator();
comm.allReduce(&norm_max_equivalent_stress, 1, _so_max);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMSawToothDamage<spatial_dimension>::
findMaxNormalizedEquivalentStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (ghost_type == _not_ghost) {
const Array<Real> & e_stress = equivalent_stress(el_type);
Array<Real>::const_iterator<Real> equivalent_stress_it = e_stress.begin();
Array<Real>::const_iterator<Real> equivalent_stress_end = e_stress.end();
Array<Real> & dam = this->damage(el_type);
Array<Real>::iterator<Real> dam_it = dam.begin();
Array<UInt> & sub_mat = this->sub_material(el_type);
Array<UInt>::iterator<UInt> sub_mat_it = sub_mat.begin();
for (; equivalent_stress_it != equivalent_stress_end;
++equivalent_stress_it, ++dam_it, ++sub_mat_it) {
/// check if max equivalent stress for this element type is greater than
/// the current norm_max_eq_stress and if the element is not already fully
/// damaged
if ((*equivalent_stress_it > norm_max_equivalent_stress &&
*dam_it < max_damage) &&
*sub_mat_it != 0) {
norm_max_equivalent_stress = *equivalent_stress_it;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMSawToothDamage<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent::computeStress(el_type, ghost_type);
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeDamageAndStressOnQuad(sigma, *dam);
++dam;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
computeNormalizedEquivalentStress(this->gradu(el_type, ghost_type), el_type,
ghost_type);
norm_max_equivalent_stress = 0;
findMaxNormalizedEquivalentStress(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
UInt MaterialIGFEMSawToothDamage<spatial_dimension>::updateDamage() {
UInt nb_damaged_elements = 0;
AKANTU_DEBUG_ASSERT(prescribed_dam > 0.,
"Your prescribed damage must be greater than zero");
if (norm_max_equivalent_stress >= 1.) {
AKANTU_DEBUG_IN();
GhostType ghost_type = _not_ghost;
;
Mesh::type_iterator it = this->model->getMesh().firstType(
spatial_dimension, ghost_type, _ek_igfem);
Mesh::type_iterator last_type = this->model->getMesh().lastType(
spatial_dimension, ghost_type, _ek_igfem);
for (; it != last_type; ++it) {
ElementType el_type = *it;
Array<UInt> & sub_mat = this->sub_material(el_type);
Array<UInt>::iterator<UInt> sub_mat_it = sub_mat.begin();
const Array<Real> & e_stress = equivalent_stress(el_type);
Array<Real>::const_iterator<Real> equivalent_stress_it = e_stress.begin();
Array<Real>::const_iterator<Real> equivalent_stress_end = e_stress.end();
Array<Real> & dam = this->damage(el_type);
Array<Real>::iterator<Real> dam_it = dam.begin();
/// loop over all the elements of the given type
UInt nb_element = this->element_filter(el_type, ghost_type).getSize();
UInt nb_quads = this->fem->getNbIntegrationPoints(el_type, ghost_type);
bool damage_element = false;
for (UInt e = 0; e < nb_element; ++e) {
damage_element = false;
/// check if damage occurs in the element
for (UInt q = 0; q < nb_quads; ++q) {
if (*equivalent_stress_it >=
(1 - dam_tolerance) * norm_max_equivalent_stress &&
*sub_mat_it != 0) {
damage_element = true;
}
++sub_mat_it;
++equivalent_stress_it;
}
if (damage_element) {
nb_damaged_elements += 1;
/// damage the element
sub_mat_it -= nb_quads;
for (UInt q = 0; q < nb_quads; ++q) {
if (*sub_mat_it) {
if (*dam_it < dam_threshold)
*dam_it += prescribed_dam;
else
*dam_it = max_damage;
}
++sub_mat_it;
++dam_it;
}
} else {
dam_it += nb_quads;
}
}
}
}
StaticCommunicator & comm =
akantu::StaticCommunicator::getStaticCommunicator();
comm.allReduce(&nb_damaged_elements, 1, _so_sum);
AKANTU_DEBUG_OUT();
return nb_damaged_elements;
}
/* -------------------------------------------------------------------------- */
// template<UInt spatial_dimension>
// void
// MaterialIGFEMSawToothDamage<spatial_dimension>::updateEnergiesAfterDamage(ElementType
// el_type, GhostType ghost_type) {
// MaterialDamage<spatial_dimension>::updateEnergies(el_type, ghost_type);
// }
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialIGFEMSawToothDamage<spatial_dimension>::onElementsAdded(
__attribute__((unused)) const Array<Element> & element_list,
__attribute__((unused)) const NewElementsEvent & event) {
/// update elastic constants
MaterialIGFEMElastic<spatial_dimension>::onElementsAdded(element_list, event);
IGFEMInternalField<Real> quadrature_points_coordinates(
"quadrature_points_coordinates", *this);
quadrature_points_coordinates.initialize(spatial_dimension);
this->computeQuadraturePointsCoordinates(quadrature_points_coordinates,
_not_ghost);
this->computeQuadraturePointsCoordinates(quadrature_points_coordinates,
_ghost);
Array<Element>::const_iterator<Element> el_begin = element_list.begin();
Array<Element>::const_iterator<Element> el_end = element_list.end();
Element el;
el.kind = _ek_igfem;
/// loop over all the elements in the filter
for (ghost_type_t::iterator g = ghost_type_t::begin();
g != ghost_type_t::end(); ++g) {
GhostType ghost_type = *g;
/// loop over all types in the material
typedef ElementTypeMapArray<UInt>::type_iterator iterator;
iterator it = this->element_filter.firstType(spatial_dimension, ghost_type,
_ek_igfem);
iterator last_type =
this->element_filter.lastType(spatial_dimension, ghost_type, _ek_igfem);
for (; it != last_type; ++it) {
/// store the elements added to this material
std::vector<Element> new_elements;
Array<UInt> & elem_filter = this->element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
UInt nb_quads =
quadrature_points_coordinates.getFEEngine().getNbIntegrationPoints(
*it, ghost_type);
Array<Real> added_quads(0, spatial_dimension);
const Array<Real> & quads =
quadrature_points_coordinates(*it, ghost_type);
Array<Real>::const_vector_iterator quad = quads.begin(spatial_dimension);
el.type = *it;
el.ghost_type = ghost_type;
for (UInt e = 0; e < nb_element; ++e) {
/// global number of element
el.element = elem_filter(e);
if (std::find(el_begin, el_end, el) != el_end) {
new_elements.push_back(el);
for (UInt q = 0; q < nb_quads; ++q) {
added_quads.push_back(*quad);
++quad;
}
} else
quad += nb_quads;
}
/// get the extrapolated values
for (UInt i = 0; i < this->internals_to_transfer.size(); ++i) {
if (!new_elements.size())
continue;
const ID name = this->getID() + ":" + this->internals_to_transfer[i];
Array<Real> & internal =
(*(this->internal_vectors_real[name]))(*it, ghost_type);
UInt nb_component = internal.getNbComponent();
/// Array<Real>::vector_iterator internal_it =
/// internal.begin(nb_component);
Array<Real> extrapolated_internal_values(new_elements.size() * nb_quads,
nb_component);
this->model->transferInternalValues(this->internals_to_transfer[i],
new_elements, added_quads,
extrapolated_internal_values);
UInt * sub_mat_ptr = this->sub_material(*it, ghost_type).storage();
Array<Real>::const_vector_iterator extrapolated_it =
extrapolated_internal_values.begin(nb_component);
Array<Real>::vector_iterator internal_it = internal.begin(nb_component);
/// copy back the results
for (UInt j = 0; j < new_elements.size(); ++j) {
Element element_local = this->convertToLocalElement(new_elements[j]);
for (UInt q = 0; q < nb_quads; ++q, ++extrapolated_it) {
if (sub_mat_ptr[element_local.element * nb_quads + q])
internal_it[element_local.element * nb_quads + q] =
*extrapolated_it;
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
// template<UInt spatial_dimension>
// void
// MaterialIGFEMSawToothDamage<spatial_dimension>::transferInternals(Material &
// old_mat,
// std::vector<ElementPair> & element_pairs)
// {
// Element new_el_global;
// Element new_el_local;
// Element old_el_global;
// Element old_el_local;
// /// get the fe-engine of the old material
// FEEngine & fem_old_mat = old_mat.getFEEngine();
// for (UInt e = 0; e < element_pairs.size(); ++e) {
// new_el_global = element_pairs[e].first;
// old_el_global = element_pairs[e].second;
// /// get the number of the elements in their materials
// old_el_local = old_el_global;
// Array<UInt> & mat_local_numbering =
// this->model->getMaterialLocalNumbering(old_el_global.type,
// old_el_global.ghost_type);
// old_el_local.element = mat_local_numbering(old_el_global.element);
// new_el_local = this->convertToLocalElement(new_el_global);
// UInt nb_old_quads = fem_old_mat.getNbIntegrationPoints(old_el_global.type,
// old_el_global.ghost_type);
// UInt nb_new_quads = this->fem->getNbIntegrationPoints(new_el_global.type,
// new_el_global.ghost_type);
// if (old_mat.isInternal("damage", Mesh::getKind(old_el_global.type))
// && old_mat.isInternal("Sc", Mesh::getKind(old_el_global.type)) ) {
// UInt quad;
// Vector<Real> el_old_damage(nb_old_quads);
// Vector<Real> el_old_Sc(nb_old_quads);
// Vector<Real> el_new_damage(nb_new_quads);
// Vector<Real> el_new_Sc(nb_new_quads);
// const Array<Real> & old_Sc = old_mat.getArray("Sc", old_el_global.type,
// old_el_global.ghost_type);
// const Array<Real> & old_damage = old_mat.getArray("damage",
// old_el_global.type, old_el_global.ghost_type);
// Array<Real> & new_Sc = this->Sc(new_el_global.type,
// new_el_global.ghost_type);
// Array<Real> & new_damage = this->damage(new_el_global.type,
// new_el_global.ghost_type);
// for (UInt q = 0; q < nb_old_quads; ++q) {
// quad = old_el_local.element * nb_old_quads + q;
// el_old_damage(q) = old_damage(quad);
// el_old_Sc(q) = old_Sc(quad);
// }
// this->interpolateInternal(new_el_global, old_el_global, el_new_damage,
// el_old_damage, nb_new_quads, nb_old_quads);
// this->interpolateInternal(new_el_global, old_el_global, el_new_Sc,
// el_old_Sc, nb_new_quads, nb_old_quads);
// for (UInt q = 0; q < nb_new_quads; ++q) {
// quad = new_el_local.element * nb_new_quads + q;
// if (this->sub_material(new_el_global.type,new_el_global.ghost_type)(quad)) {
// new_damage(quad) = el_new_damage(q);
// new_Sc(quad) = el_new_damage(q);
// }
// }
// }
// else
// AKANTU_DEBUG_ASSERT((!old_mat.isInternal("damage",
// Mesh::getKind(old_el_global.type))
// && !old_mat.isInternal("Sc", Mesh::getKind(old_el_global.type))
// ),
// "old material has damage or Sc but not both!!!!");
// }
// }
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialIGFEMSawToothDamage);
} // namespace akantu
/* /// get the material index in the model from this current material
UInt this_mat_idx = this->model->getMaterialIndex(this->name);
/// number of elements in this event
UInt nb_new_elements = element_list.getSize();
// const Array<Element> & old_elements = igfem_event->getOldElementsList();
// std::map<UInt, std::vector<ElementPair> > elements_by_old_mat;
/// store the old elements sorted by their material
for (UInt e = 0; e < nb_new_elements; ++e) {
const Element new_el = element_list(e);
const Array<UInt> & mat_idx =
this->model->getMaterialByElement(new_el.type, new_el.ghost_type);
if ( mat_idx(new_el.element) != this_mat_idx )
continue; /// new element is not part of this material: nothing to be done
/// get the corresponding old element and store new and old one as pair
const Element old_el = old_elements(e);
ElementPair el_pair(new_el, old_el);
const Array<UInt> & old_mat_idx =
this->model->getMaterialByElement(old_el.type, old_el.ghost_type);
UInt mat_old_idx = old_mat_idx(old_el.element);
elements_by_old_mat[mat_old_idx].push_back(el_pair);
}
/// loop over all the element pairs in the map
for (std::map<UInt, std::vector<ElementPair> >::iterator map_it =
elements_by_old_mat.begin();
map_it != elements_by_old_mat.end(); ++map_it) {
/// get the vector of old and new element pairs
std::vector<ElementPair > & element_pairs = map_it->second;
Material & old_mat = this->model->getMaterial(map_it->first);
this->transferInternals(old_mat, element_pairs);
}
*/
diff --git a/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage.hh b/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage.hh
index c0e861aaf..04ecc8063 100644
--- a/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage.hh
+++ b/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage.hh
@@ -1,138 +1,138 @@
/**
* @file material_igfem_saw_tooth_damage.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Linear saw-tooth softening material model for IGFEM elements
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage.hh"
#include "material_igfem_elastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_IGFEM_SAW_TOOTH_DAMAGE_HH__
-#define __AKANTU_MATERIAL_IGFEM_SAW_TOOTH_DAMAGE_HH__
+#ifndef AKANTU_MATERIAL_IGFEM_SAW_TOOTH_DAMAGE_HH_
+#define AKANTU_MATERIAL_IGFEM_SAW_TOOTH_DAMAGE_HH_
namespace akantu {
template <UInt spatial_dimension>
class MaterialIGFEMSawToothDamage
: public MaterialDamage<spatial_dimension, MaterialIGFEMElastic> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
typedef MaterialDamage<spatial_dimension, MaterialIGFEMElastic> Parent;
public:
typedef std::pair<Element, Element> ElementPair;
MaterialIGFEMSawToothDamage(SolidMechanicsModel & model, const ID & id = "");
MaterialIGFEMSawToothDamage(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "");
virtual ~MaterialIGFEMSawToothDamage() {}
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void initMaterial();
/// virtual void updateInternalParameters();
virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
/// update internal field damage
virtual UInt updateDamage();
UInt updateDamage(UInt quad_index, const Real eq_stress,
- const ElementType & el_type, const GhostType & ghost_type);
+ ElementType el_type, GhostType ghost_type);
/// update energies after damage has been updated
// virtual void updateEnergiesAfterDamage(ElementType el_type, GhostType
// ghost_typ);
virtual void onBeginningSolveStep(const AnalysisMethod & method){};
virtual void onEndSolveStep(const AnalysisMethod & method){};
protected:
/// constitutive law for all element of a type
virtual void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// compute the equivalent stress on each Gauss point (i.e. the max prinicpal
/// stress) and normalize it by the tensile strength
virtual void
computeNormalizedEquivalentStress(const Array<Real> & grad_u,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// find max normalized equivalent stress
void findMaxNormalizedEquivalentStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma, Real & dam);
protected:
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
virtual void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get max normalized equivalent stress
AKANTU_GET_MACRO(NormMaxEquivalentStress, norm_max_equivalent_stress, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// resistance to damage
IGFEMInternalField<Real> Sc;
/// internal field to store equivalent stress on each Gauss point
IGFEMInternalField<Real> equivalent_stress;
/// damage increment
Real prescribed_dam;
/// maximum equivalent stress
Real norm_max_equivalent_stress;
/// deviation from max stress at which Gauss point will still get damaged
Real dam_tolerance;
/// define damage threshold at which damage will be set to 1
Real dam_threshold;
/// maximum damage value
Real max_damage;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_igfem_saw_tooth_damage_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_IGFEM_SAW_TOOTH_DAMAGE_HH__ */
+#endif /* AKANTU_MATERIAL_IGFEM_SAW_TOOTH_DAMAGE_HH_ */
diff --git a/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage_inline_impl.hh b/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage_inline_impl.hh
index ce35f8000..6cacd607f 100644
--- a/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage_inline_impl.hh
+++ b/extra_packages/igfem/src/material_igfem/material_igfem_saw_tooth_damage_inline_impl.hh
@@ -1,66 +1,66 @@
/**
* @file material_igfem_saw_tooth_damage_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief Implementation of inline functions of the squentially linear
* saw-tooth damage model for IGFEM elements
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void
MaterialIGFEMSawToothDamage<spatial_dimension>::computeDamageAndStressOnQuad(
Matrix<Real> & sigma, Real & dam) {
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
UInt MaterialIGFEMSawToothDamage<spatial_dimension>::updateDamage(
- UInt quad_index, const Real eq_stress, const ElementType & el_type,
- const GhostType & ghost_type) {
+ UInt quad_index, const Real eq_stress, ElementType el_type,
+ GhostType ghost_type) {
AKANTU_DEBUG_ASSERT(prescribed_dam > 0.,
"Your prescribed damage must be greater than zero");
Array<Real> & dam = this->damage(el_type, ghost_type);
Real & dam_on_quad = dam(quad_index);
/// check if damage occurs
if (equivalent_stress(el_type, ghost_type)(quad_index) >=
(1 - dam_tolerance) * norm_max_equivalent_stress) {
/// damage the entire sub-element -> get the element index
UInt el_index =
quad_index / this->element_filter(el_type, ghost_type).getSize();
UInt nb_quads = this->fem->getNbIntegrationPoints(el_type, ghost_type);
UInt start_idx = el_index * nb_quads;
Array<UInt> & sub_mat = this->sub_material(el_type, ghost_type);
UInt damaged_quads = 0;
if (dam_on_quad < dam_threshold) {
for (UInt q = 0; q < nb_quads; ++q, ++start_idx) {
if (sub_mat(start_idx)) {
dam(start_idx) += prescribed_dam;
damaged_quads += 1;
}
}
} else {
for (UInt q = 0; q < nb_quads; ++q, ++start_idx) {
if (sub_mat(start_idx)) {
dam(start_idx) += max_damage;
damaged_quads += 1;
}
}
}
return damaged_quads;
}
return 0;
}
/* -------------------------------------------------------------------------- */
diff --git a/extra_packages/igfem/src/mesh_igfem_spherical_growing_gel.hh b/extra_packages/igfem/src/mesh_igfem_spherical_growing_gel.hh
index eb196d463..7604a0118 100644
--- a/extra_packages/igfem/src/mesh_igfem_spherical_growing_gel.hh
+++ b/extra_packages/igfem/src/mesh_igfem_spherical_growing_gel.hh
@@ -1,220 +1,220 @@
/**
* @file mesh_igfem_spherical_growing_gel.hh
*
* @author Clement Roux-Langlois <clement.roux@epfl.ch>
*
* @date creation: Mon Jul 13 2015
*
* @brief Computation of mesh intersection with sphere(s) and growing of these
* spheres. This class handle the intersectors templated for every
* element
* types.
*
*
* Copyright (©) 2010-2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
//#if 0
-#ifndef __AKANTU_MESH_IGFEM_SPHERICAL_GROWING_GEL_HH__
-#define __AKANTU_MESH_IGFEM_SPHERICAL_GROWING_GEL_HH__
+#ifndef AKANTU_MESH_IGFEM_SPHERICAL_GROWING_GEL_HH_
+#define AKANTU_MESH_IGFEM_SPHERICAL_GROWING_GEL_HH_
#include "aka_common.hh"
#include "mesh_sphere_intersector.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* classes for new igfem elements mesh events */
/* -------------------------------------------------------------------------- */
class NewIGFEMElementsEvent : public NewElementsEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(OldElementsList, old_elements, Array<Element> &);
AKANTU_GET_MACRO(OldElementsList, old_elements, const Array<Element> &);
protected:
Array<Element> old_elements;
};
class NewIGFEMNodesEvent : public NewNodesEvent {
public:
void setNewNodePerElem(const Array<UInt> & new_node_per_elem) {
this->new_node_per_elem = &new_node_per_elem;
}
void setType(ElementType new_type) { type = new_type; }
void setGhostType(GhostType new_type) { ghost_type = new_type; }
AKANTU_GET_MACRO(NewNodePerElem, *new_node_per_elem, const Array<UInt> &);
AKANTU_GET_MACRO(ElementType, type, ElementType);
AKANTU_GET_MACRO(GhostType, ghost_type, GhostType);
protected:
ElementType type;
GhostType ghost_type;
const Array<UInt> * new_node_per_elem;
};
/* -------------------------------------------------------------------------- */
template <UInt dim> class MeshIgfemSphericalGrowingGel {
// definition of the element list
#define ELEMENT_LIST (_triangle_3)(_igfem_triangle_4)(_igfem_triangle_5)
// Solution 1
/* #define INTERSECTOR_DEFINITION(type) \
MeshSphereIntersector<2, type> intersector##type(mesh);*/
// Solution 2
#define INSTANTIATOR(_type) \
intersectors(_type, ghost_type) = \
new MeshSphereIntersector<dim, _type>(this->mesh)
/* --------------------------------------------------------------------------
*/
/* Constructor/Destructor */
/* --------------------------------------------------------------------------
*/
public:
/// Construct from mesh
MeshIgfemSphericalGrowingGel(Mesh & mesh);
/// Destructor
~MeshIgfemSphericalGrowingGel() {
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(dim, ghost_type, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType(dim, ghost_type, _ek_not_defined);
for (; it != end; ++it) {
delete intersectors(*it, ghost_type);
}
}
}
/* --------------------------------------------------------------------------
*/
/* Methods */
/* --------------------------------------------------------------------------
*/
public:
void init();
/// Remove the additionnal nodes
void removeAdditionalNodes();
/// Compute the intersection points between the mesh and the query list for
/// all element types and send the NewNodeEvent
void computeMeshQueryListIntersectionPoint(
const std::list<SK::Sphere_3> & query_list);
/// increase sphere radius and build the new intersection points between the
/// mesh and the query list for all element types and send the NewNodeEvent
void computeMeshQueryListIntersectionPoint(
const std::list<SK::Sphere_3> & query_list, Real inf_fact) {
std::list<SK::Sphere_3>::const_iterator query_it = query_list.begin(),
query_end = query_list.end();
std::list<SK::Sphere_3> sphere_list;
for (; query_it != query_end; ++query_it) {
SK::Sphere_3 sphere(query_it->center(),
query_it->squared_radius() * inf_fact * inf_fact);
sphere_list.push_back(sphere);
}
computeMeshQueryListIntersectionPoint(sphere_list);
}
/// Build the IGFEM mesh from intersection points
void buildIGFEMMesh();
/// Build the IGFEM mesh from spheres
void buildIGFEMMeshFromSpheres(const std::list<SK::Sphere_3> & query_list) {
computeMeshQueryListIntersectionPoint(query_list);
buildIGFEMMesh();
}
/// Build the IGFEM mesh from spheres with increase factor
void buildIGFEMMeshFromSpheres(const std::list<SK::Sphere_3> & query_list,
Real inf_fact) {
computeMeshQueryListIntersectionPoint(query_list, inf_fact);
buildIGFEMMesh();
}
/// set the distributed synchronizer
void setDistributedSynchronizer(DistributedSynchronizer * dist) {
synchronizer = dist;
buildSegmentConnectivityToNodeType();
}
/// update node type
void updateNodeType(const Array<UInt> & nodes_list,
const Array<UInt> & new_node_per_elem, ElementType type,
GhostType ghost_type);
protected:
/// Build the unordered_map needed to assign the node type to new nodes in
/// parallel
void buildSegmentConnectivityToNodeType();
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
AKANTU_GET_MACRO(NbStandardNodes, nb_nodes_fem, UInt);
AKANTU_GET_MACRO(NbEnrichedNodes, nb_enriched_nodes, UInt);
/* --------------------------------------------------------------------------
*/
/* Class Members */
/* --------------------------------------------------------------------------
*/
protected:
/// Mesh used to construct the primitives
Mesh & mesh;
/// number of fem nodes in the initial mesh
UInt nb_nodes_fem;
/// number of enriched nodes before intersection
UInt nb_enriched_nodes;
// Solution 2
/// map of the elements types in the mesh and the corresponding intersectors
ElementTypeMap<MeshAbstractIntersector<SK::Sphere_3> *> intersectors;
/// Map linking pairs of nodes to a node type. The pairs of nodes
/// contain the connectivity of the primitive segments that are
/// intersected.
unordered_map<std::pair<UInt, UInt>, Int>::type segment_conn_to_node_type;
/// Pointer to the distributed synchronizer of the model
DistributedSynchronizer * synchronizer;
};
} // namespace akantu
#include "mesh_igfem_spherical_growing_gel_tmpl.hh"
-#endif // __AKANTU_MESH_IGFEM_SPHERICAL_GROWING_GEL_HH__
+#endif // AKANTU_MESH_IGFEM_SPHERICAL_GROWING_GEL_HH_
//#endif //
diff --git a/extra_packages/igfem/src/non_local_manager_igfem.cc b/extra_packages/igfem/src/non_local_manager_igfem.cc
index 81dbaa5f3..5f1b2b851 100644
--- a/extra_packages/igfem/src/non_local_manager_igfem.cc
+++ b/extra_packages/igfem/src/non_local_manager_igfem.cc
@@ -1,307 +1,307 @@
/**
* @file non_local_manager_igfem.cc
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Mon Sep 21 15:32:10 2015
*
* @brief Implementation of non-local manager igfem
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_DAMAGE_NON_LOCAL
#include "non_local_manager_igfem.hh"
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLocalManagerIGFEM::NonLocalManagerIGFEM(SolidMechanicsModelIGFEM & model,
const ID & id,
const MemoryID & memory_id)
: NonLocalManager(model, id, memory_id) {
Mesh & mesh = this->model.getMesh();
/// initialize the element type map array
/// it will be resized to nb_quad * nb_element during the computation of
/// coords
mesh.initElementTypeMapArray(quad_positions, spatial_dimension,
spatial_dimension, false, _ek_igfem, true);
}
/* -------------------------------------------------------------------------- */
NonLocalManagerIGFEM::~NonLocalManagerIGFEM() {}
/* -------------------------------------------------------------------------- */
void NonLocalManagerIGFEM::init() {
/// store the number of current ghost elements for each type in the mesh
ElementTypeMap<UInt> nb_ghost_protected;
Mesh & mesh = this->model.getMesh();
for (UInt k = _ek_regular; k <= _ek_igfem; ++k) {
ElementKind el_kind = (ElementKind)k;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost, el_kind);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, _ghost, el_kind);
for (; it != last_type; ++it)
nb_ghost_protected(mesh.getNbElement(*it, _ghost), *it, _ghost);
}
/// exchange the missing ghosts for the non-local neighborhoods
this->createNeighborhoodSynchronizers();
/// insert the ghost quadrature points of the non-local materials into the
/// non-local neighborhoods
for (UInt m = 0; m < this->non_local_materials.size(); ++m) {
switch (spatial_dimension) {
case 1:
dynamic_cast<MaterialNonLocal<1> &>(*(this->non_local_materials[m]))
.insertQuadsInNeighborhoods(_ghost);
break;
case 2:
dynamic_cast<MaterialNonLocal<2> &>(*(this->non_local_materials[m]))
.insertQuadsInNeighborhoods(_ghost);
break;
case 3:
dynamic_cast<MaterialNonLocal<3> &>(*(this->non_local_materials[m]))
.insertQuadsInNeighborhoods(_ghost);
break;
}
}
FEEngine & fee_regular = this->model.getFEEngine();
FEEngine & fee_igfem = this->model.getFEEngine("IGFEMFEEngine");
this->updatePairLists();
/// cleanup the unneccessary ghost elements
this->cleanupExtraGhostElements(nb_ghost_protected);
this->initElementTypeMap(1, volumes, fee_regular, _ek_regular);
this->initElementTypeMap(1, volumes, fee_igfem, _ek_igfem);
this->setJacobians(fee_regular, _ek_regular);
this->setJacobians(fee_igfem, _ek_igfem);
this->initNonLocalVariables();
this->computeWeights();
}
/* -------------------------------------------------------------------------- */
void NonLocalManagerIGFEM::computeAllNonLocalStresses() {
/// update the flattened version of the internals
std::map<ID, NonLocalVariable *>::iterator non_local_variable_it =
non_local_variables.begin();
std::map<ID, NonLocalVariable *>::iterator non_local_variable_end =
non_local_variables.end();
for (; non_local_variable_it != non_local_variable_end;
++non_local_variable_it) {
- non_local_variable_it->second->local.clear();
- non_local_variable_it->second->non_local.clear();
+ non_local_variable_it->second->local.zero();
+ non_local_variable_it->second->non_local.zero();
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType)gt;
this->flattenInternal(non_local_variable_it->second->local, ghost_type,
_ek_regular);
this->flattenInternal(non_local_variable_it->second->local, ghost_type,
_ek_igfem);
}
}
- this->volumes.clear();
+ this->volumes.zero();
/// loop over all the neighborhoods and compute intiate the
/// exchange of the non-local_variables
std::set<ID>::const_iterator global_neighborhood_it =
global_neighborhoods.begin();
NeighborhoodMap::iterator it;
for (; global_neighborhood_it != global_neighborhoods.end();
++global_neighborhood_it) {
it = neighborhoods.find(*global_neighborhood_it);
if (it != neighborhoods.end())
it->second->getSynchronizerRegistry().asynchronousSynchronize(
SynchronizationTag::_mnl_for_average);
else
dummy_synchronizers[*global_neighborhood_it]->asynchronousSynchronize(
dummy_accessor, SynchronizationTag::_mnl_for_average);
}
this->averageInternals(_not_ghost);
AKANTU_DEBUG_INFO("Wait distant non local stresses");
/// loop over all the neighborhoods and block until all non-local
/// variables have been exchanged
global_neighborhood_it = global_neighborhoods.begin();
it = neighborhoods.begin();
for (; global_neighborhood_it != global_neighborhoods.end();
++global_neighborhood_it) {
it = neighborhoods.find(*global_neighborhood_it);
if (it != neighborhoods.end())
it->second->getSynchronizerRegistry().waitEndSynchronize(
SynchronizationTag::_mnl_for_average);
else
dummy_synchronizers[*global_neighborhood_it]->waitEndSynchronize(
dummy_accessor, SynchronizationTag::_mnl_for_average);
}
this->averageInternals(_ghost);
/// copy the results in the materials
this->distributeInternals(_ek_regular);
/// loop over all the materials and update the weights
for (UInt m = 0; m < this->non_local_materials.size(); ++m) {
switch (spatial_dimension) {
case 1:
dynamic_cast<MaterialNonLocal<1> &>(*(this->non_local_materials[m]))
.computeNonLocalStresses(_not_ghost);
break;
case 2:
dynamic_cast<MaterialNonLocal<2> &>(*(this->non_local_materials[m]))
.computeNonLocalStresses(_not_ghost);
break;
case 3:
dynamic_cast<MaterialNonLocal<3> &>(*(this->non_local_materials[m]))
.computeNonLocalStresses(_not_ghost);
break;
}
}
++this->compute_stress_calls;
}
/* -------------------------------------------------------------------------- */
void NonLocalManagerIGFEM::cleanupExtraGhostElements(
ElementTypeMap<UInt> & nb_ghost_protected) {
typedef std::set<Element> ElementSet;
ElementSet relevant_ghost_elements;
ElementSet to_keep_per_neighborhood;
/// loop over all the neighborhoods and get their protected ghosts
NeighborhoodMap::iterator neighborhood_it = neighborhoods.begin();
NeighborhoodMap::iterator neighborhood_end = neighborhoods.end();
for (; neighborhood_it != neighborhood_end; ++neighborhood_it) {
neighborhood_it->second->cleanupExtraGhostElements(
to_keep_per_neighborhood);
ElementSet::const_iterator it = to_keep_per_neighborhood.begin();
for (; it != to_keep_per_neighborhood.end(); ++it)
relevant_ghost_elements.insert(*it);
- to_keep_per_neighborhood.clear();
+ to_keep_per_neighborhood.zero();
}
/// remove all unneccessary ghosts from the mesh
/// Create list of element to remove and new numbering for element to keep
Mesh & mesh = this->model.getMesh();
ElementSet ghost_to_erase;
RemovedElementsEvent remove_elem(mesh);
Element element;
for (UInt k = _ek_regular; k < _ek_igfem; ++k) {
ElementKind el_kind = (ElementKind)k;
element.kind = _ek_igfem;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost, el_kind);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, _ghost, el_kind);
element.ghost_type = _ghost;
for (; it != last_type; ++it) {
element.type = *it;
UInt nb_ghost_elem = mesh.getNbElement(*it, _ghost);
UInt nb_ghost_elem_protected = 0;
try {
nb_ghost_elem_protected = nb_ghost_protected(*it, _ghost);
} catch (...) {
}
if (!remove_elem.getNewNumbering().exists(*it, _ghost))
remove_elem.getNewNumbering().alloc(nb_ghost_elem, 1, *it, _ghost);
else
remove_elem.getNewNumbering(*it, _ghost).resize(nb_ghost_elem);
Array<UInt> & new_numbering = remove_elem.getNewNumbering(*it, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
element.element = g;
if (element.element >= nb_ghost_elem_protected &&
relevant_ghost_elements.find(element) ==
relevant_ghost_elements.end()) {
remove_elem.getList().push_back(element);
new_numbering(element.element) = UInt(-1);
}
}
/// renumber remaining ghosts
UInt ng = 0;
for (UInt g = 0; g < nb_ghost_elem; ++g) {
if (new_numbering(g) != UInt(-1)) {
new_numbering(g) = ng;
++ng;
}
}
}
}
for (UInt k = _ek_regular; k < _ek_igfem; ++k) {
ElementKind el_kind = (ElementKind)k;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost, el_kind);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, _ghost, el_kind);
for (; it != last_type; ++it) {
UInt nb_elem = mesh.getNbElement(*it, _not_ghost);
if (!remove_elem.getNewNumbering().exists(*it, _not_ghost))
remove_elem.getNewNumbering().alloc(nb_elem, 1, *it, _not_ghost);
Array<UInt> & new_numbering =
remove_elem.getNewNumbering(*it, _not_ghost);
for (UInt e = 0; e < nb_elem; ++e) {
new_numbering(e) = e;
}
}
}
mesh.sendEvent(remove_elem);
}
/* -------------------------------------------------------------------------- */
void NonLocalManagerIGFEM::onElementsAdded(__attribute__((unused))
const Array<Element> & element_list,
__attribute__((unused))
const NewElementsEvent & event) {
FEEngine & fee = this->model.getFEEngine("IGFEMFEEngine");
this->resizeElementTypeMap(1, volumes, fee, _ek_igfem);
this->resizeElementTypeMap(spatial_dimension, quad_positions, fee, _ek_igfem);
NonLocalManager::onElementsAdded(element_list, event);
}
/* -------------------------------------------------------------------------- */
void NonLocalManagerIGFEM::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
FEEngine & fee = this->model.getFEEngine("IGFEMFEEngine");
this->removeIntegrationPointsFromMap(event.getNewNumbering(),
spatial_dimension, quad_positions, fee,
_ek_igfem);
this->removeIntegrationPointsFromMap(event.getNewNumbering(), 1, volumes, fee,
_ek_igfem);
NonLocalManager::onElementsRemoved(element_list, new_numbering, event);
}
} // namespace akantu
#endif /* AKANTU_DAMAGE_NON_LOCAL */
diff --git a/extra_packages/igfem/src/non_local_manager_igfem.hh b/extra_packages/igfem/src/non_local_manager_igfem.hh
index e66a4bd71..1937a2c86 100644
--- a/extra_packages/igfem/src/non_local_manager_igfem.hh
+++ b/extra_packages/igfem/src/non_local_manager_igfem.hh
@@ -1,97 +1,97 @@
/**
* @file non_local_manager_igfem.hh
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Mon Sep 21 14:21:33 2015
*
* @brief Class that manages all the non-local neighborhoods for IGFEM
* simulations
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_DAMAGE_NON_LOCAL
-#ifndef __AKANTU_NON_LOCAL_MANAGER_IGFEM_HH__
-#define __AKANTU_NON_LOCAL_MANAGER_IGFEM_HH__
+#ifndef AKANTU_NON_LOCAL_MANAGER_IGFEM_HH_
+#define AKANTU_NON_LOCAL_MANAGER_IGFEM_HH_
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_igfem.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class NonLocalManagerIGFEM : public NonLocalManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalManagerIGFEM(SolidMechanicsModelIGFEM & model,
const ID & id = "non_local_manager_igfem",
const MemoryID & memory_id = 0);
virtual ~NonLocalManagerIGFEM();
/* --------------------------------------------------------------------------
*/
/* Methods */
/* --------------------------------------------------------------------------
*/
public:
/// initialize the non-local manager: compute pair lists and weights for all
/// neighborhoods
virtual void init();
/// average the internals and compute the non-local stresses
virtual void computeAllNonLocalStresses();
/* --------------------------------------------------------------------------
*/
/* MeshEventHandler inherited members */
/* --------------------------------------------------------------------------
*/
virtual void
onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
virtual void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event);
private:
/// cleanup unneccessary ghosts
virtual void
cleanupExtraGhostElements(ElementTypeMap<UInt> & nb_ghost_protected);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_NON_LOCAL_MANAGER_IGFEM_HH__ */
+#endif /* AKANTU_NON_LOCAL_MANAGER_IGFEM_HH_ */
#endif /* AKANTU_DAMAGE_NON_LOCAL */
diff --git a/extra_packages/igfem/src/shape_igfem.cc b/extra_packages/igfem/src/shape_igfem.cc
index 5818616db..d698a9cdb 100644
--- a/extra_packages/igfem/src/shape_igfem.cc
+++ b/extra_packages/igfem/src/shape_igfem.cc
@@ -1,96 +1,96 @@
/**
* @file shape_igfem_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief ShapeIGFEM inline implementation
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
//#include "mesh.hh"
#include "shape_igfem.hh"
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IGFEM)
namespace akantu {
/* -------------------------------------------------------------------------- */
ShapeLagrange<_ek_igfem>::ShapeLagrange(const Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: ShapeFunctions(mesh, id, memory_id),
shapes("shapes_generic", id, memory_id),
shapes_derivatives("shapes_derivatives_generic", id, memory_id),
igfem_integration_points("igfem_integration_points", id, memory_id),
shapes_at_enrichments("shapes_at_enrichments", id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/*-------------------------------------------------------------------------- */
void ShapeLagrange<_ek_igfem>::extractValuesAtStandardNodes(
const Array<Real> & nodal_values, Array<Real> & extracted_values,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_ASSERT(nodal_values.getNbComponent() ==
extracted_values.getNbComponent(),
"The arrays are not of the same size!!!!!");
- extracted_values.clear();
+ extracted_values.zero();
UInt spatial_dimension = mesh.getSpatialDimension();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_igfem);
Mesh::type_iterator end =
mesh.lastType(spatial_dimension, ghost_type, _ek_igfem);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_elements = mesh.getNbElement(type, ghost_type);
UInt nb_parent_nodes = 0;
UInt nb_nodes_per_element = 0;
#define GET_NODES_INFO(type) \
const ElementType parent_type = \
ElementClassProperty<type>::parent_element_type; \
nb_parent_nodes = \
ElementClass<parent_type>::getNbNodesPerInterpolationElement(); \
nb_nodes_per_element = \
ElementClass<type>::getNbNodesPerInterpolationElement();
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(GET_NODES_INFO);
#undef GET_NODES_INFO
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
for (UInt e = 0; e < nb_elements; ++e) {
/// copy the value at standard nodes
UInt offset = e * nb_nodes_per_element;
for (UInt n = 0; n < nb_parent_nodes; ++n) {
UInt node = conn_val[offset + n];
for (UInt i = 0; i < nodal_values.getNbComponent(); ++i)
extracted_values(node, i) = nodal_values(node, i);
}
}
}
}
/* -------------------------------------------------------------------------- */
void ShapeLagrange<_ek_igfem>::printself(std::ostream & stream,
int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Shapes Lagrange [" << std::endl;
ShapeFunctions::printself(stream, indent + 1);
shapes.printself(stream, indent + 1);
shapes_derivatives.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
} // namespace akantu
#endif
diff --git a/extra_packages/igfem/src/shape_igfem.hh b/extra_packages/igfem/src/shape_igfem.hh
index 591819dc9..a3db5d3dd 100644
--- a/extra_packages/igfem/src/shape_igfem.hh
+++ b/extra_packages/igfem/src/shape_igfem.hh
@@ -1,200 +1,200 @@
/**
* @file shape_igfem.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief shape functions for interface-enriched generalized FEM
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "shape_functions.hh"
-#ifndef __AKANTU_SHAPE_IGFEM_HH__
-#define __AKANTU_SHAPE_IGFEM_HH__
+#ifndef AKANTU_SHAPE_IGFEM_HH_
+#define AKANTU_SHAPE_IGFEM_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <> class ShapeLagrange<_ek_igfem> : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, const ID & id = "shape_igfem",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
const Matrix<Real> & integration_points_1,
const Matrix<Real> & integration_points_2,
- const ElementType & type,
- const GhostType & ghost_type);
+ ElementType type,
+ GhostType ghost_type);
inline void
interpolateEnrichmentsAllTypes(const Array<Real> & src, Array<Real> & dst,
- const ElementType & type,
- const GhostType & ghost_type) const;
+ ElementType type,
+ GhostType ghost_type) const;
template <ElementType type>
inline void precomputeShapesOnEnrichedNodes(const Array<Real> & nodes,
- const GhostType & ghost_type);
+ GhostType ghost_type);
template <ElementType type>
void interpolateAtEnrichedNodes(const Array<Real> & src, Array<Real> & dst,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// pre compute all shape derivatives on the element integration points from
/// natural coordinates
template <ElementType type>
void precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// interpolate on physical point
template <ElementType type>
void interpolate(const Vector<Real> & real_coords, UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// compute the gradient of u on the integration points
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// multiply a field by shape functions @f$ fts_{ij} = f_i * \varphi_j @f$
template <ElementType type>
void fieldTimesShapes(const Array<Real> & field,
Array<Real> & field_times_shapes,
GhostType ghost_type) const;
/// find natural coords in parent element from real coords provided an element
template <ElementType type>
void inverseMap(const Vector<Real> & real_coords, UInt element,
Vector<Real> & natural_coords,
- const GhostType & ghost_type = _not_ghost) const;
+ GhostType ghost_type = _not_ghost) const;
/// find natural coords in sub-element from real coords provided an element
template <ElementType type>
void inverseMap(const Vector<Real> & real_coords, UInt element,
Vector<Real> & natural_coords, UInt sub_element,
- const GhostType & ghost_type = _not_ghost) const;
+ GhostType ghost_type = _not_ghost) const;
/// return true if the coordinates provided are inside the element, false
/// otherwise
template <ElementType type>
bool contains(const Vector<Real> & real_coords, UInt elem,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// compute the shape on a provided point
template <ElementType type>
void computeShapes(const Vector<Real> & real_coords, UInt elem,
- Vector<Real> & shapes, const GhostType & ghost_type) const;
+ Vector<Real> & shapes, GhostType ghost_type) const;
/// compute the shape derivatives on a provided point
template <ElementType type>
void computeShapeDerivatives(const Matrix<Real> & real_coords, UInt elem,
Tensor3<Real> & shapes,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// interpolate a field on a given physical point
template <ElementType type>
void interpolateOnPhysicalPoint(const Vector<Real> & real_coords, UInt elem,
const Array<Real> & field,
Vector<Real> & interpolated,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// function to extract values at standard nodes and zero-out enriched values
/// of a nodal field
void extractValuesAtStandardNodes(const Array<Real> & nodal_values,
Array<Real> & extracted_values,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute the shape derivatives on integration points for a given element
template <ElementType type>
inline void
computeShapeDerivativesOnCPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get a the shapes vector
inline const Array<Real> &
- getShapes(const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ getShapes(ElementType el_type,
+ GhostType ghost_type = _not_ghost) const;
/// get a the shapes derivatives vector
inline const Array<Real> &
- getShapesDerivatives(const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ getShapesDerivatives(ElementType el_type,
+ GhostType ghost_type = _not_ghost) const;
/// get a the shapes vector
inline const Array<Real> &
- getShapesAtEnrichedNodes(const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ getShapesAtEnrichedNodes(ElementType el_type,
+ GhostType ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// shape functions for all elements
ElementTypeMapArray<Real, InterpolationType> shapes;
/// shape functions derivatives for all elements
ElementTypeMapArray<Real, InterpolationType> shapes_derivatives;
/// additional integration points for the IGFEM formulation
ElementTypeMapArray<Real> igfem_integration_points;
/// values of shape functions for all elements on the enriched nodes
ElementTypeMapArray<Real, InterpolationType> shapes_at_enrichments;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "shape_igfem_inline_impl.hh"
/// standard output stream operator
// template <class ShapeFunction>
// inline std::ostream & operator <<(std::ostream & stream, const
// ShapeIGFEM<ShapeFunction> & _this)
// {
// _this.printself(stream);
// return stream;
// }
-#endif /* __AKANTU_SHAPE_IGFEM_HH__ */
+#endif /* AKANTU_SHAPE_IGFEM_HH_ */
diff --git a/extra_packages/igfem/src/shape_igfem_inline_impl.hh b/extra_packages/igfem/src/shape_igfem_inline_impl.hh
index f7d08f220..e72aaba33 100644
--- a/extra_packages/igfem/src/shape_igfem_inline_impl.hh
+++ b/extra_packages/igfem/src/shape_igfem_inline_impl.hh
@@ -1,733 +1,733 @@
/**
* @file shape_igfem_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief ShapeIGFEM inline implementation
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_IGFEM_INLINE_IMPL_HH__
-#define __AKANTU_SHAPE_IGFEM_INLINE_IMPL_HH__
+#ifndef AKANTU_SHAPE_IGFEM_INLINE_IMPL_HH_
+#define AKANTU_SHAPE_IGFEM_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline const Array<Real> &
-ShapeLagrange<_ek_igfem>::getShapes(const ElementType & el_type,
- const GhostType & ghost_type) const {
+ShapeLagrange<_ek_igfem>::getShapes(ElementType el_type,
+ GhostType ghost_type) const {
return shapes(FEEngine::getInterpolationType(el_type), ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const Array<Real> & ShapeLagrange<_ek_igfem>::getShapesDerivatives(
- const ElementType & el_type, const GhostType & ghost_type) const {
+ ElementType el_type, GhostType ghost_type) const {
return shapes_derivatives(FEEngine::getInterpolationType(el_type),
ghost_type);
}
/* -------------------------------------------------------------------------- */
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
setIntegrationPointsByType<ElementClassProperty<type>::sub_element_type_1>( \
integration_points_1, ghost_type); \
setIntegrationPointsByType<ElementClassProperty<type>::sub_element_type_2>( \
integration_points_2, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
if (ElementClass<type>::getNaturalSpaceDimension() == \
mesh.getSpatialDimension()) \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type); \
precomputeShapesOnEnrichedNodes<type>(nodes, ghost_type);
inline void ShapeLagrange<_ek_igfem>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
const Matrix<Real> & integration_points_1,
- const Matrix<Real> & integration_points_2, const ElementType & type,
- const GhostType & ghost_type) {
+ const Matrix<Real> & integration_points_2, ElementType type,
+ GhostType ghost_type) {
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
#undef INIT_SHAPE_FUNCTIONS
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeLagrange<_ek_igfem>::computeShapeDerivativesOnCPointsByElement(
const Matrix<Real> & node_coords, const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const {
AKANTU_DEBUG_IN();
// compute dnds
Tensor3<Real> dnds(node_coords.rows(), node_coords.cols(),
natural_coords.cols());
ElementClass<type>::computeDNDS(natural_coords, dnds);
// compute dxds
Tensor3<Real> J(node_coords.rows(), natural_coords.rows(),
natural_coords.cols());
ElementClass<type>::computeJMat(dnds, node_coords, J);
// compute shape derivatives
ElementClass<type>::computeShapeDerivatives(J, dnds, shapesd);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::inverseMap(const Vector<Real> & real_coords,
UInt elem,
Vector<Real> & natural_coords,
UInt sub_element,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
/// typedef for the two subelement_types and the parent element type
const ElementType sub_type_1 = ElementClassProperty<type>::sub_element_type_1;
const ElementType sub_type_2 = ElementClassProperty<type>::sub_element_type_2;
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
if (!sub_element) {
UInt nb_nodes_sub_el =
ElementClass<sub_type_1>::getNbNodesPerInterpolationElement();
Matrix<Real> sub_el_coords(spatial_dimension, nb_nodes_sub_el);
ElementClass<type>::getSubElementCoords(nodes_coord, sub_el_coords,
sub_element);
ElementClass<sub_type_1>::inverseMap(real_coords, sub_el_coords,
natural_coords);
}
else {
UInt nb_nodes_sub_el =
ElementClass<sub_type_2>::getNbNodesPerInterpolationElement();
Matrix<Real> sub_el_coords(spatial_dimension, nb_nodes_sub_el);
ElementClass<type>::getSubElementCoords(nodes_coord, sub_el_coords,
sub_element);
ElementClass<sub_type_2>::inverseMap(real_coords, sub_el_coords,
natural_coords);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::inverseMap(const Vector<Real> & real_coords,
UInt elem,
Vector<Real> & natural_coords,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
/// map point into parent reference domain
AKANTU_DEBUG_IN();
const ElementType parent_type =
ElementClassProperty<type>::parent_element_type;
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
UInt nb_nodes_parent_el =
ElementClass<parent_type>::getNbNodesPerInterpolationElement();
Matrix<Real> parent_coords(spatial_dimension, nb_nodes_parent_el);
ElementClass<type>::getParentCoords(nodes_coord, parent_coords);
ElementClass<parent_type>::inverseMap(real_coords, parent_coords,
natural_coords);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
bool ShapeLagrange<_ek_igfem>::contains(const Vector<Real> & real_coords,
UInt elem,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> natural_coords(spatial_dimension);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
return ElementClass<type>::contains(natural_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::interpolate(const Vector<Real> & real_coords,
UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
UInt nb_shapes = ElementClass<type>::getShapeSize();
Vector<Real> shapes(nb_shapes);
computeShapes<type>(real_coords, elem, shapes, ghost_type);
ElementClass<type>::interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::computeShapes(
const Vector<Real> & real_coords, UInt elem, Vector<Real> & shapes,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
/// typedef for the two subelement_types and the parent element type
const ElementType sub_type_1 = ElementClassProperty<type>::sub_element_type_1;
const ElementType sub_type_2 = ElementClassProperty<type>::sub_element_type_2;
const ElementType parent_type =
ElementClassProperty<type>::parent_element_type;
UInt spatial_dimension = mesh.getSpatialDimension();
/// parent contribution
/// get the size of the parent shapes
UInt size_of_parent_shapes = ElementClass<parent_type>::getShapeSize();
Vector<Real> parent_shapes(size_of_parent_shapes);
/// compute parent shapes -> map shapes in the physical domain of the parent
Vector<Real> natural_coords(spatial_dimension);
Real tol = Math::getTolerance();
Math::setTolerance(1e-14);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
ElementClass<parent_type>::computeShapes(natural_coords, parent_shapes);
- natural_coords.clear();
+ natural_coords.zero();
/// sub-element contribution
/// check which sub-element contains the physical point
/// check if point is in sub-element 1
inverseMap<type>(real_coords, elem, natural_coords, 0, ghost_type);
if (ElementClass<sub_type_1>::contains(natural_coords)) {
UInt size_of_sub_shapes = ElementClass<sub_type_1>::getShapeSize();
Vector<Real> sub_shapes(size_of_sub_shapes);
ElementClass<sub_type_1>::computeShapes(natural_coords, sub_shapes);
/// assemble shape functions
ElementClass<type>::assembleShapes(parent_shapes, sub_shapes, shapes, 0);
} else {
- natural_coords.clear();
+ natural_coords.zero();
inverseMap<type>(real_coords, elem, natural_coords, 1, ghost_type);
AKANTU_DEBUG_ASSERT(ElementClass<sub_type_2>::contains(natural_coords),
"Physical point not contained in any element");
UInt size_of_sub_shapes = ElementClass<sub_type_2>::getShapeSize();
Vector<Real> sub_shapes(size_of_sub_shapes);
ElementClass<sub_type_2>::computeShapes(natural_coords, sub_shapes);
/// assemble shape functions
ElementClass<type>::assembleShapes(parent_shapes, sub_shapes, shapes, 1);
}
Math::setTolerance(tol);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::computeShapeDerivatives(
const Matrix<Real> & real_coords, UInt elem, Tensor3<Real> & shapesd,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::precomputeShapesOnIntegrationPoints(
__attribute__((unused)) const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
/// typedef for the two subelement_types and the parent element type
const ElementType sub_type_1 = ElementClassProperty<type>::sub_element_type_1;
const ElementType sub_type_2 = ElementClassProperty<type>::sub_element_type_2;
const ElementType parent_type =
ElementClassProperty<type>::parent_element_type;
/// get the spatial dimension for the given element type
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
/// get the integration points for the subelements
Matrix<Real> & natural_coords_sub_1 =
integration_points(sub_type_1, ghost_type);
Matrix<Real> & natural_coords_sub_2 =
integration_points(sub_type_2, ghost_type);
/// store the number of quadrature points on each subelement and the toal
/// number
UInt nb_points_sub_1 = natural_coords_sub_1.cols();
UInt nb_points_sub_2 = natural_coords_sub_2.cols();
UInt nb_total_points = nb_points_sub_1 + nb_points_sub_2;
// get the integration points for the parent element
UInt nb_element = mesh.getConnectivity(type, ghost_type).getSize();
Array<Real> & natural_coords_parent = igfem_integration_points.alloc(
nb_element * nb_total_points, spatial_dimension, type, ghost_type);
Array<Real>::matrix_iterator natural_coords_parent_it =
natural_coords_parent.begin_reinterpret(spatial_dimension,
nb_total_points, nb_element);
/// get the size of the shapes
UInt size_of_shapes = ElementClass<type>::getShapeSize();
UInt size_of_parent_shapes = ElementClass<parent_type>::getShapeSize();
UInt size_of_sub_1_shapes = ElementClass<sub_type_1>::getShapeSize();
UInt size_of_sub_2_shapes = ElementClass<sub_type_2>::getShapeSize();
/// initialize the matrices to store the shape functions of the subelements
/// and the parent
Matrix<Real> sub_1_shapes(size_of_sub_1_shapes, nb_points_sub_1);
Matrix<Real> sub_2_shapes(size_of_sub_2_shapes, nb_points_sub_2);
Matrix<Real> parent_1_shapes(size_of_parent_shapes, nb_points_sub_1);
Matrix<Real> parent_2_shapes(size_of_parent_shapes, nb_points_sub_2);
/// compute the shape functions of the subelements
ElementClass<sub_type_1>::computeShapes(natural_coords_sub_1, sub_1_shapes);
ElementClass<sub_type_2>::computeShapes(natural_coords_sub_2, sub_2_shapes);
/// get the nodal coordinates per element
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
Array<Real>::matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
/// allocate the shapes for the given element type
Array<Real> & shapes_tmp = shapes.alloc(nb_element * nb_total_points,
size_of_shapes, itp_type, ghost_type);
Array<Real>::matrix_iterator shapes_it = shapes_tmp.begin_reinterpret(
ElementClass<type>::getNbNodesPerInterpolationElement(), nb_total_points,
nb_element);
Matrix<Real> physical_points_1(spatial_dimension, nb_points_sub_1);
Matrix<Real> physical_points_2(spatial_dimension, nb_points_sub_2);
Matrix<Real> parent_natural_coords_1(spatial_dimension, nb_points_sub_1);
Matrix<Real> parent_natural_coords_2(spatial_dimension, nb_points_sub_2);
/// intialize the matrices for the parent and subelement coordinates
UInt nb_nodes_parent_el =
ElementClass<parent_type>::getNbNodesPerInterpolationElement();
UInt nb_nodes_sub_el_1 =
ElementClass<sub_type_1>::getNbNodesPerInterpolationElement();
UInt nb_nodes_sub_el_2 =
ElementClass<sub_type_2>::getNbNodesPerInterpolationElement();
Matrix<Real> parent_coords(spatial_dimension, nb_nodes_parent_el);
Matrix<Real> sub_el_1_coords(spatial_dimension, nb_nodes_sub_el_1);
Matrix<Real> sub_el_2_coords(spatial_dimension, nb_nodes_sub_el_2);
/// loop over all elements of the given type and compute the shape functions
Vector<Real> all_shapes(size_of_shapes);
for (UInt elem = 0; elem < nb_element;
++elem, ++shapes_it, ++x_it, ++natural_coords_parent_it) {
Matrix<Real> & N = *shapes_it;
const Matrix<Real> & X = *x_it;
Matrix<Real> & nc_parent = *natural_coords_parent_it;
/// map the sub element integration points into the parent reference domain
ElementClass<type>::mapFromSubRefToParentRef(
X, sub_el_1_coords, parent_coords, sub_1_shapes, physical_points_1,
parent_natural_coords_1, 0);
ElementClass<type>::mapFromSubRefToParentRef(
X, sub_el_2_coords, parent_coords, sub_2_shapes, physical_points_2,
parent_natural_coords_2, 1);
/// compute the parent shape functions on all integration points
ElementClass<sub_type_1>::computeShapes(parent_natural_coords_1,
parent_1_shapes);
ElementClass<sub_type_1>::computeShapes(parent_natural_coords_2,
parent_2_shapes);
/// copy the results into the shape functions iterator and natural coords
/// iterator
for (UInt i = 0; i < nb_points_sub_1; ++i) {
ElementClass<type>::assembleShapes(parent_1_shapes(i), sub_1_shapes(i),
all_shapes, 0);
N(i) = all_shapes;
nc_parent(i) = parent_natural_coords_1(i);
}
for (UInt i = 0; i < nb_points_sub_2; ++i) {
ElementClass<type>::assembleShapes(parent_2_shapes(i), sub_2_shapes(i),
all_shapes, 1);
N(i + nb_points_sub_1) = all_shapes;
/// N(i + nb_points_sub_2) = all_shapes;
nc_parent(i + nb_points_sub_1) = parent_natural_coords_2(i);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::precomputeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// typedef for the two subelement_types and the parent element type
const ElementType sub_type_1 = ElementClassProperty<type>::sub_element_type_1;
const ElementType sub_type_2 = ElementClassProperty<type>::sub_element_type_2;
const ElementType parent_type =
ElementClassProperty<type>::parent_element_type;
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
UInt spatial_dimension = mesh.getSpatialDimension();
/// get the integration points for the subelements
Matrix<Real> & natural_coords_sub_1 =
integration_points(sub_type_1, ghost_type);
Matrix<Real> & natural_coords_sub_2 =
integration_points(sub_type_2, ghost_type);
/// store the number of quadrature points on each subelement and the toal
/// number
UInt nb_points_sub_1 = natural_coords_sub_1.cols();
UInt nb_points_sub_2 = natural_coords_sub_2.cols();
UInt nb_points_total = nb_points_sub_1 + nb_points_sub_2;
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
/// intialize the matrices for the parent and subelement coordinates
UInt nb_nodes_parent_el =
ElementClass<parent_type>::getNbNodesPerInterpolationElement();
UInt nb_nodes_sub_el_1 =
ElementClass<sub_type_1>::getNbNodesPerInterpolationElement();
UInt nb_nodes_sub_el_2 =
ElementClass<sub_type_2>::getNbNodesPerInterpolationElement();
Matrix<Real> parent_coords(spatial_dimension, nb_nodes_parent_el);
Matrix<Real> sub_el_1_coords(spatial_dimension, nb_nodes_sub_el_1);
Matrix<Real> sub_el_2_coords(spatial_dimension, nb_nodes_sub_el_2);
UInt nb_element = mesh.getConnectivity(type, ghost_type).getSize();
Array<Real> & shapes_derivatives_tmp = shapes_derivatives.alloc(
nb_element * nb_points_total, size_of_shapesd, itp_type, ghost_type);
/// get an iterator to the coordiantes of the elements
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
Real * shapesd_val = shapes_derivatives_tmp.storage();
Array<Real>::matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
/// get an iterator to the integration points of the parent element
Array<Real> & natural_coords_parent =
igfem_integration_points(type, ghost_type);
Array<Real>::matrix_iterator natural_coords_parent_it =
natural_coords_parent.begin_reinterpret(spatial_dimension,
nb_points_total, nb_element);
Tensor3<Real> B_sub_1(spatial_dimension, nb_nodes_sub_el_1, nb_points_sub_1);
Tensor3<Real> B_sub_2(spatial_dimension, nb_nodes_sub_el_2, nb_points_sub_2);
Tensor3<Real> B_parent(spatial_dimension, nb_nodes_parent_el,
nb_points_total);
/// assemble the shape derivatives
Matrix<Real> all_shapes(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element;
++elem, ++x_it, ++natural_coords_parent_it) {
Matrix<Real> & X = *x_it;
Matrix<Real> & nc_parent = *natural_coords_parent_it;
Tensor3<Real> B(shapesd_val, spatial_dimension, nb_nodes_per_element,
nb_points_total);
/// get the coordinates of the two sub elements and the parent element
ElementClass<type>::getSubElementCoords(X, sub_el_1_coords, 0);
ElementClass<type>::getSubElementCoords(X, sub_el_2_coords, 1);
ElementClass<type>::getParentCoords(X, parent_coords);
/// compute the subelements' shape derivatives and the parent shape
/// derivatives
computeShapeDerivativesOnCPointsByElement<sub_type_1>(
sub_el_1_coords, natural_coords_sub_1, B_sub_1);
computeShapeDerivativesOnCPointsByElement<sub_type_2>(
sub_el_2_coords, natural_coords_sub_2, B_sub_2);
computeShapeDerivativesOnCPointsByElement<parent_type>(parent_coords,
nc_parent, B_parent);
for (UInt i = 0; i < nb_points_sub_1; ++i) {
ElementClass<type>::assembleShapeDerivatives(B_parent(i), B_sub_1(i),
all_shapes, 0);
B(i) = all_shapes;
}
for (UInt i = 0; i < nb_points_sub_2; ++i) {
ElementClass<type>::assembleShapeDerivatives(B_parent(i), B_sub_2(i),
all_shapes, 1);
B(i + nb_points_sub_1) = all_shapes;
}
shapesd_val += size_of_shapesd * nb_points_total;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(shapes.exists(itp_type, ghost_type),
"No shapes for the type "
<< shapes.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->interpolateElementalFieldOnIntegrationPoints<type>(
u_el, out_uq, ghost_type, shapes(itp_type, ghost_type), filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::gradientOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_nablauq,
UInt nb_degree_of_freedom, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(
shapes_derivatives.exists(itp_type, ghost_type),
"No shapes derivatives for the type "
<< shapes_derivatives.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->gradientElementalFieldOnIntegrationPoints<type>(
u_el, out_nablauq, ghost_type, shapes_derivatives(itp_type, ghost_type),
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::fieldTimesShapes(
const Array<Real> & field, Array<Real> & field_times_shapes,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
field_times_shapes.resize(field.getSize());
UInt size_of_shapes = ElementClass<type>::getShapeSize();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
UInt nb_degree_of_freedom = field.getNbComponent();
const Array<Real> & shape = shapes(itp_type, ghost_type);
Array<Real>::const_matrix_iterator field_it =
field.begin(nb_degree_of_freedom, 1);
Array<Real>::const_matrix_iterator shapes_it = shape.begin(1, size_of_shapes);
Array<Real>::matrix_iterator it =
field_times_shapes.begin(nb_degree_of_freedom, size_of_shapes);
Array<Real>::matrix_iterator end =
field_times_shapes.end(nb_degree_of_freedom, size_of_shapes);
for (; it != end; ++it, ++field_it, ++shapes_it) {
it->mul<false, false>(*field_it, *shapes_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::interpolateOnPhysicalPoint(
const Vector<Real> & real_coords, UInt elem, const Array<Real> & field,
- Vector<Real> & interpolated, const GhostType & ghost_type) const {
+ Vector<Real> & interpolated, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
Vector<Real> shapes(ElementClass<type>::getShapeSize());
computeShapes<type>(real_coords, elem, shapes, ghost_type);
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_val(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(field, nodes_val.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
ElementClass<type>::interpolate(nodes_val, shapes, interpolated);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::precomputeShapesOnEnrichedNodes(
__attribute__((unused)) const Array<Real> & nodes,
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
const ElementType parent_type =
ElementClassProperty<type>::parent_element_type;
const ElementType sub_type = ElementClassProperty<type>::sub_element_type_1;
/// get the spatial dimension for the given element type
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
// get the integration points for the parent element
UInt nb_element = mesh.getConnectivity(type, ghost_type).getSize();
/// get the size of the shapes
UInt nb_enriched_nodes = ElementClass<type>::getNbEnrichments();
UInt nb_parent_nodes =
ElementClass<parent_type>::getNbNodesPerInterpolationElement();
UInt size_of_shapes = ElementClass<type>::getShapeSize();
UInt size_of_parent_shapes = ElementClass<parent_type>::getShapeSize();
UInt size_of_sub_shapes = ElementClass<sub_type>::getShapeSize();
Vector<Real> parent_shapes(size_of_parent_shapes);
Vector<Real> sub_shapes(size_of_sub_shapes);
Vector<Real> shapes(size_of_shapes);
/// get the nodal coordinates per element
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
Array<Real>::matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
/// allocate the shapes for the given element type
Array<Real> & shapes_tmp = shapes_at_enrichments.alloc(
nb_element * nb_enriched_nodes, size_of_shapes, itp_type, ghost_type);
Array<Real>::matrix_iterator shapes_it = shapes_tmp.begin_reinterpret(
ElementClass<type>::getNbNodesPerInterpolationElement(),
nb_enriched_nodes, nb_element);
Vector<Real> real_coords(spatial_dimension);
Vector<Real> natural_coords(spatial_dimension);
Matrix<Real> parent_coords(spatial_dimension, nb_parent_nodes);
UInt * sub_element_enrichments =
ElementClass<type>::getSubElementEnrichments();
/// loop over all elements
for (UInt elem = 0; elem < nb_element; ++elem, ++shapes_it, ++x_it) {
Matrix<Real> & N = *shapes_it;
const Matrix<Real> & X = *x_it;
for (UInt i = 0; i < nb_enriched_nodes; ++i) {
/// get the parent element coordinates
ElementClass<type>::getParentCoords(X, parent_coords);
/// get the physical coords of the enriched node
real_coords = X(nb_parent_nodes + i);
/// map the physical point into the parent ref domain
ElementClass<parent_type>::inverseMap(real_coords, parent_coords,
natural_coords);
/// compute the parent shape functions
ElementClass<parent_type>::computeShapes(natural_coords, parent_shapes);
/// Sub-element contribution
- sub_shapes.clear();
+ sub_shapes.zero();
sub_shapes(sub_element_enrichments[i]) = 1.;
ElementClass<type>::assembleShapes(parent_shapes, sub_shapes, shapes, 0);
N(i) = shapes;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_igfem>::interpolateAtEnrichedNodes(
const Array<Real> & src, Array<Real> & dst,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
const ElementType parent_type =
ElementClassProperty<type>::parent_element_type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_parent_nodes =
ElementClass<parent_type>::getNbNodesPerInterpolationElement();
UInt nb_enrichments = ElementClass<type>::getNbEnrichments();
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
UInt spatial_dimension = mesh.getSpatialDimension();
Matrix<Real> nodes_val(spatial_dimension, nb_nodes_per_element);
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
const Array<Real> & shapes = shapes_at_enrichments(itp_type, ghost_type);
Array<Real>::const_matrix_iterator shapes_it = shapes.begin_reinterpret(
nb_nodes_per_element, nb_enrichments, nb_element);
Array<Real>::vector_iterator dst_vect = dst.begin(spatial_dimension);
Vector<Real> interpolated(spatial_dimension);
for (UInt e = 0; e < nb_element; ++e, ++shapes_it) {
const Matrix<Real> & el_shapes = *shapes_it;
mesh.extractNodalValuesFromElement(src, nodes_val.storage(),
elem_val + e * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
;
for (UInt i = 0; i < nb_enrichments; ++i) {
ElementClass<type>::interpolate(nodes_val, el_shapes(i), interpolated);
UInt enr_node_idx =
elem_val[e * nb_nodes_per_element + nb_parent_nodes + i];
dst_vect[enr_node_idx] = interpolated;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#define COMPUTE_ENRICHED_VALUES(type) \
interpolateAtEnrichedNodes<type>(src, dst, ghost_type);
inline void ShapeLagrange<_ek_igfem>::interpolateEnrichmentsAllTypes(
- const Array<Real> & src, Array<Real> & dst, const ElementType & type,
- const GhostType & ghost_type) const {
+ const Array<Real> & src, Array<Real> & dst, ElementType type,
+ GhostType ghost_type) const {
AKANTU_BOOST_IGFEM_ELEMENT_SWITCH(COMPUTE_ENRICHED_VALUES);
}
#undef COMPUTE_ENRICHED_VALUES
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_SHAPE_IGFEM_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SHAPE_IGFEM_INLINE_IMPL_HH_ */
diff --git a/extra_packages/igfem/src/solid_mechanics_model_igfem.cc b/extra_packages/igfem/src/solid_mechanics_model_igfem.cc
index fabff0a65..f7dfab8e3 100644
--- a/extra_packages/igfem/src/solid_mechanics_model_igfem.cc
+++ b/extra_packages/igfem/src/solid_mechanics_model_igfem.cc
@@ -1,586 +1,586 @@
/**
* @file solid_mechanics_model_igfem.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief solid mechanics model for IGFEM analysis
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_igfem.hh"
#include "dumpable_inline_impl.hh"
#include "group_manager_inline_impl.hh"
#include "igfem_helper.hh"
#include "material_igfem.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_igfem_element_partition.hh"
#include "dumper_igfem_elemental_field.hh"
#include "dumper_igfem_material_internal_field.hh"
#include "dumper_material_padders.hh"
#include "dumper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
const SolidMechanicsModelIGFEMOptions
default_solid_mechanics_model_igfem_options(_static, false);
SolidMechanicsModelIGFEM::SolidMechanicsModelIGFEM(Mesh & mesh, UInt dim,
const ID & id,
const MemoryID & memory_id)
: SolidMechanicsModel(mesh, dim, id, memory_id), IGFEMEnrichment(mesh),
global_ids_updater(NULL) {
AKANTU_DEBUG_IN();
delete material_selector;
material_selector = new DefaultMaterialIGFEMSelector(*this);
this->registerEventHandler(*this);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("igfem elements", id);
this->mesh.addDumpMeshToDumper("igfem elements", mesh, spatial_dimension,
_not_ghost, _ek_igfem);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModelIGFEM::~SolidMechanicsModelIGFEM() {
AKANTU_DEBUG_IN();
if (global_ids_updater)
delete global_ids_updater;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::initFull(const ModelOptions & options) {
AKANTU_DEBUG_IN();
/// intialize the IGFEM enrichment
this->initialize();
SolidMechanicsModel::initFull(options);
// set the initial condition to 0
real_force->clear();
real_displacement->clear();
real_residual->clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Allocate all the needed vectors. By default their are not necessarily set to
* 0
*
*/
void SolidMechanicsModelIGFEM::initArrays() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_rdisp;
sstr_rdisp << id << ":real_displacement";
std::stringstream sstr_rforc;
sstr_rforc << id << ":real_force";
std::stringstream sstr_rresi;
sstr_rresi << id << ":real_residual";
real_displacement = &(alloc<Real>(sstr_rdisp.str(), nb_nodes,
spatial_dimension, REAL_INIT_VALUE));
real_force = &(alloc<Real>(sstr_rforc.str(), nb_nodes, spatial_dimension,
REAL_INIT_VALUE));
real_residual = &(alloc<Real>(sstr_rresi.str(), nb_nodes, spatial_dimension,
REAL_INIT_VALUE));
SolidMechanicsModel::initArrays();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::initParallel(MeshPartition * partition,
DataAccessor * data_accessor) {
SolidMechanicsModel::initParallel(partition, data_accessor);
this->intersector_sphere.setDistributedSynchronizer(synch_parallel);
if (mesh.isDistributed())
global_ids_updater = new GlobalIdsUpdater(mesh, synch_parallel);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::initMaterials() {
AKANTU_DEBUG_IN();
// make sure the material are instantiated
if (!are_materials_instantiated)
instantiateMaterials();
/// find the first igfem material
UInt igfem_index = 0;
while ((dynamic_cast<MaterialIGFEM *>(materials[igfem_index]) == NULL) &&
igfem_index <= materials.size())
++igfem_index;
AKANTU_DEBUG_ASSERT(igfem_index != materials.size(),
"No igfem materials in the material input file");
DefaultMaterialIGFEMSelector * igfem_mat_selector =
dynamic_cast<DefaultMaterialIGFEMSelector *>(material_selector);
if (igfem_mat_selector != NULL)
igfem_mat_selector->setIGFEMFallback(igfem_index);
SolidMechanicsModel::initMaterials();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the model, basically pre-compute the shapes, shapes derivatives
* and jacobian
*
*/
void SolidMechanicsModelIGFEM::initModel() {
AKANTU_DEBUG_IN();
SolidMechanicsModel::initModel();
registerFEEngineObject<MyFEEngineIGFEMType>("IGFEMFEEngine", mesh,
spatial_dimension);
/// insert the two feengines associated with the model in the map
this->fe_engines_per_kind[_ek_regular] = &(this->getFEEngine());
this->fe_engines_per_kind[_ek_igfem] = &(this->getFEEngine("IGFEMFEEngine"));
/// add the igfem type connectivities
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType type_ghost = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, type_ghost);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, type_ghost);
for (; it != last; ++it) {
const Array<UInt> & connectivity = mesh.getConnectivity(*it, type_ghost);
if (connectivity.getSize() != 0) {
ElementType type = *it;
Vector<ElementType> types_igfem = FEEngine::getIGFEMElementTypes(type);
for (UInt i = 0; i < types_igfem.size(); ++i)
mesh.addConnectivityType(types_igfem(i), type_ghost);
}
}
}
getFEEngine("IGFEMFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("IGFEMFEEngine").initShapeFunctions(_ghost);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::onElementsAdded(const Array<Element> & elements,
const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
const NewIGFEMElementsEvent * igfem_event =
dynamic_cast<const NewIGFEMElementsEvent *>(&event);
/// insert the new and old elements in the map
if (igfem_event != NULL) {
- this->element_map.clear();
+ this->element_map.zero();
const Array<Element> & old_elements = igfem_event->getOldElementsList();
for (UInt e = 0; e < elements.getSize(); ++e) {
this->element_map[elements(e)] = old_elements(e);
}
}
/// update shape functions
getFEEngine("IGFEMFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("IGFEMFEEngine").initShapeFunctions(_ghost);
SolidMechanicsModel::onElementsAdded(elements, event);
this->reassignMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
this->getFEEngine("IGFEMFEEngine").initShapeFunctions(_not_ghost);
this->getFEEngine("IGFEMFEEngine").initShapeFunctions(_ghost);
SolidMechanicsModel::onElementsRemoved(element_list, new_numbering, event);
if (synch_parallel)
synch_parallel->computeAllBufferSizes(*this);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
const NewIGFEMNodesEvent * igfem_event =
dynamic_cast<const NewIGFEMNodesEvent *>(&event);
// update the node type
if (igfem_event != NULL) {
intersector_sphere.updateNodeType(
nodes_list, igfem_event->getNewNodePerElem(),
igfem_event->getElementType(), igfem_event->getGhostType());
}
UInt nb_nodes = mesh.getNbNodes();
if (real_displacement)
real_displacement->resize(nb_nodes);
if (real_force)
real_force->resize(nb_nodes);
if (real_residual)
real_residual->resize(nb_nodes);
if (mesh.isDistributed())
mesh.getGlobalNodesIds().resize(mesh.getNbNodes());
if (displacement)
displacement->resize(nb_nodes);
if (mass)
mass->resize(nb_nodes);
if (velocity)
velocity->resize(nb_nodes);
if (acceleration)
acceleration->resize(nb_nodes);
if (force)
force->resize(nb_nodes);
if (residual)
residual->resize(nb_nodes);
if (blocked_dofs)
blocked_dofs->resize(nb_nodes);
if (previous_displacement)
previous_displacement->resize(nb_nodes);
if (increment_acceleration)
increment_acceleration->resize(nb_nodes);
if (increment)
increment->resize(nb_nodes);
if (current_position)
current_position->resize(nb_nodes);
std::vector<Material *>::iterator mat_it;
for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
(*mat_it)->onNodesAdded(nodes_list, event);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::onNodesRemoved(const Array<UInt> & nodes_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) {
if (real_displacement)
mesh.removeNodesFromArray(*real_displacement, new_numbering);
if (real_force)
mesh.removeNodesFromArray(*real_force, new_numbering);
if (real_residual)
mesh.removeNodesFromArray(*real_residual, new_numbering);
// communicate global connectivity for slave nodes
if (global_ids_updater)
global_ids_updater->updateGlobalIDs(
mesh.getNbNodes() - intersector_sphere.getNbStandardNodes());
SolidMechanicsModel::onNodesRemoved(nodes_list, new_numbering, event);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::addDumpGroupFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
- const std::string & group_name, const ElementKind & element_kind,
+ const std::string & group_name, ElementKind element_kind,
bool padding_flag) {
AKANTU_DEBUG_IN();
ElementKind _element_kind = element_kind;
if (dumper_name == "igfem elements") {
_element_kind = _ek_igfem;
}
SolidMechanicsModel::addDumpGroupFieldToDumper(
dumper_name, field_id, group_name, _element_kind, padding_flag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::onDump() {
this->computeValuesOnEnrichedNodes();
this->flattenAllRegisteredInternals(_ek_igfem);
SolidMechanicsModel::onDump();
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
dumpers::Field * SolidMechanicsModelIGFEM::createElementalField(
const std::string & field_name, const std::string & group_name,
bool padding_flag, const UInt & spatial_dimension,
- const ElementKind & kind) {
+ ElementKind kind) {
dumpers::Field * field = NULL;
if (kind != _ek_igfem)
field = SolidMechanicsModel::createElementalField(
field_name, group_name, padding_flag, spatial_dimension, kind);
else {
if (field_name == "partitions")
field =
mesh.createElementalField<UInt, dumpers::IGFEMElementPartitionField>(
mesh.getConnectivities(), group_name, spatial_dimension, kind);
else if (field_name == "material_index")
field =
mesh.createElementalField<UInt, Vector, dumpers::IGFEMElementalField>(
material_index, group_name, spatial_dimension, kind);
else {
// this copy of field_name is used to compute derivated data such as
// strain and von mises stress that are based on grad_u and stress
std::string field_name_copy(field_name);
if (field_name == "strain" || field_name == "Green strain" ||
field_name == "principal strain" ||
field_name == "principal Green strain")
field_name_copy = "grad_u";
else if (field_name == "Von Mises stress")
field_name_copy = "stress";
bool is_internal = this->isInternal(field_name_copy, kind);
if (is_internal) {
ElementTypeMap<UInt> nb_data_per_elem =
this->getInternalDataPerElem(field_name_copy, kind);
ElementTypeMapArray<Real> & internal_flat =
this->flattenInternal(field_name_copy, kind);
field =
mesh.createElementalField<Real, dumpers::IGFEMInternalMaterialField>(
internal_flat, group_name, spatial_dimension, kind,
nb_data_per_elem);
if (field_name == "strain") {
dumpers::ComputeStrain<false> * foo =
new dumpers::ComputeStrain<false>(*this);
field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "Von Mises stress") {
dumpers::ComputeVonMisesStress * foo =
new dumpers::ComputeVonMisesStress(*this);
field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "Green strain") {
dumpers::ComputeStrain<true> * foo =
new dumpers::ComputeStrain<true>(*this);
field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "principal strain") {
dumpers::ComputePrincipalStrain<false> * foo =
new dumpers::ComputePrincipalStrain<false>(*this);
field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "principal Green strain") {
dumpers::ComputePrincipalStrain<true> * foo =
new dumpers::ComputePrincipalStrain<true>(*this);
field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
}
/// treat the paddings
if (padding_flag) {
if (field_name == "stress") {
if (spatial_dimension == 2) {
dumpers::StressPadder<2> * foo =
new dumpers::StressPadder<2>(*this);
field =
dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
}
} else if (field_name == "strain" || field_name == "Green strain") {
if (spatial_dimension == 2) {
dumpers::StrainPadder<2> * foo =
new dumpers::StrainPadder<2>(*this);
field =
dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
}
}
}
// homogenize the field
dumpers::ComputeFunctorInterface * foo =
dumpers::HomogenizerProxy::createHomogenizer(*field);
field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
}
}
}
// }
return field;
}
/* -------------------------------------------------------------------------- */
dumpers::Field *
SolidMechanicsModelIGFEM::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["real_displacement"] = real_displacement;
dumpers::Field * field = NULL;
if (padding_flag)
field = mesh.createNodalField(real_nodal_fields[field_name], group_name, 3);
else
field = mesh.createNodalField(real_nodal_fields[field_name], group_name);
if (field == NULL)
return SolidMechanicsModel::createNodalFieldReal(field_name, group_name,
padding_flag);
return field;
}
#else
/* -------------------------------------------------------------------------- */
dumpers::Field * SolidMechanicsModelIGFEM::createElementalField(
const std::string & field_name, const std::string & group_name,
bool padding_flag, const UInt & spatial_dimension,
- const ElementKind & kind) {
+ ElementKind kind) {
return NULL;
}
/* -------------------------------------------------------------------------- */
dumpers::Field *
SolidMechanicsModelIGFEM::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
return NULL;
}
#endif
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::computeValuesOnEnrichedNodes() {
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
for (UInt s = 0; s < spatial_dimension; ++s)
(*real_displacement)(n, s) = (*displacement)(n, s);
}
Element element;
Vector<Real> real_coords(spatial_dimension);
Vector<Real> interpolated(spatial_dimension);
Array<Real>::const_vector_iterator r_displ_it =
this->real_displacement->begin(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
element.ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, *gt, _ek_igfem);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, *gt, _ek_igfem);
for (; it != last; ++it) {
element.type = *it;
UInt nb_element = mesh.getNbElement(*it, *gt);
if (!nb_element)
continue;
UInt * elem_val = mesh.getConnectivity(*it, *gt).storage();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(*it);
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
Matrix<Real> displ_val(spatial_dimension, nb_nodes_per_element);
UInt nb_enriched_nodes = IGFEMHelper::getNbEnrichedNodes(*it);
UInt nb_parent_nodes = IGFEMHelper::getNbParentNodes(*it);
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
/// get the node coordinates of the element
mesh.extractNodalValuesFromElement(
mesh.getNodes(), nodes_coord.storage(),
elem_val + el * nb_nodes_per_element, nb_nodes_per_element,
spatial_dimension);
/// get the displacement values at the nodes of the element
mesh.extractNodalValuesFromElement(
*(this->displacement), displ_val.storage(),
elem_val + el * nb_nodes_per_element, nb_nodes_per_element,
spatial_dimension);
for (UInt i = 0; i < nb_enriched_nodes; ++i) {
/// coordinates of enriched node
real_coords = nodes_coord(nb_parent_nodes + i);
/// global index of the enriched node
UInt idx = elem_val[el * nb_nodes_per_element + nb_parent_nodes + i];
/// compute the real displacement value
this->getFEEngine("IGFEMFEEngine")
.interpolate(real_coords, displ_val, interpolated, element);
r_displ_it[idx] = interpolated;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::transferInternalValues(
const ID & internal, std::vector<Element> & new_elements,
Array<Real> & added_quads, Array<Real> & internal_values) {
/// @todo sort the new elements by their corresponding old element type and
/// old material!!!
/// get the number of elements for which iternals need to be transfered
UInt nb_new_elements = new_elements.size();
UInt nb_new_quads = added_quads.getSize() / nb_new_elements;
Array<Real>::const_matrix_iterator quad_coords =
added_quads.begin_reinterpret(this->spatial_dimension, nb_new_quads,
nb_new_elements);
UInt nb_internal_component = internal_values.getNbComponent();
Array<Real>::matrix_iterator internal_val = internal_values.begin_reinterpret(
nb_internal_component, nb_new_quads, nb_new_elements);
Vector<Real> default_values(nb_internal_component, 0.);
for (UInt e = 0; e < nb_new_elements; ++e, ++quad_coords, ++internal_val) {
Element new_element = new_elements[e];
Element old_element = this->element_map[new_element];
UInt mat_idx = (this->material_index(
old_element.type, old_element.ghost_type))(old_element.element);
Material & old_material = *(this->materials[mat_idx]);
old_material.extrapolateInternal(internal, old_element, *quad_coords,
*internal_val);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelIGFEM::applyEigenGradU(
const Matrix<Real> & prescribed_eigen_grad_u, const ID & material_name,
const GhostType ghost_type) {
AKANTU_DEBUG_ASSERT(prescribed_eigen_grad_u.size() ==
spatial_dimension * spatial_dimension,
"The prescribed grad_u is not of the good size");
std::vector<Material *>::iterator mat_it;
for (mat_it = this->materials.begin(); mat_it != this->materials.end();
++mat_it) {
MaterialIGFEM * mat_igfem = dynamic_cast<MaterialIGFEM *>(*mat_it);
if (mat_igfem != NULL)
mat_igfem->applyEigenGradU(prescribed_eigen_grad_u, material_name,
ghost_type);
else if ((*mat_it)->getName() == material_name)
(*mat_it)->applyEigenGradU(prescribed_eigen_grad_u, ghost_type);
}
}
} // namespace akantu
diff --git a/extra_packages/igfem/src/solid_mechanics_model_igfem.hh b/extra_packages/igfem/src/solid_mechanics_model_igfem.hh
index 77a2f01df..101e40b67 100644
--- a/extra_packages/igfem/src/solid_mechanics_model_igfem.hh
+++ b/extra_packages/igfem/src/solid_mechanics_model_igfem.hh
@@ -1,197 +1,197 @@
/**
* @file solid_mechanics_model_igfem.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief solid mechanics model for IGFEM analysis
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLID_MECHANICS_MODEL_IGFEM_HH__
-#define __AKANTU_SOLID_MECHANICS_MODEL_IGFEM_HH__
+#ifndef AKANTU_SOLID_MECHANICS_MODEL_IGFEM_HH_
+#define AKANTU_SOLID_MECHANICS_MODEL_IGFEM_HH_
#include "global_ids_updater.hh"
#include "igfem_enrichment.hh"
#include "solid_mechanics_model.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
struct SolidMechanicsModelIGFEMOptions : public SolidMechanicsModelOptions {
SolidMechanicsModelIGFEMOptions(AnalysisMethod analysis_method = _static,
bool no_init_materials = false)
: SolidMechanicsModelOptions(analysis_method, no_init_materials) {}
};
extern const SolidMechanicsModelIGFEMOptions
default_solid_mechanics_model_igfem_options;
/* -------------------------------------------------------------------------- */
/* Solid Mechanics Model for IGFEM analysis */
/* -------------------------------------------------------------------------- */
class SolidMechanicsModelIGFEM : public SolidMechanicsModel,
public SolidMechanicsModelEventHandler,
public IGFEMEnrichment {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_igfem>
MyFEEngineIGFEMType;
typedef std::map<Element, Element> ElementMap;
typedef std::map<ElementKind, FEEngine *> FEEnginesPerKindMap;
SolidMechanicsModelIGFEM(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model_igfem",
const MemoryID & memory_id = 0);
virtual ~SolidMechanicsModelIGFEM();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the cohesive model
virtual void initFull(const ModelOptions & options =
default_solid_mechanics_model_igfem_options);
/// initialize the model
virtual void initModel();
/// initialize igfem material
virtual void initMaterials();
/// register the tags associated with the parallel synchronizer
virtual void initParallel(MeshPartition * partition,
DataAccessor * data_accessor = NULL);
/// allocate all vectors
virtual void initArrays();
/// transfer internals from old to new elements
void transferInternalValues(const ID & internal,
std::vector<Element> & new_elements,
Array<Real> & added_quads,
Array<Real> & internal_values);
/// compute the barycenter for a sub-element
inline void getSubElementBarycenter(UInt element, UInt sub_element,
- const ElementType & type,
+ ElementType type,
Vector<Real> & barycenter,
GhostType ghost_type) const;
/// apply a constant eigen_grad_u on all quadrature points of a given material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const ID & material_name,
const GhostType ghost_type = _not_ghost);
private:
/// compute the real values of displacement, force, etc. on the enriched nodes
void computeValuesOnEnrichedNodes();
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
virtual void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event);
virtual void onNodesRemoved(const Array<UInt> & element_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event);
virtual void onElementsAdded(const Array<Element> & nodes_list,
const NewElementsEvent & event);
virtual void
onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
virtual void onDump();
virtual void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
- const ElementKind & element_kind,
+ ElementKind element_kind,
bool padding_flag);
virtual dumpers::Field * createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
const UInt & spatial_dimension,
- const ElementKind & kind);
+ ElementKind kind);
virtual dumpers::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
/// get the fe-engines per kind
AKANTU_GET_MACRO(FEEnginesPerKind, fe_engines_per_kind,
const FEEnginesPerKindMap &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// real displacements array
Array<Real> * real_displacement;
/// real forces array
Array<Real> * real_force;
/// real residuals array
Array<Real> * real_residual;
/// map between and new elements (needed when the interface is moving)
ElementMap element_map;
/// global connectivity ids updater
GlobalIdsUpdater * global_ids_updater;
/// map between element kind and corresponding FEEngine object
FEEnginesPerKindMap fe_engines_per_kind;
};
/* -------------------------------------------------------------------------- */
/* IGFEMMaterialSelector */
/* -------------------------------------------------------------------------- */
class DefaultMaterialIGFEMSelector : public DefaultMaterialSelector {
public:
DefaultMaterialIGFEMSelector(const SolidMechanicsModelIGFEM & model)
: DefaultMaterialSelector(model.getMaterialByElement()),
fallback_value_igfem(0) {}
virtual UInt operator()(const Element & element) {
if (Mesh::getKind(element.type) == _ek_igfem)
return fallback_value_igfem;
else
return DefaultMaterialSelector::operator()(element);
}
void setIGFEMFallback(UInt f) { this->fallback_value_igfem = f; }
protected:
UInt fallback_value_igfem;
};
} // namespace akantu
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "solid_mechanics_model_igfem_inline_impl.hh"
#endif
-#endif /* __AKANTU_SOLID_MECHANICS_MODEL_IGFEM_HH__ */
+#endif /* AKANTU_SOLID_MECHANICS_MODEL_IGFEM_HH_ */
diff --git a/extra_packages/igfem/src/solid_mechanics_model_igfem_inline_impl.hh b/extra_packages/igfem/src/solid_mechanics_model_igfem_inline_impl.hh
index b9413da96..4c708c938 100644
--- a/extra_packages/igfem/src/solid_mechanics_model_igfem_inline_impl.hh
+++ b/extra_packages/igfem/src/solid_mechanics_model_igfem_inline_impl.hh
@@ -1,59 +1,59 @@
/**
* @file solid_mechanics_model_igfem_inline_impl.hh
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Wed Nov 4 15:53:52 2015
*
* @brief Implementation on inline functions for SMMIGFEM
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLID_MECHANICS_MODEL_IGFEM_INLINE_IMPL_HH__
-#define __AKANTU_SOLID_MECHANICS_MODEL_IGFEM_INLINE_IMPL_HH__
+#ifndef AKANTU_SOLID_MECHANICS_MODEL_IGFEM_INLINE_IMPL_HH_
+#define AKANTU_SOLID_MECHANICS_MODEL_IGFEM_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModelIGFEM::getSubElementBarycenter(
- UInt element, UInt sub_element, const ElementType & type,
+ UInt element, UInt sub_element, ElementType type,
Vector<Real> & barycenter, GhostType ghost_type) const {
UInt * conn_val = this->mesh.getConnectivity(type, ghost_type).storage();
UInt nb_sub_element_nodes =
IGFEMHelper::getNbNodesPerSubElement(type, sub_element);
UInt * sub_el_conn =
IGFEMHelper::getSubElementConnectivity(type, sub_element);
UInt nb_nodes_per_element = this->mesh.getNbNodesPerElement(type);
const Array<Real> & node_coords = this->mesh.getNodes();
Real local_coord[spatial_dimension * nb_sub_element_nodes];
UInt offset = element * nb_nodes_per_element;
for (UInt n = 0; n < nb_sub_element_nodes; ++n) {
UInt index = conn_val[offset + sub_el_conn[n]];
memcpy(local_coord + n * spatial_dimension,
node_coords.storage() + index * spatial_dimension,
spatial_dimension * sizeof(Real));
}
Math::barycenter(local_coord, nb_sub_element_nodes, spatial_dimension,
barycenter.storage());
}
} // namespace akantu
-#endif /* __AKANTU_SOLID_MECHANICS_MODEL_IGFEM_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SOLID_MECHANICS_MODEL_IGFEM_INLINE_IMPL_HH_ */
diff --git a/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_ASR_damage.cc b/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_ASR_damage.cc
index e6667a3c4..8f6dd15d0 100644
--- a/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_ASR_damage.cc
+++ b/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_ASR_damage.cc
@@ -1,210 +1,210 @@
/**
* @file test_ASR_damage.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief test the solidmechancis model for IGFEM analysis
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "solid_mechanics_model_igfem.hh"
/* -------------------------------------------------------------------------- */
#include "material_damage_iterative.hh"
#include "material_igfem_saw_tooth_damage.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/// function declaration
void applyBoundaryConditions(SolidMechanicsModelIGFEM & model);
class ASRMaterialSelector : public MaterialSelector {
public:
ASRMaterialSelector(SolidMechanicsModelIGFEM & model) : model(model) {}
UInt operator()(const Element & elem) {
if (Mesh::getKind(elem.type) == _ek_igfem)
/// choose IGFEM material
return 2;
const Mesh & mesh = model.getMesh();
UInt spatial_dimension = model.getSpatialDimension();
Vector<Real> barycenter(spatial_dimension);
mesh.getBarycenter(elem, barycenter);
if (model.isInside(barycenter))
return 1;
return 0;
}
protected:
SolidMechanicsModelIGFEM & model;
};
typedef Spherical SK;
int main(int argc, char * argv[]) {
initialize("material_ASR.dat", argc, argv);
/// problem dimension
const UInt spatial_dimension = 2;
StaticCommunicator & comm =
akantu::StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// mesh creation
Mesh mesh(spatial_dimension);
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
mesh.read("one_inclusion.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
/// model creation
SolidMechanicsModelIGFEM model(mesh);
model.initParallel(partition);
delete partition;
/// register the gel pocket list in the model
std::list<SK::Sphere_3> gel_pocket_list;
model.registerGeometryObject(gel_pocket_list, "gel");
ASRMaterialSelector * mat_selector;
mat_selector = new ASRMaterialSelector(model);
model.setMaterialSelector(*mat_selector);
model.initFull();
/// add fields that should be dumped
model.setBaseName("regular_elements");
model.addDumpField("material_index");
model.addDumpField("damage");
model.addDumpField("Sc");
model.addDumpField("partitions");
model.addDumpField("eigen_grad_u");
model.addDumpField("blocked_dofs");
model.setBaseNameToDumper("igfem elements", "igfem elements");
model.addDumpFieldToDumper("igfem elements", "material_index");
model.addDumpFieldToDumper("igfem elements", "Sc");
model.addDumpFieldToDumper("igfem elements", "damage");
model.addDumpFieldToDumper("igfem elements", "lambda");
model.addDumpFieldToDumper("igfem elements", "eigen_grad_u");
model.addDumpFieldToDumper("igfem elements", "blocked_dofs");
/// dump before the interface generation
model.dump();
model.dump("igfem elements");
/// weaken one element to enforce damage there
Array<Real> & Sc =
model.getMaterial(0).getInternal<Real>("Sc")(_triangle_3, _not_ghost);
Sc(11) = 1;
/// create the gel pocket
Real initial_gel_radius = 0.1;
SK::Sphere_3 sphere_1(SK::Point_3(0., 0., 0.),
initial_gel_radius * initial_gel_radius);
gel_pocket_list.push_back(sphere_1);
/// create the interface
model.update("gel");
/// apply eigenstrain the eigenstrain in the inclusions
Matrix<Real> prestrain(spatial_dimension, spatial_dimension, 0.);
for (UInt i = 0; i < spatial_dimension; ++i)
prestrain(i, i) = 0.05;
model.applyEigenGradU(prestrain, "gel", _not_ghost);
applyBoundaryConditions(model);
/// dump
model.dump("igfem elements");
model.dump();
/// Instantiate objects of class MyDamageso
MaterialDamageIterative<spatial_dimension> & mat_aggregate =
dynamic_cast<MaterialDamageIterative<spatial_dimension> &>(
model.getMaterial(0));
MaterialIGFEMSawToothDamage<spatial_dimension> & mat_igfem =
dynamic_cast<MaterialIGFEMSawToothDamage<spatial_dimension> &>(
model.getMaterial(2));
bool factorize = false;
bool converged = false;
Real error;
UInt nb_damaged_elements = 0;
Real max_eq_stress_aggregate = 0;
Real max_igfem = 0;
const Array<Real> & stress =
model.getMaterial(2).getStress(_igfem_triangle_5, _not_ghost);
Array<Real>::const_matrix_iterator stress_it =
stress.begin(spatial_dimension, spatial_dimension);
do {
converged = model.solveStep<_scm_newton_raphson_tangent,
SolveConvergenceCriteria::_increment>(
1e-6, error, 2, factorize);
/// compute damage
max_eq_stress_aggregate = mat_aggregate.getNormMaxEquivalentStress();
max_igfem = mat_igfem.getNormMaxEquivalentStress();
if (max_eq_stress_aggregate > max_igfem)
nb_damaged_elements = mat_aggregate.updateDamage();
else
nb_damaged_elements = mat_igfem.updateDamage();
std::cout << "damaged elements: " << nb_damaged_elements << std::endl;
for (UInt i = 0; i < 5; ++i) {
std::cout << *stress_it << std::endl;
++stress_it;
}
model.dump();
model.dump("igfem elements");
} while (nb_damaged_elements);
model.dump();
model.dump("igfem elements");
finalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void applyBoundaryConditions(SolidMechanicsModelIGFEM & model) {
/// boundary conditions
Mesh & mesh = model.getMesh();
mesh.computeBoundingBox();
const Vector<Real> & lowerBounds = mesh.getLowerBounds();
const Vector<Real> & upperBounds = mesh.getUpperBounds();
Real bottom = lowerBounds(1);
Real top = upperBounds(1);
Real left = lowerBounds(0);
// Real right = upperBounds(0);
Real eps = std::abs((top - bottom) * 1e-12);
const Array<Real> & pos = mesh.getNodes();
Array<Real> & disp = model.getDisplacement();
Array<bool> & boun = model.getBlockedDOFs();
- disp.clear();
- boun.clear();
+ disp.zero();
+ boun.zero();
/// free expansion
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
if (std::abs(pos(i, 1) - bottom) < eps) {
boun(i, 1) = true;
disp(i, 1) = 0.0;
}
if (std::abs(pos(i, 0) - left) < eps) {
boun(i, 0) = true;
disp(i, 0) = 0.0;
}
}
}
diff --git a/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_solid_mechanics_model_igfem.cc b/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_solid_mechanics_model_igfem.cc
index 23d7a7e6e..75826b39b 100644
--- a/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_solid_mechanics_model_igfem.cc
+++ b/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_solid_mechanics_model_igfem.cc
@@ -1,337 +1,337 @@
/**
* @file test_solid_mechanics_model_igfem.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief test the solidmechancis model for IGFEM analysis
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dumper_paraview.hh"
#include "material_elastic.hh"
#include "mesh_geom_common.hh"
#include "solid_mechanics_model_igfem.hh"
#include <cmath>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <math.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
void outputArray(const Mesh & mesh, const Array<Real> & array) {
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_global_nodes = mesh.getNbGlobalNodes();
Array<Real> solution(nb_global_nodes, spatial_dimension, 0.);
Array<Real>::vector_iterator solution_begin =
solution.begin(spatial_dimension);
Array<Real>::const_vector_iterator array_it = array.begin(spatial_dimension);
for (UInt n = 0; n < mesh.getNbNodes(); ++n, ++array_it) {
if (mesh.isLocalOrMasterNode(n))
solution_begin[mesh.getNodeGlobalId(n)] = *array_it;
}
comm.allReduce(solution.storage(),
solution.getSize() * solution.getNbComponent(), _so_sum);
std::cout << std::fixed;
std::cout << std::setprecision(6);
if (prank == 0) {
Array<Real>::const_vector_iterator sol_it =
solution.begin(spatial_dimension);
for (UInt n = 0; n < nb_global_nodes; ++n, ++sol_it)
// Print absolute values to avoid parasite negative sign in machine
// precision zeros
std::cout << std::abs((*sol_it)(0)) << "," << std::abs((*sol_it)(1))
<< std::endl;
}
}
/* -------------------------------------------------------------------------- */
class Sphere {
public:
Sphere(const Vector<Real> & center, Real radius, Real tolerance = 0.)
: center(center), radius(radius), tolerance(tolerance) {}
bool isInside(const Vector<Real> & point) const {
return (point.distance(center) < radius + tolerance);
}
const Vector<Real> & getCenter() const { return center; }
Real & getRadius() { return radius; }
protected:
Vector<Real> center;
Real radius, tolerance;
};
void growGel(std::list<SK::Sphere_3> & query_list, Real new_radius) {
std::list<SK::Sphere_3>::const_iterator query_it = query_list.begin(),
query_end = query_list.end();
std::list<SK::Sphere_3> sphere_list;
for (; query_it != query_end; ++query_it) {
SK::Sphere_3 sphere(query_it->center(), new_radius * new_radius);
sphere_list.push_back(sphere);
}
- query_list.clear();
+ query_list.zero();
query_list = sphere_list;
}
Real computeAlpha(Real inner_radius, Real outer_radius,
const Vector<Real> & lambda, const Vector<Real> & mu) {
Real alpha = (lambda(1) + mu(1) + mu(0)) * outer_radius * outer_radius /
((lambda(0) + mu(0)) * inner_radius * inner_radius +
(lambda(1) + mu(1)) * (outer_radius * outer_radius -
inner_radius * inner_radius) +
(mu(0) * outer_radius * outer_radius));
return alpha;
}
void applyBoundaryConditions(SolidMechanicsModelIGFEM & model,
Real inner_radius, Real outer_radius,
const Vector<Real> & lambda,
const Vector<Real> & mu) {
/// boundary conditions for circular inclusion:
Real alpha = computeAlpha(inner_radius, outer_radius, lambda, mu);
Mesh & mesh = model.getMesh();
mesh.computeBoundingBox();
const Vector<Real> & lowerBounds = mesh.getLowerBounds();
const Vector<Real> & upperBounds = mesh.getUpperBounds();
Real bottom = lowerBounds(1);
Real top = upperBounds(1);
Real left = lowerBounds(0);
Real right = upperBounds(0);
Real eps = std::abs((top - bottom) * 1e-12);
const Array<Real> & pos = mesh.getNodes();
Array<Real> & disp = model.getDisplacement();
Array<bool> & boun = model.getBlockedDOFs();
Real radius = 0;
Real phi = 0;
- disp.clear();
- boun.clear();
+ disp.zero();
+ boun.zero();
/// absolute confinement
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
if (std::abs(pos(i, 0) - left) < eps) {
radius = std::sqrt(pos(i, 0) * pos(i, 0) + pos(i, 1) * pos(i, 1));
phi = std::atan2(pos(i, 1), pos(i, 0));
boun(i, 0) = true;
disp(i, 0) = cos(phi) * ((radius - 4. / radius) * alpha + 4. / radius);
boun(i, 1) = true;
disp(i, 1) = sin(phi) * ((radius - 4. / radius) * alpha + 4. / radius);
}
if (std::abs(pos(i, 0) - right) < eps) {
radius = std::sqrt(pos(i, 0) * pos(i, 0) + pos(i, 1) * pos(i, 1));
phi = std::atan2(pos(i, 1), pos(i, 0));
boun(i, 0) = true;
disp(i, 0) = cos(phi) * ((radius - 4. / radius) * alpha + 4. / radius);
boun(i, 1) = true;
disp(i, 1) = sin(phi) * ((radius - 4. / radius) * alpha + 4. / radius);
}
if (std::abs(pos(i, 1) - top) < eps) {
radius = std::sqrt(pos(i, 0) * pos(i, 0) + pos(i, 1) * pos(i, 1));
phi = std::atan2(pos(i, 1), pos(i, 0));
boun(i, 0) = true;
disp(i, 0) = cos(phi) * ((radius - 4. / radius) * alpha + 4. / radius);
boun(i, 1) = true;
disp(i, 1) = sin(phi) * ((radius - 4. / radius) * alpha + 4. / radius);
}
if (std::abs(pos(i, 1) - bottom) < eps) {
radius = std::sqrt(pos(i, 0) * pos(i, 0) + pos(i, 1) * pos(i, 1));
phi = std::atan2(pos(i, 1), pos(i, 0));
boun(i, 0) = true;
disp(i, 0) = cos(phi) * ((radius - 4. / radius) * alpha + 4. / radius);
boun(i, 1) = true;
disp(i, 1) = sin(phi) * ((radius - 4. / radius) * alpha + 4. / radius);
}
}
}
class SphereMaterialSelector : public DefaultMaterialIGFEMSelector {
public:
SphereMaterialSelector(std::vector<Sphere> & sphere_list,
SolidMechanicsModelIGFEM & model)
: DefaultMaterialIGFEMSelector(model), model(model),
spheres(sphere_list) {}
UInt operator()(const Element & elem) {
if (Mesh::getKind(elem.type) == _ek_igfem)
return this->fallback_value_igfem;
// return 2;//2model.getMaterialIndex(2);
const Mesh & mesh = model.getMesh();
UInt spatial_dimension = model.getSpatialDimension();
Vector<Real> barycenter(spatial_dimension);
mesh.getBarycenter(elem, barycenter);
std::vector<Sphere>::const_iterator iit = spheres.begin();
std::vector<Sphere>::const_iterator eit = spheres.end();
for (; iit != eit; ++iit) {
const Sphere & sp = *iit;
if (sp.isInside(barycenter)) {
return 1; // model.getMaterialIndex("inside");;
}
}
return 0;
// return DefaultMaterialSelector::operator()(elem);
}
void update(Real new_radius) {
std::vector<Sphere>::iterator iit = spheres.begin();
std::vector<Sphere>::iterator eit = spheres.end();
for (; iit != eit; ++iit) {
Real & radius = iit->getRadius();
radius = new_radius;
}
}
protected:
SolidMechanicsModelIGFEM & model;
std::vector<Sphere> spheres;
};
typedef Spherical SK;
/// the following modeling problem is explained in:
/// T.-P. Fries "A corrected XFEM approximation without problems in blending
/// elements", 2008
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
/// problem dimension
const UInt spatial_dimension = 2;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// mesh creation
Mesh mesh(spatial_dimension);
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
mesh.read("plate.msh");
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
/// model creation
SolidMechanicsModelIGFEM model(mesh);
model.initParallel(partition);
delete partition;
Math::setTolerance(1e-14);
/// geometry of IGFEM interface: circular inclusion
Real radius_inclusion = 0.401;
Vector<Real> center(spatial_dimension, 0.);
/// @todo: Simplify this: need to create two type of spheres:
/// one for the geometry and one for the material selector
SK::Sphere_3 sphere(SK::Point_3(center(0), center(1), 0),
radius_inclusion * radius_inclusion);
std::list<SK::Sphere_3> sphere_list;
sphere_list.push_back(sphere);
ID domain_name = "gel";
SphereMaterialSelector * mat_selector;
/// set material selector and initialize the model completely
std::vector<Sphere> spheres;
spheres.push_back(Sphere(center, radius_inclusion, 1.e-12));
mat_selector = new SphereMaterialSelector(spheres, model);
model.setMaterialSelector(*mat_selector);
model.initFull();
/// register the sphere list in the model
model.registerGeometryObject(sphere_list, domain_name);
/// add fields that should be dumped
model.setBaseName("regular_elements");
model.setBaseNameToDumper("igfem elements", "igfem elements");
model.addDumpField("material_index");
model.addDumpField("partitions");
model.addDumpFieldVector("displacement");
model.addDumpField("blocked_dofs");
model.addDumpField("stress");
model.addDumpFieldToDumper("igfem elements", "lambda");
model.addDumpFieldVectorToDumper("igfem elements", "real_displacement");
model.addDumpFieldVectorToDumper("igfem elements", "displacement");
model.addDumpFieldToDumper("igfem elements", "material_index");
model.addDumpFieldToDumper("igfem elements", "stress");
model.addDumpFieldToDumper("igfem elements", "partitions");
/// dump mesh before the IGFEM interface is created
model.dump();
model.dump("igfem elements");
/// create the interface
model.update(domain_name);
/* --------------------------------------------------------------------------
*/
/// apply exact solution for the displacement along the outer boundary
Real outer_radius = 2.0;
/// get the Lame constants for the two non-igfem materials (frist two
/// materials in the material file):
/// Needed for compuation of boundary conditions
Vector<Real> lambda(2);
Vector<Real> mu(2);
for (UInt m = 0; m < 2; ++m) {
MaterialElastic<spatial_dimension> & mat =
dynamic_cast<MaterialElastic<spatial_dimension> &>(
model.getMaterial(m));
lambda(m) = mat.getLambda();
mu(m) = mat.getMu();
}
applyBoundaryConditions(model, radius_inclusion, outer_radius, lambda, mu);
/// dump the mesh after the IGFEM interface has been created
model.dump();
model.dump("igfem elements");
/// solve the system
bool factorize = false;
bool converged = false;
Real error;
converged = model.solveStep<_scm_newton_raphson_tangent,
SolveConvergenceCriteria::_increment>(
1e-12, error, 2, factorize);
if (!converged) {
std::cout << "Solving step did not yield a converged solution, error: "
<< error << std::endl;
return EXIT_FAILURE;
}
/// dump the solution
model.dump();
model.dump("igfem elements");
/// output the displacement in parallel
outputArray(mesh, model.getDisplacement());
finalize();
return EXIT_SUCCESS;
}
diff --git a/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_transfer_internals.cc b/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_transfer_internals.cc
index 01b798658..36416e5af 100644
--- a/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_transfer_internals.cc
+++ b/extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_transfer_internals.cc
@@ -1,298 +1,298 @@
/**
* @file test_transfer_internals.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
*
* @brief test to test the transfer of internals such as damage
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dumper_paraview.hh"
#include "mesh_geom_common.hh"
#include "solid_mechanics_model_igfem.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
bool checkResults(Real & error, UInt & counter, SolidMechanicsModel & model,
Real diagonal);
class ASRMaterialSelector : public DefaultMaterialIGFEMSelector {
public:
ASRMaterialSelector(SolidMechanicsModelIGFEM & model)
: DefaultMaterialIGFEMSelector(model), model(model) {}
UInt operator()(const Element & elem) {
if (Mesh::getKind(elem.type) == _ek_igfem)
/// choose IGFEM material
return this->fallback_value_igfem;
const Mesh & mesh = model.getMesh();
UInt spatial_dimension = model.getSpatialDimension();
Vector<Real> barycenter(spatial_dimension);
mesh.getBarycenter(elem, barycenter);
if (model.isInside(barycenter))
return 1;
return 0;
}
protected:
SolidMechanicsModelIGFEM & model;
};
typedef Spherical SK;
int main(int argc, char * argv[]) {
initialize("material_damage.dat", argc, argv);
StaticCommunicator & comm =
akantu::StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// problem dimension
UInt spatial_dimension = 2;
/// mesh creation and partioning
Mesh mesh(spatial_dimension);
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
mesh.read("fine_mesh.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
/// model creation and initialization
SolidMechanicsModelIGFEM model(mesh);
model.initParallel(partition);
delete partition;
/// create the list to store the gel pockets
std::list<SK::Sphere_3> gel_pocket_list;
model.registerGeometryObject(gel_pocket_list, "mat_1");
/// set the material selector
ASRMaterialSelector * mat_selector = new ASRMaterialSelector(model);
model.setMaterialSelector(*mat_selector);
model.initFull();
/// add fields that should be dumped
model.setBaseName("regular_elements");
model.addDumpField("material_index");
model.addDumpField("damage");
model.addDumpField("Sc");
model.addDumpField("partitions");
model.setBaseNameToDumper("igfem elements", "igfem elements");
model.addDumpFieldToDumper("igfem elements", "material_index");
model.addDumpFieldToDumper("igfem elements", "Sc");
model.addDumpFieldToDumper("igfem elements", "damage");
model.addDumpFieldToDumper("igfem elements", "lambda");
model.addDumpFieldToDumper("igfem elements", "partitions");
/// set damage state as a function of the position of the quadrature
/// point the damage state is the absolute value of bary center
/// position normalized by the half of the diagonal of the mesh (which is a
/// square)
/// compute the mesh diagonal
mesh.computeBoundingBox();
const Vector<Real> & lower_bounds = mesh.getLowerBounds();
const Vector<Real> & upper_bounds = mesh.getUpperBounds();
Real diagonal = upper_bounds.distance(lower_bounds);
/// compute barycenters and set damage state
GhostType ghost_type = _not_ghost;
ElementType el_type = _triangle_3;
UInt nb_element = mesh.getNbElement(el_type, ghost_type);
Array<Real> barycenter(nb_element, spatial_dimension);
Array<Real>::iterator<Vector<Real>> bary_it =
barycenter.begin(spatial_dimension);
for (UInt elem = 0; elem < nb_element; ++elem) {
mesh.getBarycenter(elem, el_type, bary_it->storage(), ghost_type);
UInt mat_index =
model.getMaterialByElement(el_type, ghost_type).begin()[elem];
UInt local_index =
model.getMaterialLocalNumbering(el_type, ghost_type).begin()[elem];
Material & mat = model.getMaterial(mat_index);
Array<Real> & damage = mat.getArray<Real>("damage", el_type, ghost_type);
Array<Real>::scalar_iterator damage_it = damage.begin();
damage_it[local_index] = (*bary_it).norm() / (0.5 * diagonal);
++bary_it;
}
/// dump
model.dump("igfem elements");
model.dump();
/// create the inclusions
SK::Sphere_3 sphere_1(SK::Point_3(0., 0., 0.), 0.13 * 0.13);
SK::Sphere_3 sphere_2(SK::Point_3(0.5, 0.5, 0.), 0.4 * 0.4);
SK::Sphere_3 sphere_3(SK::Point_3(-0.75, -0.75, 0.), 0.12 * 0.12);
SK::Sphere_3 sphere_4(SK::Point_3(0.625, -0.625, 0.), 0.25 * 0.25);
gel_pocket_list.push_back(sphere_1);
gel_pocket_list.push_back(sphere_2);
gel_pocket_list.push_back(sphere_3);
gel_pocket_list.push_back(sphere_4);
/// create the interface
model.update("mat_1");
/// dump
model.dump("igfem elements");
model.dump();
/// check that internals have been transferred correctly
Real error = 0.;
UInt counter = 0;
bool check_passed = checkResults(error, counter, model, diagonal);
if (!check_passed) {
finalize();
return EXIT_FAILURE;
}
comm.allReduce(&error, 1, _so_sum);
comm.allReduce(&counter, 1, _so_sum);
if (prank == 0) {
std::cout << "The error is: " << error << std::endl;
std::cout << "There are " << counter
<< " igfem quads with damage material in the mesh" << std::endl;
std::cout
<< "There should be 156 igfem quads with damage material in the mesh"
<< std::endl;
}
if (error > 1e-14 || counter != 156) {
finalize();
return EXIT_FAILURE;
}
// /// grow two of the gel pockets (gel pocket 1 and 3) and repeat the test
std::list<SK::Sphere_3> new_gel_pocket_list;
/// grow sphere 2
SK::Sphere_3 sphere_5(SK::Point_3(0., 0., 0.), 0.15 * 0.15);
/// grow sphere 3
SK::Sphere_3 sphere_6(SK::Point_3(-0.75, -0.75, 0.), 0.5 * 0.5);
new_gel_pocket_list.push_back(sphere_5);
new_gel_pocket_list.push_back(sphere_2);
new_gel_pocket_list.push_back(sphere_6);
new_gel_pocket_list.push_back(sphere_4);
- gel_pocket_list.clear();
+ gel_pocket_list.zero();
gel_pocket_list = new_gel_pocket_list;
model.update("mat_1");
/// check again that internals have been transferred correctly
error = 0.;
counter = 0;
check_passed = checkResults(error, counter, model, diagonal);
if (!check_passed) {
finalize();
return EXIT_FAILURE;
}
comm.allReduce(&error, 1, _so_sum);
comm.allReduce(&counter, 1, _so_sum);
if (prank == 0) {
std::cout << "The error is: " << error << std::endl;
std::cout << "There are " << counter
<< " igfem quads with damage material in the mesh" << std::endl;
std::cout
<< "There should be 150 igfem quads with damage material in the mesh"
<< std::endl;
}
if (error > 1e-14 || counter != 150) {
finalize();
return EXIT_FAILURE;
}
/// dump
model.dump("igfem elements");
model.dump();
finalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
bool checkResults(Real & error, UInt & counter, SolidMechanicsModel & model,
Real diagonal) {
/// check that damage values have been correctly transferred
FEEngine & fee = model.getFEEngine("IGFEMFEEngine");
GhostType ghost_type = _not_ghost;
Mesh & mesh = model.getMesh();
UInt spatial_dimension = model.getSpatialDimension();
bool check_passed = true;
/// loop over all IGFEM elements of type _not_ghost
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_igfem);
Mesh::type_iterator last =
mesh.lastType(spatial_dimension, ghost_type, _ek_igfem);
for (; it != last; ++it) {
ElementType igfem_el_type = *it;
UInt nb_igfem_element = mesh.getNbElement(igfem_el_type);
UInt nb_quads = fee.getNbIntegrationPoints(igfem_el_type, ghost_type);
Array<Real> barycenter_igfem(nb_igfem_element, spatial_dimension);
Array<Real>::vector_iterator bary_it =
barycenter_igfem.begin(spatial_dimension);
UInt * conn_val = mesh.getConnectivity(igfem_el_type, ghost_type).storage();
Array<Real> & nodes = mesh.getNodes();
UInt nb_parent_nodes = IGFEMHelper::getNbParentNodes(igfem_el_type);
/// compute the bary center of the underlying parent element
UInt nb_el_nodes = mesh.getNbNodesPerElement(igfem_el_type);
for (UInt elem = 0; elem < nb_igfem_element; ++elem) {
Real local_coord[spatial_dimension * nb_parent_nodes];
UInt offset = elem * nb_el_nodes;
for (UInt n = 0; n < nb_parent_nodes; ++n) {
memcpy(local_coord + n * spatial_dimension,
nodes.storage() + conn_val[offset + n] * spatial_dimension,
spatial_dimension * sizeof(Real));
}
Math::barycenter(local_coord, nb_parent_nodes, spatial_dimension,
bary_it->storage());
UInt mat_index =
model.getMaterialByElement(igfem_el_type, ghost_type).begin()[elem];
Material & mat = model.getMaterial(mat_index);
UInt local_index =
model.getMaterialLocalNumbering(igfem_el_type, ghost_type)
.begin()[elem];
Array<Real> & damage =
mat.getArray<Real>("damage", igfem_el_type, ghost_type);
Array<UInt> & sub_mat =
mat.getArray<UInt>("sub_material", igfem_el_type, ghost_type);
Array<Real> & strength =
mat.getArray<Real>("Sc", igfem_el_type, ghost_type);
Array<Real>::scalar_iterator damage_it = damage.begin();
Array<UInt>::scalar_iterator sub_mat_it = sub_mat.begin();
Array<Real>::scalar_iterator Sc_it = strength.begin();
for (UInt q = 0; q < nb_quads; ++q) {
UInt q_global = local_index * nb_quads + q;
if (sub_mat_it[q_global] == 1) {
if (std::abs(Sc_it[q_global] - 100) > 1e-15) {
check_passed = false;
return check_passed;
}
error += std::abs(
(damage_it[q_global] - (*bary_it).norm() / (0.5 * diagonal)));
++counter;
} else if ((std::abs(Sc_it[q_global]) > Math::getTolerance()) ||
(std::abs(damage_it[q_global]) > Math::getTolerance())) {
check_passed = false;
return check_passed;
}
}
++bary_it;
}
}
return check_passed;
}
diff --git a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/force_based_dirichlet.hh b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/force_based_dirichlet.hh
index e0f753d91..7f1cc31c4 100644
--- a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/force_based_dirichlet.hh
+++ b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/force_based_dirichlet.hh
@@ -1,128 +1,128 @@
/**
* @file force_based_dirichlet.hh
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief dirichlet boundary condition that tries
* to keep the force at a given value
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_FORCE_BASED_DIRICHLET_HH__
-#define __AST_FORCE_BASED_DIRICHLET_HH__
+#ifndef AST_FORCE_BASED_DIRICHLET_HH_
+#define AST_FORCE_BASED_DIRICHLET_HH_
// akantu
#include "aka_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class ForceBasedDirichlet : public BC::Dirichlet::IncrementValue {
protected:
typedef const Array<Real> * RealArrayPtr;
typedef const Array<Int> * IntArrayPtr;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ForceBasedDirichlet(SolidMechanicsModel & model, BC::Axis ax, Real target_f,
Real mass = 0.)
: IncrementValue(0., ax), model(model), mass(mass), velocity(0.),
target_force(target_f), total_residual(0.) {}
virtual ~ForceBasedDirichlet() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void updateTotalResidual() {
this->total_residual = 0.;
for (auto && subboundary : this->subboundaries) {
this->total_residual +=
integrateResidual(subboundary, this->model, this->axis);
}
}
virtual Real update() {
AKANTU_DEBUG_IN();
this->updateTotalResidual();
Real total_force = this->target_force + this->total_residual;
Real a = total_force / this->mass;
Real dt = model.getTimeStep();
this->velocity += 0.5 * dt * a;
this->value =
this->velocity * dt + 0.5 * dt * dt * a; // increment position dx
this->velocity += 0.5 * dt * a;
AKANTU_DEBUG_OUT();
return this->total_residual;
}
Real applyYourself() {
AKANTU_DEBUG_IN();
Real reaction = this->update();
for (auto && subboundary : this->subboundaries) {
this->model.applyBC(*this, subboundary);
}
AKANTU_DEBUG_OUT();
return reaction;
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_SET_MACRO(Mass, mass, Real);
AKANTU_SET_MACRO(TargetForce, target_force, Real);
void insertSubBoundary(const std::string & sb_name) {
this->subboundaries.insert(sb_name);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
typedef std::set<std::string> SubBoundarySet;
protected:
SolidMechanicsModel & model;
SubBoundarySet subboundaries;
Real mass;
Real velocity;
Real target_force;
Real total_residual;
};
} // namespace akantu
-#endif /* __AST_FORCE_BASED_DIRICHLET_HH__ */
+#endif /* AST_FORCE_BASED_DIRICHLET_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/inclined_flat_dirichlet.hh b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/inclined_flat_dirichlet.hh
index fb6f92af3..3d88444a3 100644
--- a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/inclined_flat_dirichlet.hh
+++ b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/inclined_flat_dirichlet.hh
@@ -1,80 +1,80 @@
/**
* @file inclined_flat_dirichlet.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief inclined dirichlet
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_INCLINED_FLAT_DIRICHLET_HH__
-#define __AST_INCLINED_FLAT_DIRICHLET_HH__
+#ifndef AST_INCLINED_FLAT_DIRICHLET_HH_
+#define AST_INCLINED_FLAT_DIRICHLET_HH_
// akantu
#include "aka_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class InclinedFlatDirichlet : public BC::Dirichlet::DirichletFunctor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
InclinedFlatDirichlet(Real val, BC::Axis ax, BC::Axis incl_ax,
Real center_coord, Real tang)
: DirichletFunctor(ax), value(val), incl_ax(incl_ax),
center_coord(center_coord), tang(tang){};
virtual ~InclinedFlatDirichlet() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline void operator()(UInt node, Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const {
AKANTU_DEBUG_IN();
Real dist = coord(incl_ax) - this->center_coord;
flags(axis) = true;
primal(axis) = this->value + this->tang * dist;
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
Real value;
BC::Axis incl_ax;
Real center_coord;
Real tang;
};
} // namespace akantu
-#endif /* __AST_INCLINED_FLAT_DIRICHLET_HH__ */
+#endif /* AST_INCLINED_FLAT_DIRICHLET_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/spring_bc.hh b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/spring_bc.hh
index f20b57832..62c3f790b 100644
--- a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/spring_bc.hh
+++ b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/spring_bc.hh
@@ -1,141 +1,141 @@
/**
* @file spring_bc.hh
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief spring boundary condition
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_SPRING_BC_HH__
-#define __AST_SPRING_BC_HH__
+#ifndef AST_SPRING_BC_HH_
+#define AST_SPRING_BC_HH_
// simtools
#include "force_based_dirichlet.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class SpringBC : public ForceBasedDirichlet {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SpringBC(SolidMechanicsModel & model, BC::Axis ax, Real stiffness,
Real mass = 0.)
: ForceBasedDirichlet(model, ax, 0., mass), stiffness(stiffness),
elongation(0.) {}
virtual ~SpringBC() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual Real update() {
AKANTU_DEBUG_IN();
this->target_force = -this->stiffness * this->elongation;
Real reaction = ForceBasedDirichlet::update();
this->elongation += this->value;
AKANTU_DEBUG_OUT();
return reaction;
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Elongation, elongation, Real);
inline void setToEquilibrium() {
AKANTU_DEBUG_IN();
this->updateTotalResidual();
this->target_force = -this->total_residual;
this->elongation = -this->target_force / this->stiffness;
AKANTU_DEBUG_OUT();
}
/// change elongation
/// dx > 0 -> target_force < 0
inline void incrementElongation(Real dx) {
AKANTU_DEBUG_IN();
this->elongation += dx;
AKANTU_DEBUG_OUT();
}
// friend std::ostream& operator<<(std::ostream& out, const SpringBC &
// spring);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
Real stiffness;
Real elongation;
};
// class SpringBCRestricted : public SpringBC {
// public:
// SpringBCRestricted(BC::Axis ax, Real target_force, BC::Axis surface_axis,
// Real min, Real max)
// :SpringBC(ax, target_force), surface_axis(surface_axis), min(min),
// max(max) {}
// virtual ~SpringBCRestricted() {}
// public:
// inline void operator()(UInt node, Vector<bool> & flags, Vector<Real> &
// primal, const Vector<Real> & coord) const {
// if(coord(surface_axis) > min && coord(surface_axis) < max) {
// SpringBC::operator()(node, flags, primal, coord);
// }
// }
// private:
// BC::Axis surface_axis;
// Real min;
// Real max;
// };
// std::ostream& operator<<(std::ostream& out, const SpringBC & spring) {
// out << "Real total_residual: " << *spring.total_residual << std::endl;
// out << "Real mass: " << spring.mass << std::endl;
// out << "Real k: " << spring.k << std::endl;
// out << "Real delta_x: " << spring.delta_x << std::endl;
// out << "Real dt: " << spring.dt << std::endl;
// out << "Real v: " << spring.v << std::endl;
// out << "Real dx: " << spring.dx << std::endl;
// out << "Real forcing_vel: " << spring.forcing_vel << std::endl;
// return out;
// }
} // namespace akantu
-#endif /* __AST_SPRING_BC_HH__ */
+#endif /* AST_SPRING_BC_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.hh b/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.hh
index a5f152a21..5dbaf6f2f 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.hh
+++ b/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.hh
@@ -1,109 +1,109 @@
/**
* @file parameter_reader.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief for simulations to read parameters from an input file
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_PARAMETER_READER_HH__
-#define __AST_PARAMETER_READER_HH__
+#ifndef AST_PARAMETER_READER_HH_
+#define AST_PARAMETER_READER_HH_
/* -------------------------------------------------------------------------- */
// std
#include <map>
#include <set>
// akantu
#include "aka_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class ParameterReader {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ParameterReader();
virtual ~ParameterReader(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read input file
void readInputFile(std::string file_name);
/// write input file
void writeInputFile(std::string file_name) const;
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
///
template <typename T> T get(std::string key) const;
template <typename T> bool has(std::string key) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// type of data available
std::set<std::string> data_types;
/// data
std::map<std::string, akantu::ElementType> element_type_data;
std::map<std::string, std::string> string_data;
std::map<std::string, akantu::Int> int_data;
std::map<std::string, akantu::UInt> uint_data;
std::map<std::string, akantu::Real> real_data;
std::map<std::string, bool> bool_data;
/// convert string to element type
std::map<std::string, ElementType> _input_to_akantu_element_types;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "parameter_reader_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ParameterReader & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AST_PARAMETER_READER_HH__ */
+#endif /* AST_PARAMETER_READER_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.cc b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.cc
index 8a49ec80f..9b1ad7454 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.cc
+++ b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.cc
@@ -1,243 +1,241 @@
/**
* @file synchronized_array.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief implementation of synchronized array function
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// std
#include <fstream>
#include <iostream>
// simtools
#include "synchronized_array.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class T>
-SynchronizedArray<T>::SynchronizedArray(
- UInt size, UInt nb_component, SynchronizedArray<T>::const_reference value,
- const ID & id, SynchronizedArray<T>::const_reference default_value,
- const std::string restart_name)
+SynchronizedArray<T>::SynchronizedArray(UInt size, UInt nb_component,
+ const_reference value, const ID & id,
+ const_reference default_value,
+ const std::string & restart_name)
: SynchronizedArrayBase(), Array<T>(size, nb_component, value, id),
default_value(default_value), restart_name(restart_name),
deleted_elements(0), nb_added_elements(size), depending_arrays(0) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T>
void SynchronizedArray<T>::syncElements(SyncChoice sync_choice) {
AKANTU_DEBUG_IN();
if (sync_choice == _deleted) {
std::vector<SynchronizedArrayBase *>::iterator it;
for (it = depending_arrays.begin(); it != depending_arrays.end(); ++it) {
UInt vec_size = (*it)->syncDeletedElements(this->deleted_elements);
AKANTU_DEBUG_ASSERT(vec_size == this->size_,
"Synchronized arrays do not have the same length"
<< "(may be a double synchronization)");
}
this->deleted_elements.clear();
}
else if (sync_choice == _added) {
std::vector<SynchronizedArrayBase *>::iterator it;
for (it = depending_arrays.begin(); it != depending_arrays.end(); ++it) {
UInt vec_size = (*it)->syncAddedElements(this->nb_added_elements);
AKANTU_DEBUG_ASSERT(vec_size == this->size_,
"Synchronized arrays do not have the same length"
<< "(may be a double synchronization)");
}
this->nb_added_elements = 0;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T>
UInt SynchronizedArray<T>::syncDeletedElements(
std::vector<UInt> & del_elements) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
- nb_added_elements == 0 && deleted_elements.size() == 0,
+ nb_added_elements == 0 and deleted_elements.empty(),
"Cannot sync with a SynchronizedArray if it has already been modified");
std::vector<UInt>::const_iterator it;
for (it = del_elements.begin(); it != del_elements.end(); ++it) {
erase(*it);
}
syncElements(_deleted);
AKANTU_DEBUG_OUT();
return this->size_;
}
/* -------------------------------------------------------------------------- */
template <class T>
UInt SynchronizedArray<T>::syncAddedElements(UInt nb_add_elements) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
- nb_added_elements == 0 && deleted_elements.size() == 0,
+ nb_added_elements == 0 and deleted_elements.empty(),
"Cannot sync with a SynchronizedArray if it has already been modified");
for (UInt i = 0; i < nb_add_elements; ++i) {
push_back(this->default_value);
}
syncElements(_added);
AKANTU_DEBUG_OUT();
return this->size_;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SynchronizedArray<T>::registerDependingArray(
SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->depending_arrays.push_back(&array);
array.syncAddedElements(this->size_);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SynchronizedArray<T>::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
- std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
- ;
+ std::string space(indent, AKANTU_INDENT);
stream << space << "SynchronizedArray<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
stream << space << " + default_value : " << this->default_value
<< std::endl;
stream << space << " + nb_added_elements : " << this->nb_added_elements
<< std::endl;
stream << space << " + deleted_elements : ";
- for (std::vector<UInt>::const_iterator it = this->deleted_elements.begin();
- it != this->deleted_elements.end(); ++it)
- stream << *it << " ";
+ for (auto && deleted_element : deleted_elements) {
+ stream << deleted_element << " ";
+ }
stream << std::endl;
stream << space << " + depending_arrays : ";
- for (std::vector<SynchronizedArrayBase *>::const_iterator it =
- this->depending_arrays.begin();
- it != this->depending_arrays.end(); ++it)
- stream << (*it)->getID() << " ";
+ for (auto && depending_array : this->depending_arrays) {
+ stream << depending_array->getID() << " ";
+ }
stream << std::endl;
Array<T>::printself(stream, indent + 1);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
-void SynchronizedArray<T>::dumpRestartFile(std::string file_name) const {
+void SynchronizedArray<T>::dumpRestartFile(const std::string & file_name) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
- nb_added_elements == 0 && deleted_elements.size() == 0,
+ nb_added_elements == 0 and deleted_elements.empty(),
"Restart File for SynchronizedArray "
<< this->id << " should not be dumped as it is not synchronized yet");
std::stringstream name;
name << file_name << "-" << this->restart_name << ".rs";
std::ofstream out_restart;
out_restart.open(name.str().c_str());
out_restart << this->size_ << " " << this->nb_component << std::endl;
Real size_comp = this->size_ * this->nb_component;
- for (UInt i = 0; i < size_comp; ++i)
+ for (UInt i = 0; i < size_comp; ++i) {
out_restart << std::setprecision(12) << this->values[i] << " ";
+ }
// out_restart << std::hex << std::setprecision(12) << this->values[i] << "
// ";
out_restart << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
-void SynchronizedArray<T>::readRestartFile(std::string file_name) {
+void SynchronizedArray<T>::readRestartFile(const std::string & file_name) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
- nb_added_elements == 0 && deleted_elements.size() == 0,
+ nb_added_elements == 0 and deleted_elements.empty(),
"Restart File for SynchronizedArray "
<< this->id << " should not be read as it is not synchronized yet");
std::stringstream name;
name << file_name << "-" << this->restart_name << ".rs";
std::ifstream infile;
infile.open(name.str().c_str());
std::string line;
// get size and nb_component info
AKANTU_DEBUG_ASSERT(infile.good(), "Could not read restart file for "
<< "SynchronizedArray " << this->id);
getline(infile, line);
std::stringstream size_comp(line);
size_comp >> this->size_;
size_comp >> this->nb_component;
// get elements in array
getline(infile, line);
std::stringstream data(line);
for (UInt i = 0; i < this->size_ * this->nb_component; ++i) {
AKANTU_DEBUG_ASSERT(
!data.eof(),
"Read SynchronizedArray "
<< this->id
<< " got to the end of the file before having read all data!");
data >> this->values[i];
// data >> std::hex >> this->values[i];
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template class SynchronizedArray<Real>;
template class SynchronizedArray<UInt>;
template class SynchronizedArray<Int>;
template class SynchronizedArray<bool>;
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.hh b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.hh
index ff186132c..70fa0eedf 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.hh
+++ b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.hh
@@ -1,202 +1,202 @@
/**
* @file synchronized_array.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief synchronized array: a array can be registered to another (hereafter
* called top) array. If an element is added to or removed from the top array,
* the registered array removes or adds at the same position an element. The two
* arrays stay therefore synchronized.
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_SYNCHRONIZED_ARRAY_HH__
-#define __AST_SYNCHRONIZED_ARRAY_HH__
+#ifndef AST_SYNCHRONIZED_ARRAY_HH_
+#define AST_SYNCHRONIZED_ARRAY_HH_
/* -------------------------------------------------------------------------- */
// std
#include <vector>
// akantu
#include "aka_array.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
enum SyncChoice { _added, _deleted };
/* -------------------------------------------------------------------------- */
class SynchronizedArrayBase {
public:
- SynchronizedArrayBase(){};
- ~SynchronizedArrayBase(){};
+ SynchronizedArrayBase() = default;
+ ~SynchronizedArrayBase() = default;
virtual ID getID() const { return "call should be virtual"; };
virtual UInt syncDeletedElements(std::vector<UInt> & delete_el) = 0;
virtual UInt syncAddedElements(UInt nb_added_el) = 0;
};
/* -------------------------------------------------------------------------- */
template <class T>
class SynchronizedArray : public SynchronizedArrayBase, protected Array<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- typedef typename Array<T>::value_type value_type;
- typedef typename Array<T>::reference reference;
- typedef typename Array<T>::pointer_type pointer_type;
- typedef typename Array<T>::const_reference const_reference;
+ using value_type = typename Array<T>::value_type;
+ using reference = typename Array<T>::reference;
+ using pointer_type = typename Array<T>::pointer_type;
+ using const_reference = typename Array<T>::const_reference;
SynchronizedArray(UInt size, UInt nb_component, const_reference value,
const ID & id, const_reference default_value,
- const std::string restart_name);
- virtual ~SynchronizedArray(){};
+ const std::string & restart_name);
+ ~SynchronizedArray() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// push_back
template <typename P> inline void push_back(P && value);
/// erase
inline void erase(UInt i);
// template<typename R>
// inline void erase(const iterator<R> & it);
/// synchronize elements
void syncElements(SyncChoice sync_choice);
/// dump restart file
- void dumpRestartFile(std::string file_name) const;
+ void dumpRestartFile(const std::string & file_name) const;
/// read restart file
- void readRestartFile(std::string file_name);
+ void readRestartFile(const std::string & file_name);
/// register depending array
void registerDependingArray(SynchronizedArrayBase & array);
/// function to print the contain of the class
- virtual void printself(std::ostream & stream, int indent = 0) const;
+ void printself(std::ostream & stream, int indent = 0) const override;
/// find position of element
Int find(const T & elem) const { return Array<T>::find(elem); };
/// set values to zero
- inline void clear() { Array<T>::clear(); };
+ inline void zero() { Array<T>::zero(); };
// inline void clear() { memset(values, 0, size*nb_component*sizeof(T)); };
/// set all entries of the array to the value t
/// @param t value to fill the array with
inline void set(T t) { Array<T>::set(t); }
/// set
template <template <typename> class C> inline void set(const C<T> & vm) {
Array<T>::set(vm);
}
/// set all entries of the array to value t and set default value
inline void setAndChangeDefault(T t) {
this->set(t);
this->default_value = t;
}
/// copy the content of an other array
void copy(const SynchronizedArray<T> & vect) { Array<T>::copy(vect); };
/// give the address of the memory allocated for this array
T * storage() const { return Array<T>::storage(); };
// T * storage() const { return this->values; };
// get nb component
UInt getNbComponent() const { return Array<T>::getNbComponent(); };
protected:
- UInt syncDeletedElements(std::vector<UInt> & del_elements);
- UInt syncAddedElements(UInt nb_add_elements);
+ UInt syncDeletedElements(std::vector<UInt> & del_elements) override;
+ UInt syncAddedElements(UInt nb_add_elements) override;
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
inline reference operator()(UInt i, UInt j = 0) {
return Array<T>::operator()(i, j);
}
inline const_reference operator()(UInt i, UInt j = 0) const {
return Array<T>::operator()(i, j);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_SET_MACRO(DefaultValue, default_value, T);
UInt size() const { return this->size_; };
- ID getID() const { return Array<T>::getID(); };
+ ID getID() const override { return Array<T>::getID(); };
const Array<T> & getArray() const {
const Array<T> & a = *(dynamic_cast<const Array<T> *>(this));
return a;
};
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// init value when new elements added
T default_value;
/// restart file_name
const std::string restart_name;
/// elements that have been deleted
std::vector<UInt> deleted_elements;
/// number of elements to add
UInt nb_added_elements;
/// pointers to arrays to be updated
std::vector<SynchronizedArrayBase *> depending_arrays;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const SynchronizedArray<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "synchronized_array_inline_impl.hh"
-#endif /* __AST_SYNCHRONIZED_ARRAY_HH__ */
+#endif /* AST_SYNCHRONIZED_ARRAY_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.hh b/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.hh
index 35bdcabd4..2652b1843 100644
--- a/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.hh
+++ b/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.hh
@@ -1,54 +1,54 @@
/**
* @file boundary_functions.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Fri Feb 23 2018
*
* @brief functions for boundaries
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_BOUNDARY_FUNCTIONS_HH__
-#define __AKANTU_BOUNDARY_FUNCTIONS_HH__
+#ifndef AKANTU_BOUNDARY_FUNCTIONS_HH_
+#define AKANTU_BOUNDARY_FUNCTIONS_HH_
namespace akantu {
class SolidMechanicsModel;
}
namespace akantu {
Real integrateResidual(const std::string & sub_boundary_name,
const SolidMechanicsModel & model, UInt dir);
/// this is a fix so that all subboundaries exist on all procs
void boundaryFix(Mesh & mesh,
const std::vector<std::string> & sub_boundary_names);
} // namespace akantu
-#endif /* __AKANTU_BOUNDARY_FUNCTIONS_HH__ */
+#endif /* AKANTU_BOUNDARY_FUNCTIONS_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/functions/node_filter.hh b/extra_packages/traction-at-split-node-contact/src/functions/node_filter.hh
index 3ac491e38..0cbc2f7ff 100644
--- a/extra_packages/traction-at-split-node-contact/src/functions/node_filter.hh
+++ b/extra_packages/traction-at-split-node-contact/src/functions/node_filter.hh
@@ -1,112 +1,112 @@
/**
* @file node_filter.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Tue Feb 20 2018
*
* @brief to filter nodes with functors
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NODE_FILTER_HH__
-#define __AST_NODE_FILTER_HH__
+#ifndef AST_NODE_FILTER_HH_
+#define AST_NODE_FILTER_HH_
/* -------------------------------------------------------------------------- */
// akantu
#include "aka_common.hh"
#include "mesh_filter.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class GeometryFilter : public NodeFilterFunctor {
public:
GeometryFilter(const Mesh & mesh, UInt dir, Real limit)
: NodeFilterFunctor(), mesh(mesh), dir(dir), limit(limit) {
this->positions = &(mesh.getNodes());
};
~GeometryFilter(){};
bool operator()(UInt node) { AKANTU_TO_IMPLEMENT(); };
protected:
const Mesh & mesh;
UInt dir;
Real limit;
const Array<Real> * positions;
};
/* -------------------------------------------------------------------------- */
class FilterPositionsGreaterThan : public GeometryFilter {
public:
FilterPositionsGreaterThan(const Mesh & mesh, UInt dir, Real limit)
: GeometryFilter(mesh, dir, limit){};
~FilterPositionsGreaterThan(){};
bool operator()(UInt node) {
AKANTU_DEBUG_IN();
bool to_filter = true;
if ((*this->positions)(node, this->dir) > this->limit)
to_filter = false;
AKANTU_DEBUG_OUT();
return to_filter;
};
};
/* -------------------------------------------------------------------------- */
class FilterPositionsLessThan : public GeometryFilter {
public:
FilterPositionsLessThan(const Mesh & mesh, UInt dir, Real limit)
: GeometryFilter(mesh, dir, limit){};
~FilterPositionsLessThan(){};
bool operator()(UInt node) {
AKANTU_DEBUG_IN();
bool to_filter = true;
if ((*this->positions)(node, this->dir) < this->limit)
to_filter = false;
AKANTU_DEBUG_OUT();
return to_filter;
};
};
/* -------------------------------------------------------------------------- */
// this filter is erase because the convention of filter has changed!!
// filter == true -> keep node
// template<class FilterType>
// void applyNodeFilter(Array<UInt> & nodes, FilterType & filter) {
// Array<UInt>::iterator<> it = nodes.begin();
// for (; it != nodes.end(); ++it) {
// if (filter(*it)) {
// it = nodes.erase(it);
// }
// }
// };
} // namespace akantu
-#endif /* __AST_NODE_FILTER_HH__ */
+#endif /* AST_NODE_FILTER_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh
index 6378e3804..29ac24991 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh
@@ -1,107 +1,107 @@
/**
* @file ntn_friclaw_coulomb.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief coulomb friction with \mu_s = \mu_k (constant)
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_FRICLAW_COULOMB_HH__
-#define __AST_NTN_FRICLAW_COULOMB_HH__
+#ifndef AST_NTN_FRICLAW_COULOMB_HH_
+#define AST_NTN_FRICLAW_COULOMB_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_no_regularisation.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation = NTNFricRegNoRegularisation>
class NTNFricLawCoulomb : public Regularisation {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricLawCoulomb(NTNBaseContact & contact, const ID & id = "coulomb",
const MemoryID & memory_id = 0);
virtual ~NTNFricLawCoulomb(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register synchronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// friction coefficient
SynchronizedArray<Real> mu;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFricLawCoulomb<Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friclaw_coulomb_tmpl.hh"
-#endif /* __AST_NTN_FRICLAW_COULOMB_HH__ */
+#endif /* AST_NTN_FRICLAW_COULOMB_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh
index 5f3901953..5d86d0636 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh
@@ -1,114 +1,114 @@
/**
* @file ntn_friclaw_linear_cohesive.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief linear cohesive law
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_FRICLAW_LINEAR_COHESIVE_HH__
-#define __AST_NTN_FRICLAW_LINEAR_COHESIVE_HH__
+#ifndef AST_NTN_FRICLAW_LINEAR_COHESIVE_HH_
+#define AST_NTN_FRICLAW_LINEAR_COHESIVE_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_no_regularisation.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation = NTNFricRegNoRegularisation>
class NTNFricLawLinearCohesive : public Regularisation {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricLawLinearCohesive(NTNBaseContact & contact,
const ID & id = "linear_cohesive",
const MemoryID & memory_id = 0);
virtual ~NTNFricLawLinearCohesive(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register synchronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// fracture energy
SynchronizedArray<Real> G_c;
// peak value of cohesive law
SynchronizedArray<Real> tau_c;
// residual value of cohesive law (for slip > d_c)
SynchronizedArray<Real> tau_r;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFricLawLinearCohesive<Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friclaw_linear_cohesive_tmpl.hh"
-#endif /* __AST_NTN_FRICLAW_LINEAR_COHESIVE_HH__ */
+#endif /* AST_NTN_FRICLAW_LINEAR_COHESIVE_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh
index 399ac06ed..d12963771 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh
@@ -1,116 +1,116 @@
/**
* @file ntn_friclaw_linear_slip_weakening.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief linear slip weakening
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_HH__
-#define __AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_HH__
+#ifndef AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_HH_
+#define AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_friclaw_coulomb.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation = NTNFricRegNoRegularisation>
class NTNFricLawLinearSlipWeakening : public NTNFricLawCoulomb<Regularisation> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricLawLinearSlipWeakening(NTNBaseContact & contact,
const ID & id = "linear_slip_weakening",
const MemoryID & memory_id = 0);
virtual ~NTNFricLawLinearSlipWeakening(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register synchronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength();
/// computes the friction coefficient as a function of slip
virtual void computeFrictionCoefficient();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// static coefficient of friction
SynchronizedArray<Real> mu_s;
// kinetic coefficient of friction
SynchronizedArray<Real> mu_k;
// Dc the length over which slip weakening happens
SynchronizedArray<Real> d_c;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFricLawLinearSlipWeakening<Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friclaw_linear_slip_weakening_tmpl.hh"
-#endif /* __AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_HH__ */
+#endif /* AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh
index 2403f3005..e6e44ba10 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh
@@ -1,95 +1,95 @@
/**
* @file ntn_friclaw_linear_slip_weakening_no_healing.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief linear slip weakening
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_NO_HEALING_HH__
-#define __AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_NO_HEALING_HH__
+#ifndef AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_NO_HEALING_HH_
+#define AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_NO_HEALING_HH_
/* -------------------------------------------------------------------------- */
#include "ntn_friclaw_linear_slip_weakening.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation = NTNFricRegNoRegularisation>
class NTNFricLawLinearSlipWeakeningNoHealing
: public NTNFricLawLinearSlipWeakening<Regularisation> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricLawLinearSlipWeakeningNoHealing(
NTNBaseContact & contact,
const ID & id = "linear_slip_weakening_no_healing",
const MemoryID & memory_id = 0);
virtual ~NTNFricLawLinearSlipWeakeningNoHealing(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// computes the friction coefficient as a function of slip
virtual void computeFrictionCoefficient();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Regularisation>
inline std::ostream & operator<<(
std::ostream & stream,
const NTNFricLawLinearSlipWeakeningNoHealing<Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friclaw_linear_slip_weakening_no_healing_tmpl.hh"
-#endif /* __AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_NO_HEALING_HH__ */
+#endif /* AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_NO_HEALING_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh
index a4b3c97eb..f7df9f108 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh
@@ -1,133 +1,133 @@
/**
* @file ntn_fricreg_no_regularisation.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief regularisation that does nothing
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_FRICREG_NO_REGULARISATION_HH__
-#define __AST_NTN_FRICREG_NO_REGULARISATION_HH__
+#ifndef AST_NTN_FRICREG_NO_REGULARISATION_HH_
+#define AST_NTN_FRICREG_NO_REGULARISATION_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_friction.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTNFricRegNoRegularisation : public NTNBaseFriction {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricRegNoRegularisation(NTNBaseContact & contact,
const ID & id = "no_regularisation",
const MemoryID & memory_id = 0);
virtual ~NTNFricRegNoRegularisation(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set to steady state for no regularisation -> do nothing
virtual void setToSteadyState(){};
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
virtual void dumpRestart(const std::string & file_name) const;
virtual void readRestart(const std::string & file_name);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
virtual void computeFrictionalContactPressure();
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength(){};
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
protected:
/// get the is_in_contact array
virtual const SynchronizedArray<bool> & internalGetIsInContact() {
return this->contact.getIsInContact();
};
/// get the contact pressure (the norm: scalar value)
virtual const SynchronizedArray<Real> & internalGetContactPressure();
/// get the frictional strength array
virtual SynchronizedArray<Real> & internalGetFrictionalStrength() {
return this->frictional_strength;
};
/// get the is_sticking array
virtual SynchronizedArray<bool> & internalGetIsSticking() {
return this->is_sticking;
}
/// get the slip array
virtual SynchronizedArray<Real> & internalGetSlip() { return this->slip; }
/// get the slip array
virtual SynchronizedArray<Real> & internalGetCumulativeSlip() {
return this->cumulative_slip;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// contact pressure (absolut value) for computation of friction
SynchronizedArray<Real> frictional_contact_pressure;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_fricreg_no_regularisation_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNFricRegNoRegularisation & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AST_NTN_FRICREG_NO_REGULARISATION_HH__ */
+#endif /* AST_NTN_FRICREG_NO_REGULARISATION_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh
index e8a6e197d..71593c4b8 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh
@@ -1,101 +1,101 @@
/**
* @file ntn_fricreg_rubin_ampuero.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief regularisation that regularizes the contact pressure
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_FRICREG_RUBIN_AMPUERO_HH__
-#define __AST_NTN_FRICREG_RUBIN_AMPUERO_HH__
+#ifndef AST_NTN_FRICREG_RUBIN_AMPUERO_HH_
+#define AST_NTN_FRICREG_RUBIN_AMPUERO_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_no_regularisation.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTNFricRegRubinAmpuero : public NTNFricRegNoRegularisation {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricRegRubinAmpuero(NTNBaseContact & contact,
const ID & id = "rubin_ampuero",
const MemoryID & memory_id = 0);
virtual ~NTNFricRegRubinAmpuero(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
virtual void dumpRestart(const std::string & file_name) const;
virtual void readRestart(const std::string & file_name);
virtual void setToSteadyState();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
protected:
/// get the contact pressure (the norm: scalar value)
virtual const SynchronizedArray<Real> & internalGetContactPressure();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
SynchronizedArray<Real> t_star;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_fricreg_rubin_ampuero_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNFricRegRubinAmpuero & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AST_NTN_FRICREG_RUBIN_AMPUERO_HH__ */
+#endif /* AST_NTN_FRICREG_RUBIN_AMPUERO_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh
index 24f23f284..c513fdeca 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh
@@ -1,112 +1,112 @@
/**
* @file ntn_fricreg_simplified_prakash_clifton.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief regularisation that regularizes the frictional strength with one
* parameter
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_FRICREG_SIMPLIFIED_PRAKASH_CLIFTON_HH__
-#define __AST_NTN_FRICREG_SIMPLIFIED_PRAKASH_CLIFTON_HH__
+#ifndef AST_NTN_FRICREG_SIMPLIFIED_PRAKASH_CLIFTON_HH_
+#define AST_NTN_FRICREG_SIMPLIFIED_PRAKASH_CLIFTON_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_no_regularisation.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTNFricRegSimplifiedPrakashClifton : public NTNFricRegNoRegularisation {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricRegSimplifiedPrakashClifton(
NTNBaseContact & contact, const ID & id = "simplified_prakash_clifton",
const MemoryID & memory_id = 0);
virtual ~NTNFricRegSimplifiedPrakashClifton(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
virtual void dumpRestart(const std::string & file_name) const;
virtual void readRestart(const std::string & file_name);
virtual void setToSteadyState();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
protected:
/// get the frictional strength array
virtual SynchronizedArray<Real> & internalGetFrictionalStrength() {
return this->spc_internal;
};
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
SynchronizedArray<Real> t_star;
// to get the incremental frictional strength
SynchronizedArray<Real> spc_internal;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_fricreg_simplified_prakash_clifton_inline_impl.hh"
/// standard output stream operator
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFricRegSimplifiedPrakashClifton & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AST_NTN_FRICREG_SIMPLIFIED_PRAKASH_CLIFTON_HH__ */
+#endif /* AST_NTN_FRICREG_SIMPLIFIED_PRAKASH_CLIFTON_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.hh
index ac49a11ad..3d2855cc6 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.hh
@@ -1,90 +1,90 @@
/**
* @file mIIasym_contact.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief contact for mode II anti-symmetric simulations
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_MIIASYM_CONTACT_HH__
-#define __AST_MIIASYM_CONTACT_HH__
+#ifndef AST_MIIASYM_CONTACT_HH_
+#define AST_MIIASYM_CONTACT_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntrf_contact.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class MIIASYMContact : public NTRFContact {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MIIASYMContact(SolidMechanicsModel & model, const ID & id = "contact",
const MemoryID & memory_id = 0);
virtual ~MIIASYMContact() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// update the impedance matrix
virtual void updateImpedance();
/// compute contact pressure -> do nothing because can only compute it in
/// equilibrium
virtual void computeContactPressure(){};
/// compute relative normal field (only value that has to be multiplied with
/// the normal)
/// WARNING: this is only valid for the acceleration in equilibrium
virtual void computeRelativeNormalField(const Array<Real> & field,
Array<Real> & rel_normal_field) const;
/// compute relative tangential field (complet array)
/// relative to master nodes
virtual void
computeRelativeTangentialField(const Array<Real> & field,
Array<Real> & rel_tang_field) const;
/// compute contact pressure that is used over the entire time
virtual void computeContactPressureInEquilibrium();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const MIIASYMContact & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AST_MIIASYM_CONTACT_HH__ */
+#endif /* AST_MIIASYM_CONTACT_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.cc
index fe03420a8..4f9c385a6 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.cc
@@ -1,568 +1,567 @@
/**
* @file ntn_base_contact.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief implementation of ntn base contact
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "ntn_base_contact.hh"
#include "dof_manager_default.hh"
#include "dumpable_inline_impl.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
#include "non_linear_solver_lumped.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
// NTNContactSynchElementFilter::NTNContactSynchElementFilter(
// NTNBaseContact & contact)
// : contact(contact),
// connectivity(contact.getModel().getMesh().getConnectivities()) {
// AKANTU_DEBUG_IN();
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
// bool NTNContactSynchElementFilter::operator()(const Element & e) {
// AKANTU_DEBUG_IN();
// ElementType type = e.type;
// UInt element = e.element;
// GhostType ghost_type = e.ghost_type;
// // loop over all nodes of this element
// bool need_element = false;
// UInt nb_nodes = Mesh::getNbNodesPerElement(type);
// for (UInt n = 0; n < nb_nodes; ++n) {
// UInt nn = this->connectivity(type, ghost_type)(element, n);
// // if one nodes is in this contact, we need this element
// if (this->contact.getNodeIndex(nn) >= 0) {
// need_element = true;
// break;
// }
// }
// AKANTU_DEBUG_OUT();
// return need_element;
// }
/* -------------------------------------------------------------------------- */
NTNBaseContact::NTNBaseContact(SolidMechanicsModel & model, const ID & id,
const MemoryID & memory_id)
: Memory(id, memory_id), Dumpable(), model(model),
slaves(0, 1, 0, id + ":slaves", std::numeric_limits<UInt>::quiet_NaN(),
"slaves"),
normals(0, model.getSpatialDimension(), 0, id + ":normals",
std::numeric_limits<Real>::quiet_NaN(), "normals"),
contact_pressure(
0, model.getSpatialDimension(), 0, id + ":contact_pressure",
std::numeric_limits<Real>::quiet_NaN(), "contact_pressure"),
is_in_contact(0, 1, false, id + ":is_in_contact", false, "is_in_contact"),
lumped_boundary_slaves(0, 1, 0, id + ":lumped_boundary_slaves",
std::numeric_limits<Real>::quiet_NaN(),
"lumped_boundary_slaves"),
impedance(0, 1, 0, id + ":impedance",
std::numeric_limits<Real>::quiet_NaN(), "impedance"),
contact_surfaces(), slave_elements("slave_elements", id, memory_id),
node_to_elements() {
AKANTU_DEBUG_IN();
- FEEngine & boundary_fem = this->model.getFEEngineBoundary();
- for (ghost_type_t::iterator gt = ghost_type_t::begin();
- gt != ghost_type_t::end(); ++gt) {
- boundary_fem.initShapeFunctions(*gt);
+ auto & boundary_fem = this->model.getFEEngineBoundary();
+ for (auto && ghost_type : ghost_types) {
+ boundary_fem.initShapeFunctions(ghost_type);
}
- Mesh & mesh = this->model.getMesh();
- UInt spatial_dimension = this->model.getSpatialDimension();
+ auto & mesh = this->model.getMesh();
+ auto spatial_dimension = this->model.getSpatialDimension();
this->slave_elements.initialize(mesh,
_spatial_dimension = spatial_dimension - 1);
MeshUtils::buildNode2Elements(mesh, this->node_to_elements,
spatial_dimension - 1);
this->registerDumper<DumperText>("text_all", id, true);
this->addDumpFilteredMesh(mesh, slave_elements, slaves.getArray(),
spatial_dimension - 1, _not_ghost, _ek_regular);
// parallelisation
this->synch_registry = std::make_unique<SynchronizerRegistry>();
this->synch_registry->registerDataAccessor(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NTNBaseContact::~NTNBaseContact() = default;
/* -------------------------------------------------------------------------- */
void NTNBaseContact::initParallel() {
AKANTU_DEBUG_IN();
this->synchronizer = std::make_unique<ElementSynchronizer>(
this->model.getMesh().getElementSynchronizer());
this->synchronizer->filterScheme([&](auto && element) {
// loop over all nodes of this element
Vector<UInt> conn = const_cast<const Mesh &>(this->model.getMesh())
.getConnectivity(element);
for (auto & node : conn) {
// if one nodes is in this contact, we need this element
if (this->getNodeIndex(node) >= 0) {
return true;
}
}
return false;
});
this->synch_registry->registerSynchronizer(*(this->synchronizer),
SynchronizationTag::_cf_nodal);
this->synch_registry->registerSynchronizer(*(this->synchronizer),
SynchronizationTag::_cf_incr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::findBoundaryElements(
const Array<UInt> & interface_nodes, ElementTypeMapArray<UInt> & elements) {
AKANTU_DEBUG_IN();
// add connected boundary elements that have all nodes on this contact
for (const auto & node : interface_nodes) {
for (const auto & element : this->node_to_elements.getRow(node)) {
Vector<UInt> conn = const_cast<const Mesh &>(this->model.getMesh())
.getConnectivity(element);
auto nb_nodes = conn.size();
decltype(nb_nodes) nb_found_nodes = 0;
for (auto & nn : conn) {
if (interface_nodes.find(nn) != UInt(-1)) {
nb_found_nodes++;
} else {
break;
}
}
// this is an element between all contact nodes
// and is not already in the elements
if ((nb_found_nodes == nb_nodes) &&
(elements(element.type, element.ghost_type).find(element.element) ==
UInt(-1))) {
elements(element.type, element.ghost_type).push_back(element.element);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::addSplitNode(UInt node, UInt) {
AKANTU_DEBUG_IN();
UInt dim = this->model.getSpatialDimension();
// add to node arrays
this->slaves.push_back(node);
// set contact as false
this->is_in_contact.push_back(false);
// before initializing
// set contact pressure, normal, lumped_boundary to Nan
this->contact_pressure.push_back(std::numeric_limits<Real>::quiet_NaN());
this->impedance.push_back(std::numeric_limits<Real>::quiet_NaN());
this->lumped_boundary_slaves.push_back(
std::numeric_limits<Real>::quiet_NaN());
Vector<Real> nan_normal(dim, std::numeric_limits<Real>::quiet_NaN());
this->normals.push_back(nan_normal);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::registerSynchronizedArray(SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->slaves.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::dumpRestart(const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->slaves.dumpRestartFile(file_name);
this->normals.dumpRestartFile(file_name);
this->is_in_contact.dumpRestartFile(file_name);
this->contact_pressure.dumpRestartFile(file_name);
this->lumped_boundary_slaves.dumpRestartFile(file_name);
this->impedance.dumpRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::readRestart(const std::string & file_name) {
AKANTU_DEBUG_IN();
this->slaves.readRestartFile(file_name);
this->normals.readRestartFile(file_name);
this->is_in_contact.readRestartFile(file_name);
this->contact_pressure.readRestartFile(file_name);
this->lumped_boundary_slaves.readRestartFile(file_name);
this->impedance.readRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt NTNBaseContact::getNbNodesInContact() const {
AKANTU_DEBUG_IN();
UInt nb_contact = 0;
UInt nb_nodes = this->getNbContactNodes();
const Mesh & mesh = this->model.getMesh();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(this->slaves(n));
bool is_pbc_slave_node = mesh.isPeriodicSlave(this->slaves(n));
if (is_local_node && !is_pbc_slave_node && this->is_in_contact(n)) {
nb_contact++;
}
}
mesh.getCommunicator().allReduce(nb_contact, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return nb_contact;
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::updateInternalData() {
AKANTU_DEBUG_IN();
updateNormals();
updateLumpedBoundary();
updateImpedance();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::updateLumpedBoundary() {
AKANTU_DEBUG_IN();
this->internalUpdateLumpedBoundary(this->slaves.getArray(),
this->slave_elements,
this->lumped_boundary_slaves);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::internalUpdateLumpedBoundary(
const Array<UInt> & nodes, const ElementTypeMapArray<UInt> & elements,
SynchronizedArray<Real> & boundary) {
AKANTU_DEBUG_IN();
// set all values in lumped_boundary to zero
- boundary.clear();
+ boundary.zero();
UInt dim = this->model.getSpatialDimension();
// UInt nb_contact_nodes = getNbContactNodes();
const FEEngine & boundary_fem = this->model.getFEEngineBoundary();
const Mesh & mesh = this->model.getMesh();
for (auto ghost_type : ghost_types) {
for (auto & type : mesh.elementTypes(dim - 1, ghost_type)) {
UInt nb_elements = mesh.getNbElement(type, ghost_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
// get shapes and compute integral
const Array<Real> & shapes = boundary_fem.getShapes(type, ghost_type);
Array<Real> area(nb_elements, nb_nodes_per_element);
boundary_fem.integrate(shapes, area, nb_nodes_per_element, type,
ghost_type);
if (this->contact_surfaces.size() == 0) {
AKANTU_DEBUG_WARNING(
"No surfaces in ntn base contact."
<< " You have to define the lumped boundary by yourself.");
}
Array<UInt>::const_iterator<UInt> elem_it =
(elements)(type, ghost_type).begin();
Array<UInt>::const_iterator<UInt> elem_it_end =
(elements)(type, ghost_type).end();
// loop over contact nodes
for (; elem_it != elem_it_end; ++elem_it) {
for (UInt q = 0; q < nb_nodes_per_element; ++q) {
UInt node = connectivity(*elem_it, q);
UInt node_index = nodes.find(node);
AKANTU_DEBUG_ASSERT(node_index != UInt(-1), "Could not find node "
<< node
<< " in the array!");
Real area_to_add = area(*elem_it, q);
boundary(node_index) += area_to_add;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::computeAcceleration(Array<Real> & acceleration) const {
auto && dof_manager =
dynamic_cast<DOFManagerDefault &>(model.getDOFManager());
const auto & b = dof_manager.getResidual();
acceleration.resize(b.size());
const auto & blocked_dofs = dof_manager.getGlobalBlockedDOFs();
const auto & A = dof_manager.getLumpedMatrix("M");
Array<bool> blocked_dofs_bool(blocked_dofs.size());
for (auto && data : zip(blocked_dofs, blocked_dofs_bool)) {
std::get<1>(data) = std::get<0>(data);
}
// pre-compute the acceleration
// (not increment acceleration, because residual is still Kf)
NonLinearSolverLumped::solveLumped(A, acceleration, b, this->model.getF_M2A(),
blocked_dofs_bool);
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::computeContactPressure() {
AKANTU_DEBUG_IN();
UInt dim = this->model.getSpatialDimension();
Real delta_t = this->model.getTimeStep();
UInt nb_contact_nodes = getNbContactNodes();
AKANTU_DEBUG_ASSERT(delta_t > 0.,
"Cannot compute contact pressure if no time step is set");
// synchronize data
this->synch_registry->synchronize(SynchronizationTag::_cf_nodal);
Array<Real> acceleration(0, dim);
this->computeAcceleration(acceleration);
// compute relative normal fields of displacement, velocity and acceleration
Array<Real> r_disp(0, 1);
Array<Real> r_velo(0, 1);
Array<Real> r_acce(0, 1);
Array<Real> r_old_acce(0, 1);
computeNormalGap(r_disp);
// computeRelativeNormalField(this->model.getCurrentPosition(), r_disp);
computeRelativeNormalField(this->model.getVelocity(), r_velo);
computeRelativeNormalField(acceleration, r_acce);
computeRelativeNormalField(this->model.getAcceleration(), r_old_acce);
AKANTU_DEBUG_ASSERT(r_disp.size() == nb_contact_nodes,
"computeRelativeNormalField does not give back arrays "
<< "size == nb_contact_nodes. nb_contact_nodes = "
<< nb_contact_nodes
<< " | array size = " << r_disp.size());
// compute gap array for all nodes
Array<Real> gap(nb_contact_nodes, 1);
Real * gap_p = gap.storage();
Real * r_disp_p = r_disp.storage();
Real * r_velo_p = r_velo.storage();
Real * r_acce_p = r_acce.storage();
Real * r_old_acce_p = r_old_acce.storage();
for (UInt i = 0; i < nb_contact_nodes; ++i) {
*gap_p = *r_disp_p + delta_t * *r_velo_p + delta_t * delta_t * *r_acce_p -
0.5 * delta_t * delta_t * *r_old_acce_p;
// increment pointers
gap_p++;
r_disp_p++;
r_velo_p++;
r_acce_p++;
r_old_acce_p++;
}
// check if gap is negative -> is in contact
for (UInt n = 0; n < nb_contact_nodes; ++n) {
if (gap(n) <= 0.) {
for (UInt d = 0; d < dim; ++d) {
this->contact_pressure(n, d) =
this->impedance(n) * gap(n) / (2 * delta_t) * this->normals(n, d);
}
this->is_in_contact(n) = true;
} else {
for (UInt d = 0; d < dim; ++d)
this->contact_pressure(n, d) = 0.;
this->is_in_contact(n) = false;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::applyContactPressure() {
AKANTU_DEBUG_IN();
UInt nb_contact_nodes = getNbContactNodes();
UInt dim = this->model.getSpatialDimension();
Array<Real> & residual = this->model.getInternalForce();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
UInt slave = this->slaves(n);
for (UInt d = 0; d < dim; ++d) {
// residual(master,d) += this->lumped_boundary(n,0) *
// this->contact_pressure(n,d);
residual(slave, d) -=
this->lumped_boundary_slaves(n) * this->contact_pressure(n, d);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Int NTNBaseContact::getNodeIndex(UInt node) const {
return this->slaves.find(node);
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNBaseContact [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + slaves : " << std::endl;
this->slaves.printself(stream, indent + 2);
stream << space << " + normals : " << std::endl;
this->normals.printself(stream, indent + 2);
stream << space << " + contact_pressure : " << std::endl;
this->contact_pressure.printself(stream, indent + 2);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::syncArrays(SyncChoice sync_choice) {
AKANTU_DEBUG_IN();
this->slaves.syncElements(sync_choice);
this->normals.syncElements(sync_choice);
this->is_in_contact.syncElements(sync_choice);
this->contact_pressure.syncElements(sync_choice);
this->lumped_boundary_slaves.syncElements(sync_choice);
this->impedance.syncElements(sync_choice);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
const Array<UInt> & nodal_filter = this->slaves.getArray();
#define ADD_FIELD(field_id, field, type) \
internalAddDumpFieldToDumper( \
dumper_name, field_id, \
std::make_unique< \
dumpers::NodalField<type, true, Array<type>, Array<UInt>>>( \
field, 0, 0, &nodal_filter))
if (field_id == "displacement") {
ADD_FIELD(field_id, this->model.getDisplacement(), Real);
} else if (field_id == "mass") {
ADD_FIELD(field_id, this->model.getMass(), Real);
} else if (field_id == "velocity") {
ADD_FIELD(field_id, this->model.getVelocity(), Real);
} else if (field_id == "acceleration") {
ADD_FIELD(field_id, this->model.getAcceleration(), Real);
} else if (field_id == "external_force") {
ADD_FIELD(field_id, this->model.getExternalForce(), Real);
} else if (field_id == "internal_force") {
ADD_FIELD(field_id, this->model.getInternalForce(), Real);
} else if (field_id == "blocked_dofs") {
ADD_FIELD(field_id, this->model.getBlockedDOFs(), bool);
} else if (field_id == "increment") {
ADD_FIELD(field_id, this->model.getIncrement(), Real);
} else if (field_id == "normal") {
internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->normals.getArray()));
} else if (field_id == "contact_pressure") {
internalAddDumpFieldToDumper(dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->contact_pressure.getArray()));
} else if (field_id == "is_in_contact") {
internalAddDumpFieldToDumper(dumper_name, field_id,
std::make_unique<dumpers::NodalField<bool>>(
this->is_in_contact.getArray()));
} else if (field_id == "lumped_boundary_slave") {
internalAddDumpFieldToDumper(dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->lumped_boundary_slaves.getArray()));
} else if (field_id == "impedance") {
internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->impedance.getArray()));
} else {
std::cerr << "Could not add field '" << field_id
<< "' to the dumper. Just ignored it." << std::endl;
}
#undef ADD_FIELD
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.hh
index 4341cf3a2..8c9c3cf9d 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.hh
@@ -1,251 +1,251 @@
/**
* @file ntn_base_contact.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief base contact for ntn and ntrf contact
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_BASE_CONTACT_HH__
-#define __AST_NTN_BASE_CONTACT_HH__
+#ifndef AST_NTN_BASE_CONTACT_HH_
+#define AST_NTN_BASE_CONTACT_HH_
/* -------------------------------------------------------------------------- */
// akantu
#include "aka_csr.hh"
#include "solid_mechanics_model.hh"
// simtools
#include "synchronized_array.hh"
namespace akantu {
class NTNBaseContact;
/* -------------------------------------------------------------------------- */
// class NTNContactSynchElementFilter : public SynchElementFilter {
// public:
// // constructor
// NTNContactSynchElementFilter(NTNBaseContact & contact);
// // answer to: do we need this element ?
// virtual bool operator()(const Element & e);
// private:
// const NTNBaseContact & contact;
// const ElementTypeMapArray<UInt> & connectivity;
// };
/* -------------------------------------------------------------------------- */
class NTNBaseContact : protected Memory,
public DataAccessor<Element>,
public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNBaseContact(SolidMechanicsModel & model, const ID & id = "contact",
const MemoryID & memory_id = 0);
virtual ~NTNBaseContact();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initializes ntn contact parallel
virtual void initParallel();
/// add split node
virtual void addSplitNode(UInt node, UInt = 0);
/// update normals, lumped boundary, and impedance
virtual void updateInternalData();
/// update (compute the normals)
virtual void updateNormals() = 0;
/// update the lumped boundary B matrix
virtual void updateLumpedBoundary();
/// update the impedance matrix
virtual void updateImpedance() = 0;
/// compute the normal contact force
virtual void computeContactPressure();
/// impose the normal contact force
virtual void applyContactPressure() ;
/// register synchronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// compute the normal gap
virtual void computeNormalGap(Array<Real> & gap) const = 0;
/// compute relative normal field (only value that has to be multiplied with
/// the normal)
/// relative to master nodes
virtual void
computeRelativeNormalField(const Array<Real> & field,
Array<Real> & rel_normal_field) const = 0;
/// compute relative tangential field (complet array)
/// relative to master nodes
virtual void
computeRelativeTangentialField(const Array<Real> & field,
Array<Real> & rel_tang_field) const = 0;
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// computes the acceleration
void computeAcceleration(Array<Real> & acceleration) const;
protected:
/// updateLumpedBoundary
virtual void
internalUpdateLumpedBoundary(const Array<UInt> & nodes,
const ElementTypeMapArray<UInt> & elements,
SynchronizedArray<Real> & boundary);
// to find the slave_elements or master_elements
virtual void findBoundaryElements(const Array<UInt> & interface_nodes,
ElementTypeMapArray<UInt> & elements);
/// synchronize arrays
virtual void syncArrays(SyncChoice sync_choice);
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Model, model, SolidMechanicsModel &)
AKANTU_GET_MACRO(Slaves, slaves, const SynchronizedArray<UInt> &)
AKANTU_GET_MACRO(Normals, normals, const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(ContactPressure, contact_pressure,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(LumpedBoundarySlaves, lumped_boundary_slaves,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(Impedance, impedance, const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(IsInContact, is_in_contact, const SynchronizedArray<bool> &)
AKANTU_GET_MACRO(SlaveElements, slave_elements,
const ElementTypeMapArray<UInt> &)
AKANTU_GET_MACRO(SynchronizerRegistry, *synch_registry,
SynchronizerRegistry &)
/// get number of nodes that are in contact (globally, on all procs together)
/// is_in_contact = true
virtual UInt getNbNodesInContact() const;
/// get index of node in either slaves or masters array
/// if node is in neither of them, return -1
virtual Int getNodeIndex(UInt node) const;
/// get number of contact nodes: nodes in the system locally (on this proc)
/// is_in_contact = true and false, because just in the system
virtual UInt getNbContactNodes() const { return this->slaves.size(); }
bool isNTNContact() const { return this->is_ntn_contact; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
typedef std::set<const ElementGroup *> SurfacePtrSet;
SolidMechanicsModel & model;
/// array of slave nodes
SynchronizedArray<UInt> slaves;
/// array of normals
SynchronizedArray<Real> normals;
/// array indicating if nodes are in contact
SynchronizedArray<Real> contact_pressure;
/// array indicating if nodes are in contact
SynchronizedArray<bool> is_in_contact;
/// boundary matrix for slave nodes
SynchronizedArray<Real> lumped_boundary_slaves;
/// impedance matrix
SynchronizedArray<Real> impedance;
/// contact surface
SurfacePtrSet contact_surfaces;
/// element list for dump and lumped_boundary
ElementTypeMapArray<UInt> slave_elements;
CSR<Element> node_to_elements;
/// parallelisation
std::unique_ptr<SynchronizerRegistry> synch_registry;
std::unique_ptr<ElementSynchronizer> synchronizer;
bool is_ntn_contact{true};
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNBaseContact & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "ntn_base_contact_inline_impl.hh"
-#endif /* __AST_NTN_BASE_CONTACT_HH__ */
+#endif /* AST_NTN_BASE_CONTACT_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc
index e8f620915..efa895782 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc
@@ -1,380 +1,380 @@
/**
* @file ntn_base_friction.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief implementation of ntn base friction
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_friction.hh"
#include "dof_manager_default.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
#include "non_linear_solver_lumped.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
NTNBaseFriction::NTNBaseFriction(NTNBaseContact & contact, const ID & id,
const MemoryID & memory_id)
: Memory(id, memory_id), Parsable(ParserType::_friction, id), Dumpable(),
contact(contact),
is_sticking(0, 1, true, id + ":is_sticking", true, "is_sticking"),
frictional_strength(0, 1, 0., id + ":frictional_strength", 0.,
"frictional_strength"),
friction_traction(0, contact.getModel().getSpatialDimension(), 0.,
id + ":friction_traction", 0., "friction_traction"),
slip(0, 1, 0., id + ":slip", 0., "slip"),
cumulative_slip(0, 1, 0., id + ":cumulative_slip", 0., "cumulative_slip"),
slip_velocity(0, contact.getModel().getSpatialDimension(), 0.,
id + ":slip_velocity", 0., "slip_velocity") {
AKANTU_DEBUG_IN();
this->contact.registerSynchronizedArray(this->is_sticking);
this->contact.registerSynchronizedArray(this->frictional_strength);
this->contact.registerSynchronizedArray(this->friction_traction);
this->contact.registerSynchronizedArray(this->slip);
this->contact.registerSynchronizedArray(this->cumulative_slip);
this->contact.registerSynchronizedArray(this->slip_velocity);
this->registerExternalDumper(contact.getDumper().shared_from_this(),
contact.getDefaultDumperName(), true);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::updateSlip() {
AKANTU_DEBUG_IN();
SolidMechanicsModel & model = this->contact.getModel();
UInt dim = model.getSpatialDimension();
// synchronize increment
this->contact.getSynchronizerRegistry().synchronize(
SynchronizationTag::_cf_incr);
Array<Real> rel_tan_incr(0, dim);
this->contact.computeRelativeTangentialField(model.getIncrement(),
rel_tan_incr);
Array<Real>::const_iterator<Vector<Real>> it = rel_tan_incr.begin(dim);
UInt nb_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_nodes; ++n) {
if (this->is_sticking(n)) {
this->slip(n) = 0.;
} else {
const Vector<Real> & rti = it[n];
this->slip(n) += rti.norm();
this->cumulative_slip(n) += rti.norm();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::computeFrictionTraction() {
AKANTU_DEBUG_IN();
this->computeStickTraction();
this->computeFrictionalStrength();
SolidMechanicsModel & model = this->contact.getModel();
UInt dim = model.getSpatialDimension();
// get contact arrays
const SynchronizedArray<bool> & is_in_contact =
this->contact.getIsInContact();
Array<Real> & traction =
const_cast<Array<Real> &>(this->friction_traction.getArray());
Array<Real>::iterator<Vector<Real>> it_fric_trac = traction.begin(dim);
- this->is_sticking.clear(); // set to not sticking
+ this->is_sticking.zero(); // set to not sticking
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// node pair is in contact
if (is_in_contact(n)) {
Vector<Real> fric_trac = it_fric_trac[n];
// check if it is larger than frictional strength
Real abs_fric = fric_trac.norm();
if (abs_fric != 0.) {
Real alpha = this->frictional_strength(n) / abs_fric;
// larger -> sliding
if (alpha < 1.) {
fric_trac *= alpha;
} else
this->is_sticking(n) = true;
} else {
// frictional traction is already zero
this->is_sticking(n) = true;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::computeStickTraction() {
AKANTU_DEBUG_IN();
SolidMechanicsModel & model = this->contact.getModel();
UInt dim = model.getSpatialDimension();
Real delta_t = model.getTimeStep();
UInt nb_contact_nodes = this->contact.getNbContactNodes();
// get contact arrays
const SynchronizedArray<Real> & impedance = this->contact.getImpedance();
const SynchronizedArray<bool> & is_in_contact =
this->contact.getIsInContact();
Array<Real> acceleration(0, dim);
this->contact.computeAcceleration(acceleration);
// compute relative normal fields of velocity and acceleration
Array<Real> r_velo(0, dim);
Array<Real> r_acce(0, dim);
Array<Real> r_old_acce(0, dim);
this->contact.computeRelativeTangentialField(model.getVelocity(), r_velo);
this->contact.computeRelativeTangentialField(acceleration, r_acce);
this->contact.computeRelativeTangentialField(model.getAcceleration(),
r_old_acce);
AKANTU_DEBUG_ASSERT(r_velo.size() == nb_contact_nodes,
"computeRelativeNormalField does not give back arrays "
<< "size == nb_contact_nodes. nb_contact_nodes = "
<< nb_contact_nodes
<< " | array size = " << r_velo.size());
// compute tangential gap_dot array for all nodes
Array<Real> gap_dot(nb_contact_nodes, dim);
for (auto && data : zip(make_view(gap_dot), make_view(r_velo),
make_view(r_acce), make_view(r_old_acce))) {
auto & gap_dot = std::get<0>(data);
auto & r_velo = std::get<1>(data);
auto & r_acce = std::get<2>(data);
auto & r_old_acce = std::get<3>(data);
gap_dot = r_velo + delta_t * r_acce - 1. / 2. * delta_t * r_old_acce;
}
// compute friction traction to stop sliding
Array<Real> & traction =
const_cast<Array<Real> &>(this->friction_traction.getArray());
auto it_fric_trac = traction.begin(dim);
for (UInt n = 0; n < nb_contact_nodes; ++n) {
Vector<Real> fric_trac = it_fric_trac[n];
// node pair is NOT in contact
if (!is_in_contact(n)) {
- fric_trac.clear(); // set to zero
+ fric_trac.zero(); // set to zero
}
// node pair is in contact
else {
// compute friction traction
for (UInt d = 0; d < dim; ++d)
fric_trac(d) = impedance(n) * gap_dot(n, d) / 2.;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::applyFrictionTraction() {
AKANTU_DEBUG_IN();
SolidMechanicsModel & model = this->contact.getModel();
Array<Real> & residual = model.getInternalForce();
UInt dim = model.getSpatialDimension();
const SynchronizedArray<UInt> & slaves = this->contact.getSlaves();
const SynchronizedArray<Real> & lumped_boundary_slaves =
this->contact.getLumpedBoundarySlaves();
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
UInt slave = slaves(n);
for (UInt d = 0; d < dim; ++d) {
residual(slave, d) -=
lumped_boundary_slaves(n) * this->friction_traction(n, d);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::registerSynchronizedArray(SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->frictional_strength.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::dumpRestart(const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->is_sticking.dumpRestartFile(file_name);
this->frictional_strength.dumpRestartFile(file_name);
this->friction_traction.dumpRestartFile(file_name);
this->slip.dumpRestartFile(file_name);
this->cumulative_slip.dumpRestartFile(file_name);
this->slip_velocity.dumpRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::readRestart(const std::string & file_name) {
AKANTU_DEBUG_IN();
this->is_sticking.readRestartFile(file_name);
this->frictional_strength.readRestartFile(file_name);
this->friction_traction.readRestartFile(file_name);
this->cumulative_slip.readRestartFile(file_name);
this->slip_velocity.readRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::setParam(const std::string & name, UInt node,
Real value) {
AKANTU_DEBUG_IN();
SynchronizedArray<Real> & array =
this->get(name).get<SynchronizedArray<Real>>();
Int index = this->contact.getNodeIndex(node);
if (index < 0) {
AKANTU_DEBUG_WARNING("Node "
<< node << " is not a contact node. "
<< "Therefore, cannot set interface parameter!!");
} else {
array(index) = value; // put value
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt NTNBaseFriction::getNbStickingNodes() const {
AKANTU_DEBUG_IN();
UInt nb_stick = 0;
UInt nb_nodes = this->contact.getNbContactNodes();
const SynchronizedArray<UInt> & nodes = this->contact.getSlaves();
const SynchronizedArray<bool> & is_in_contact =
this->contact.getIsInContact();
const Mesh & mesh = this->contact.getModel().getMesh();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(nodes(n));
bool is_pbc_slave_node = mesh.isPeriodicSlave(nodes(n));
if (is_local_node && !is_pbc_slave_node && is_in_contact(n) &&
this->is_sticking(n)) {
nb_stick++;
}
}
mesh.getCommunicator().allReduce(nb_stick, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return nb_stick;
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNBaseFriction [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
// const SynchronizedArray<UInt> * nodal_filter =
// &(this->contact.getSlaves());
if (field_id == "is_sticking") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<bool>>(
this->is_sticking.getArray()));
} else if (field_id == "frictional_strength") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->frictional_strength.getArray()));
} else if (field_id == "friction_traction") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->friction_traction.getArray()));
} else if (field_id == "slip") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->slip.getArray()));
} else if (field_id == "cumulative_slip") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->cumulative_slip.getArray()));
} else if (field_id == "slip_velocity") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->slip_velocity.getArray()));
} else {
this->contact.addDumpFieldToDumper(dumper_name, field_id);
}
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.hh
index 051659a48..538d02f65 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.hh
@@ -1,177 +1,177 @@
/**
* @file ntn_base_friction.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief base class for ntn and ntrf friction
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_BASE_FRICTION_HH__
-#define __AST_NTN_BASE_FRICTION_HH__
+#ifndef AST_NTN_BASE_FRICTION_HH_
+#define AST_NTN_BASE_FRICTION_HH_
/* -------------------------------------------------------------------------- */
// akantu
#include "parsable.hh"
// simtools
#include "ntn_base_contact.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<akantu::SynchronizedArray<Real>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Real r = in_param;
param.setAndChangeDefault(r);
}
/* -------------------------------------------------------------------------- */
template <>
template <>
inline void ParameterTyped<akantu::SynchronizedArray<Real>>::setTyped<Real>(
const Real & value) {
param.setAndChangeDefault(value);
}
/* -------------------------------------------------------------------------- */
class NTNBaseFriction : protected Memory, public Parsable, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNBaseFriction(NTNBaseContact & contact, const ID & id = "friction",
const MemoryID & memory_id = 0);
virtual ~NTNBaseFriction() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// compute friction traction
virtual void computeFrictionTraction();
/// compute stick traction (friction traction needed to stick the nodes)
virtual void computeStickTraction();
/// apply the friction force
virtual void applyFrictionTraction();
/// compute slip
virtual void updateSlip();
/// register Syncronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// set to steady state
virtual void setToSteadyState() { AKANTU_TO_IMPLEMENT(); };
/// get the number of sticking nodes (in parallel)
/// a node that is not in contact does not count as sticking
virtual UInt getNbStickingNodes() const;
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength() = 0;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Contact, contact, const NTNBaseContact &)
AKANTU_GET_MACRO(IsSticking, is_sticking, const SynchronizedArray<bool> &)
AKANTU_GET_MACRO(FrictionalStrength, frictional_strength,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(FrictionTraction, friction_traction,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(Slip, slip, const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(CumulativeSlip, cumulative_slip,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(SlipVelocity, slip_velocity, const SynchronizedArray<Real> &)
/// set parameter of a given node
/// (if you need to set to all: used the setMixed function of the Parsable).
virtual void setParam(const std::string & name, UInt node, Real value);
// replaced by the setMixed of the Parsable
// virtual void setParam(const std::string & param, Real value) {
// AKANTU_ERROR("Friction does not know the following parameter: " <<
// param);
// };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
NTNBaseContact & contact;
// if node is sticking
SynchronizedArray<bool> is_sticking;
// frictional strength
SynchronizedArray<Real> frictional_strength;
// friction force
SynchronizedArray<Real> friction_traction;
// slip
SynchronizedArray<Real> slip;
SynchronizedArray<Real> cumulative_slip;
// slip velocity (tangential vector)
SynchronizedArray<Real> slip_velocity;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_base_friction_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNBaseFriction & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AST_NTN_BASE_FRICTION_HH__ */
+#endif /* AST_NTN_BASE_FRICTION_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc
index 5f647ce23..17a44cac8 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc
@@ -1,555 +1,555 @@
/**
* @file ntn_contact.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief implementation of ntn_contact
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_contact.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
NTNContact::NTNContact(SolidMechanicsModel & model, const ID & id,
const MemoryID & memory_id)
: NTNBaseContact(model, id, memory_id),
masters(0, 1, 0, id + ":masters", std::numeric_limits<UInt>::quiet_NaN(),
"masters"),
lumped_boundary_masters(0, 1, 0, id + ":lumped_boundary_masters",
std::numeric_limits<Real>::quiet_NaN(),
"lumped_boundary_masters"),
master_elements("master_elements", id, memory_id) {
AKANTU_DEBUG_IN();
const Mesh & mesh = this->model.getMesh();
UInt spatial_dimension = this->model.getSpatialDimension();
this->master_elements.initialize(mesh, _nb_component = 1,
_spatial_dimension = spatial_dimension - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::pairInterfaceNodes(const ElementGroup & slave_boundary,
const ElementGroup & master_boundary,
UInt surface_normal_dir, const Mesh & mesh,
Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
pairs.resize(0);
AKANTU_DEBUG_ASSERT(pairs.getNbComponent() == 2,
"Array of node pairs should have nb_component = 2,"
<< " but has nb_component = "
<< pairs.getNbComponent());
UInt dim = mesh.getSpatialDimension();
AKANTU_DEBUG_ASSERT(surface_normal_dir < dim,
"Mesh is of " << dim << " dimensions"
<< " and cannot have direction "
<< surface_normal_dir
<< " for surface normal");
// offset for projection computation
Vector<UInt> offset(dim - 1);
for (UInt i = 0, j = 0; i < dim; ++i) {
if (surface_normal_dir != i) {
offset(j) = i;
++j;
}
}
// find projected node coordinates
const Array<Real> & coordinates = mesh.getNodes();
// find slave nodes
Array<Real> proj_slave_coord(slave_boundary.getNbNodes(), dim - 1, 0.);
Array<UInt> slave_nodes(slave_boundary.getNbNodes());
UInt n(0);
for (auto && slave_node : slave_boundary.getNodeGroup().getNodes()) {
for (UInt d = 0; d < dim - 1; ++d) {
proj_slave_coord(n, d) = coordinates(slave_node, offset[d]);
slave_nodes(n) = slave_node;
}
++n;
}
// find master nodes
Array<Real> proj_master_coord(master_boundary.getNbNodes(), dim - 1, 0.);
Array<UInt> master_nodes(master_boundary.getNbNodes());
n = 0;
for (auto && master_node : master_boundary.getNodeGroup().getNodes()) {
for (UInt d = 0; d < dim - 1; ++d) {
proj_master_coord(n, d) = coordinates(master_node, offset[d]);
master_nodes(n) = master_node;
}
++n;
}
// find minimum distance between slave nodes to define tolerance
Real min_dist = std::numeric_limits<Real>::max();
for (UInt i = 0; i < proj_slave_coord.size(); ++i) {
for (UInt j = i + 1; j < proj_slave_coord.size(); ++j) {
Real dist = 0.;
for (UInt d = 0; d < dim - 1; ++d) {
dist += (proj_slave_coord(i, d) - proj_slave_coord(j, d)) *
(proj_slave_coord(i, d) - proj_slave_coord(j, d));
}
if (dist < min_dist) {
min_dist = dist;
}
}
}
min_dist = std::sqrt(min_dist);
Real local_tol = 0.1 * min_dist;
// find master slave node pairs
for (UInt i = 0; i < proj_slave_coord.size(); ++i) {
for (UInt j = 0; j < proj_master_coord.size(); ++j) {
Real dist = 0.;
for (UInt d = 0; d < dim - 1; ++d) {
dist += (proj_slave_coord(i, d) - proj_master_coord(j, d)) *
(proj_slave_coord(i, d) - proj_master_coord(j, d));
}
dist = std::sqrt(dist);
if (dist < local_tol) { // it is a pair
Vector<UInt> pair(2);
pair[0] = slave_nodes(i);
pair[1] = master_nodes(j);
pairs.push_back(pair);
continue; // found master do not need to search further for this slave
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::addSurfacePair(const ID & slave, const ID & master,
UInt surface_normal_dir) {
AKANTU_DEBUG_IN();
const Mesh & mesh = this->model.getMesh();
const ElementGroup & slave_boundary = mesh.getElementGroup(slave);
const ElementGroup & master_boundary = mesh.getElementGroup(master);
this->contact_surfaces.insert(&slave_boundary);
this->contact_surfaces.insert(&master_boundary);
Array<UInt> pairs(0, 2);
NTNContact::pairInterfaceNodes(slave_boundary, master_boundary,
surface_normal_dir, this->model.getMesh(),
pairs);
// eliminate pairs which contain a pbc slave node
Array<UInt> pairs_no_PBC_slaves(0, 2);
Array<UInt>::const_vector_iterator it = pairs.begin(2);
Array<UInt>::const_vector_iterator end = pairs.end(2);
for (; it != end; ++it) {
const Vector<UInt> & pair = *it;
if (not mesh.isPeriodicSlave(pair(0)) and
not mesh.isPeriodicSlave(pair(1))) {
pairs_no_PBC_slaves.push_back(pair);
}
}
this->addNodePairs(pairs_no_PBC_slaves);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::addNodePairs(const Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(pairs.getNbComponent() == 2,
"Array of node pairs should have nb_component = 2,"
<< " but has nb_component = "
<< pairs.getNbComponent());
UInt nb_pairs = pairs.size();
for (UInt n = 0; n < nb_pairs; ++n) {
this->addSplitNode(pairs(n, 0), pairs(n, 1));
}
// synchronize with depending nodes
findBoundaryElements(this->slaves.getArray(), this->slave_elements);
findBoundaryElements(this->masters.getArray(), this->master_elements);
updateInternalData();
syncArrays(_added);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::getNodePairs(Array<UInt> & pairs) const {
AKANTU_DEBUG_IN();
pairs.resize(0);
AKANTU_DEBUG_ASSERT(pairs.getNbComponent() == 2,
"Array of node pairs should have nb_component = 2,"
<< " but has nb_component = "
<< pairs.getNbComponent());
UInt nb_pairs = this->getNbContactNodes();
for (UInt n = 0; n < nb_pairs; ++n) {
Vector<UInt> pair{this->slaves(n), this->masters(n)};
pairs.push_back(pair);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::addSplitNode(UInt slave, UInt master) {
AKANTU_DEBUG_IN();
NTNBaseContact::addSplitNode(slave);
this->masters.push_back(master);
this->lumped_boundary_masters.push_back(
std::numeric_limits<Real>::quiet_NaN());
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/*
This function only works for surface elements with one quad point. For
surface elements with more quad points, it computes still, but the result
might not be what you are looking for.
*/
void NTNContact::updateNormals() {
AKANTU_DEBUG_IN();
// set normals to zero
- this->normals.clear();
+ this->normals.zero();
// contact information
UInt dim = this->model.getSpatialDimension();
UInt nb_contact_nodes = this->getNbContactNodes();
this->synch_registry->synchronize(
SynchronizationTag::_cf_nodal); // synchronize current pos
const Array<Real> & cur_pos = this->model.getCurrentPosition();
FEEngine & boundary_fem = this->model.getFEEngineBoundary();
const Mesh & mesh = this->model.getMesh();
for (auto ghost_type : ghost_types) {
for (auto & type : mesh.elementTypes(dim - 1, ghost_type)) {
// compute the normals
Array<Real> quad_normals(0, dim);
boundary_fem.computeNormalsOnIntegrationPoints(cur_pos, quad_normals,
type, ghost_type);
UInt nb_quad_points =
boundary_fem.getNbIntegrationPoints(type, ghost_type);
// new version: compute normals only based on master elements (and not all
// boundary elements)
// -------------------------------------------------------------------------------------
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
// loop over contact nodes
for (auto & element : (this->master_elements)(type, ghost_type)) {
for (UInt q = 0; q < nb_nodes_per_element; ++q) {
UInt node = connectivity(element, q);
UInt node_index = this->masters.find(node);
AKANTU_DEBUG_ASSERT(node_index != UInt(-1), "Could not find node "
<< node
<< " in the array!");
for (UInt q = 0; q < nb_quad_points; ++q) {
// add quad normal to master normal
for (UInt d = 0; d < dim; ++d) {
this->normals(node_index, d) +=
quad_normals(element * nb_quad_points + q, d);
}
}
}
}
}
}
Real * master_normals = this->normals.storage();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
if (dim == 2)
Math::normalize2(&(master_normals[n * dim]));
else if (dim == 3)
Math::normalize3(&(master_normals[n * dim]));
}
// // normalize normals
// auto nit = this->normals.begin();
// auto nend = this->normals.end();
// for (; nit != nend; ++nit) {
// nit->normalize();
// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::dumpRestart(const std::string & file_name) const {
AKANTU_DEBUG_IN();
NTNBaseContact::dumpRestart(file_name);
this->masters.dumpRestartFile(file_name);
this->lumped_boundary_masters.dumpRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::readRestart(const std::string & file_name) {
AKANTU_DEBUG_IN();
NTNBaseContact::readRestart(file_name);
this->masters.readRestartFile(file_name);
this->lumped_boundary_masters.readRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::updateImpedance() {
AKANTU_DEBUG_IN();
UInt nb_contact_nodes = getNbContactNodes();
Real delta_t = this->model.getTimeStep();
AKANTU_DEBUG_ASSERT(delta_t != NAN,
"Time step is NAN. Have you set it already?");
const Array<Real> & mass = this->model.getMass();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
UInt master = this->masters(n);
UInt slave = this->slaves(n);
Real imp = (this->lumped_boundary_masters(n) / mass(master)) +
(this->lumped_boundary_slaves(n) / mass(slave));
imp = 2 / delta_t / imp;
this->impedance(n) = imp;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::updateLumpedBoundary() {
AKANTU_DEBUG_IN();
internalUpdateLumpedBoundary(this->slaves.getArray(), this->slave_elements,
this->lumped_boundary_slaves);
internalUpdateLumpedBoundary(this->masters.getArray(), this->master_elements,
this->lumped_boundary_masters);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::applyContactPressure() {
AKANTU_DEBUG_IN();
UInt nb_ntn_pairs = getNbContactNodes();
UInt dim = this->model.getSpatialDimension();
Array<Real> & residual = this->model.getInternalForce();
for (UInt n = 0; n < nb_ntn_pairs; ++n) {
UInt master = this->masters(n);
UInt slave = this->slaves(n);
for (UInt d = 0; d < dim; ++d) {
residual(master, d) +=
this->lumped_boundary_masters(n) * this->contact_pressure(n, d);
residual(slave, d) -=
this->lumped_boundary_slaves(n) * this->contact_pressure(n, d);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::computeRelativeTangentialField(
const Array<Real> & field, Array<Real> & rel_tang_field) const {
AKANTU_DEBUG_IN();
// resize arrays to zero
rel_tang_field.resize(0);
UInt dim = this->model.getSpatialDimension();
auto it_field = field.begin(dim);
auto it_normal = this->normals.getArray().begin(dim);
Vector<Real> rfv(dim);
Vector<Real> np_rfv(dim);
UInt nb_contact_nodes = this->slaves.size();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// nodes
UInt slave = this->slaves(n);
UInt master = this->masters(n);
// relative field vector (slave - master)
rfv = Vector<Real>(it_field[slave]);
rfv -= Vector<Real>(it_field[master]);
// normal projection of relative field
const Vector<Real> normal_v = it_normal[n];
np_rfv = normal_v;
np_rfv *= rfv.dot(normal_v);
// subract normal projection from relative field to get the tangential
// projection
rfv -= np_rfv;
rel_tang_field.push_back(rfv);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::computeRelativeNormalField(
const Array<Real> & field, Array<Real> & rel_normal_field) const {
AKANTU_DEBUG_IN();
// resize arrays to zero
rel_normal_field.resize(0);
UInt dim = this->model.getSpatialDimension();
// Real * field_p = field.storage();
// Real * normals_p = this->normals.storage();
Array<Real>::const_iterator<Vector<Real>> it_field = field.begin(dim);
Array<Real>::const_iterator<Vector<Real>> it_normal =
this->normals.getArray().begin(dim);
Vector<Real> rfv(dim);
UInt nb_contact_nodes = this->getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// nodes
UInt slave = this->slaves(n);
UInt master = this->masters(n);
// relative field vector (slave - master)
rfv = Vector<Real>(it_field[slave]);
rfv -= Vector<Real>(it_field[master]);
// length of normal projection of relative field
const Vector<Real> normal_v = it_normal[n];
rel_normal_field.push_back(rfv.dot(normal_v));
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Int NTNContact::getNodeIndex(UInt node) const {
AKANTU_DEBUG_IN();
Int slave_i = NTNBaseContact::getNodeIndex(node);
Int master_i = this->masters.find(node);
AKANTU_DEBUG_OUT();
return std::max(slave_i, master_i);
}
/* -------------------------------------------------------------------------- */
void NTNContact::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNContact [" << std::endl;
NTNBaseContact::printself(stream, indent);
stream << space << " + masters : " << std::endl;
this->masters.printself(stream, indent + 2);
stream << space << " + lumped_boundary_mastres : " << std::endl;
this->lumped_boundary_masters.printself(stream, indent + 2);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::syncArrays(SyncChoice sync_choice) {
AKANTU_DEBUG_IN();
NTNBaseContact::syncArrays(sync_choice);
this->masters.syncElements(sync_choice);
this->lumped_boundary_masters.syncElements(sync_choice);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_IN();
/*
#ifdef AKANTU_USE_IOHELPER
const Array<UInt> & nodal_filter = this->slaves.getArray();
#define ADD_FIELD(field_id, field, type) \
internalAddDumpFieldToDumper(dumper_name, \
field_id, \
new DumperIOHelper::NodalField< type, true, \
Array<type>, \
Array<UInt> >(field, 0, 0, &nodal_filter))
*/
if (field_id == "lumped_boundary_master") {
internalAddDumpFieldToDumper(dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->lumped_boundary_masters.getArray()));
} else {
NTNBaseContact::addDumpFieldToDumper(dumper_name, field_id);
}
/*
#undef ADD_FIELD
#endif
*/
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.hh
index b5ea087cd..eb445dc20 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.hh
@@ -1,166 +1,166 @@
/**
* @file ntn_contact.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Dec 02 2014
* @date last modification: Fri Feb 23 2018
*
* @brief contact for node to node discretization
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_CONTACT_HH__
-#define __AST_NTN_CONTACT_HH__
+#ifndef AST_NTN_CONTACT_HH_
+#define AST_NTN_CONTACT_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_contact.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTNContact : public NTNBaseContact {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNContact(SolidMechanicsModel & model, const ID & id = "contact",
const MemoryID & memory_id = 0);
virtual ~NTNContact(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// add surface pair and pair nodes according to the surface normal
void addSurfacePair(const ID & slave, const ID & master,
UInt surface_normal_dir);
/// fills the pairs vector with interface node pairs (*,0)=slaves,
/// (*,1)=masters
static void pairInterfaceNodes(const ElementGroup & slave_boundary,
const ElementGroup & master_boundary,
UInt surface_normal_dir, const Mesh & mesh,
Array<UInt> & pairs);
// add node pairs from a list with pairs(*,0)=slaves and pairs(*,1)=masters
void addNodePairs(const Array<UInt> & pairs);
/// add node pair
void addSplitNode(UInt slave, UInt master) override;
/// update (compute the normals on the master nodes)
void updateNormals() override;
/// update the lumped boundary B matrix
void updateLumpedBoundary() override;
/// update the impedance matrix
void updateImpedance() override;
/// impose the normal contact force
void applyContactPressure() override;
/// dump restart file
void dumpRestart(const std::string & file_name) const override;
/// read restart file
void readRestart(const std::string & file_name) override;
/// compute the normal gap
void computeNormalGap(Array<Real> & gap) const override {
this->computeRelativeNormalField(this->model.getCurrentPosition(), gap);
};
/// compute relative normal field (only value that has to be multiplied with
/// the normal)
/// relative to master nodes
void
computeRelativeNormalField(const Array<Real> & field,
Array<Real> & rel_normal_field) const override;
/// compute relative tangential field (complet array)
/// relative to master nodes
void
computeRelativeTangentialField(const Array<Real> & field,
Array<Real> & rel_tang_field) const override;
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
protected:
/// synchronize arrays
void syncArrays(SyncChoice sync_choice) override;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) override;
// virtual void addDumpFieldVector(const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Masters, masters, const SynchronizedArray<UInt> &)
AKANTU_GET_MACRO(LumpedBoundaryMasters, lumped_boundary_masters,
const SynchronizedArray<Real> &)
/// get interface node pairs (*,0) are slaves, (*,1) are masters
void getNodePairs(Array<UInt> & pairs) const;
/// get index of node in either slaves or masters array
/// if node is in neither of them, return -1
Int getNodeIndex(UInt node) const override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// array of master nodes
SynchronizedArray<UInt> masters;
/// lumped boundary of master nodes
SynchronizedArray<Real> lumped_boundary_masters;
// element list for dump and lumped_boundary
ElementTypeMapArray<UInt> master_elements;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_contact_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNContact & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AST_NTN_CONTACT_HH__ */
+#endif /* AST_NTN_CONTACT_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh
index 18dd63799..dec3a550a 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh
@@ -1,99 +1,99 @@
/**
* @file ntn_friction.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief implementation of friction for node to node contact
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTN_FRICTION_HH__
-#define __AST_NTN_FRICTION_HH__
+#ifndef AST_NTN_FRICTION_HH_
+#define AST_NTN_FRICTION_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_friction.hh"
#include "ntn_friclaw_coulomb.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <class> class FrictionLaw = NTNFricLawCoulomb,
class Regularisation = NTNFricRegNoRegularisation>
class NTNFriction : public FrictionLaw<Regularisation> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFriction(NTNBaseContact & contact, const ID & id = "friction",
const MemoryID & memory_id = 0);
virtual ~NTNFriction(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// apply the friction force
virtual void applyFrictionTraction();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
// virtual void addDumpFieldToDumper(const std::string & dumper_name,
// const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <template <class> class FrictionLaw, class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFriction<FrictionLaw, Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friction_tmpl.hh"
-#endif /* __AST_NTN_FRICTION_HH__ */
+#endif /* AST_NTN_FRICTION_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh
index afb086b65..a56ec2067 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh
@@ -1,125 +1,125 @@
/**
* @file ntrf_contact.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief contact for node to rigid flat interface
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTRF_CONTACT_HH__
-#define __AST_NTRF_CONTACT_HH__
+#ifndef AST_NTRF_CONTACT_HH_
+#define AST_NTRF_CONTACT_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_contact.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTRFContact : public NTNBaseContact {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTRFContact(SolidMechanicsModel & model, const ID & id = "contact",
const MemoryID & memory_id = 0);
virtual ~NTRFContact(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void setReferencePoint(Real x = 0., Real y = 0., Real z = 0.);
void setNormal(Real x = 1., Real y = 0., Real z = 0.);
/// add surface and nodes according to the surface normal
void addSurface(const ID & surf);
// add nodes from a list
void addNodes(Array<UInt> & nodes);
/// update (copy the normal to all normals)
virtual void updateNormals();
/// update the impedance matrix
virtual void updateImpedance();
/// compute the normal gap
virtual void computeNormalGap(Array<Real> & gap) const;
/// compute relative normal field (only value that has to be multiplied with
/// the normal)
/// relative to master nodes
virtual void computeRelativeNormalField(const Array<Real> & field,
Array<Real> & rel_normal_field) const;
/// compute relative tangential field (complet array)
/// relative to master nodes
virtual void
computeRelativeTangentialField(const Array<Real> & field,
Array<Real> & rel_tang_field) const;
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
// virtual void addDumpFieldVector(const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// reference point for rigid flat surface
Vector<Real> reference_point;
/// outpointing normal of rigid flat surface
Vector<Real> normal;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntrf_contact_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTRFContact & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AST_NTRF_CONTACT_HH__ */
+#endif /* AST_NTRF_CONTACT_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh
index 0a10636a8..bddaa5f3d 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh
@@ -1,91 +1,91 @@
/**
* @file ntrf_friction.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 23 2018
*
* @brief friction for node to rigid flat interface
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AST_NTRF_FRICTION_HH__
-#define __AST_NTRF_FRICTION_HH__
+#ifndef AST_NTRF_FRICTION_HH_
+#define AST_NTRF_FRICTION_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_friclaw_coulomb.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <class> class FrictionLaw = NTNFricLawCoulomb,
class Regularisation = NTNFricRegNoRegularisation>
class NTRFFriction : public FrictionLaw<Regularisation> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTRFFriction(NTNBaseContact & contact, const ID & id = "friction",
const MemoryID & memory_id = 0);
virtual ~NTRFFriction(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operato
template <template <class> class FrictionLaw, class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTRFFriction<FrictionLaw, Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntrf_friction_tmpl.hh"
-#endif /* __AST_NTRF_FRICTION_HH__ */
+#endif /* AST_NTRF_FRICTION_HH_ */
diff --git a/packages/cgal.cmake b/packages/cgal.cmake
index efa064f10..80d0f5c80 100644
--- a/packages/cgal.cmake
+++ b/packages/cgal.cmake
@@ -1,86 +1,85 @@
#===============================================================================
# @file cgal.cmake
#
# @author Lucas Frerot <lucas.frerot@epfl.ch>
# @author Clement Roux <clement.roux@epfl.ch>
#
# @date creation: Thu Feb 19 2015
# @date last modification: Wed Jan 20 2016
#
# @brief package description for CGAL
#
# @section LICENSE
#
# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
-
-set(CGAL_DO_NOT_WARN_ABOUT_CMAKE_BUILD_TYPE TRUE
- CACHE INTERNAL "Tells CGAL cmake to shut up" FORCE)
-
package_declare(CGAL EXTERNAL
DESCRIPTION "Add CGAL support in akantu"
- COMPILE_FLAGS CXX -frounding-math
- #BOOST_COMPONENTS system thread
)
package_is_activated(CGAL _is_activated)
-
-if (_is_activated AND (CMAKE_BUILD_TYPE MATCHES "[Dd][Ee][Bb][Uu][Gg]"))
+package_on_enabled_script(CGAL
+ "
+ set(CGAL_DO_NOT_WARN_ABOUT_CMAKE_BUILD_TYPE TRUE
+ CACHE BOOL \"Tells CGAL cmake to shut up\")
set(CGAL_DISABLE_ROUNDING_MATH_CHECK ON
- CACHE INTERNAL "Disable rounding math check in CGAL. This permits Valgrind to run." FORCE)
-endif()
-
+ CACHE BOOL \"Disable rounding math check in CGAL. This permits Valgrind to run.\")
+ mark_as_advanced(
+ CGAL_DO_NOT_WARN_ABOUT_CMAKE_BUILD_TYPE
+ CGAL_DISABLE_ROUNDING_MATH_CHECK
+ )
+ ")
package_declare_sources(CGAL
geometry/mesh_geom_common.hh
geometry/mesh_geom_abstract.hh
geometry/mesh_geom_factory.hh
geometry/mesh_geom_factory_tmpl.hh
geometry/mesh_abstract_intersector.hh
geometry/mesh_abstract_intersector_tmpl.hh
geometry/mesh_geom_intersector.hh
geometry/mesh_geom_intersector_tmpl.hh
geometry/mesh_segment_intersector.hh
geometry/mesh_segment_intersector_tmpl.hh
geometry/mesh_sphere_intersector.hh
geometry/mesh_sphere_intersector_tmpl.hh
geometry/tree_type_helper.hh
geometry/geom_helper_functions.hh
geometry/aabb_primitives/triangle.hh
geometry/aabb_primitives/line_arc.hh
geometry/aabb_primitives/tetrahedron.hh
geometry/aabb_primitives/aabb_primitive.hh
geometry/aabb_primitives/aabb_primitive.cc
)
package_declare_documentation(CGAL
"This package allows the use of CGAL's geometry algorithms in Akantu. Note that it needs a version of CGAL $\\geq$ 4.5 and needs activation of boost's system component."
""
"CGAL checks with an assertion that the compilation flag \\shellcode{-frounding-math} is activated, which forbids the use of Valgrind on any code compilated with the package."
)
package_set_package_system_dependency(CGAL deb-src "libcgal-dev >= 4.5")
diff --git a/python/py_aka_array.hh b/python/py_aka_array.hh
index 36f6d0198..90f3b8757 100644
--- a/python/py_aka_array.hh
+++ b/python/py_aka_array.hh
@@ -1,246 +1,250 @@
/* -------------------------------------------------------------------------- */
#include <aka_array.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/numpy.h>
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
namespace _aka = akantu;
namespace akantu {
namespace detail {
template <class T> struct is_array_type : public std::false_type {};
template <class T> struct is_array_type<Vector<T>> : public std::true_type {};
template <class T> struct is_array_type<Matrix<T>> : public std::true_type {};
template <class T> struct is_array_type<Array<T>> : public std::true_type {};
/* ------------------------------------------------------------------------ */
template <typename T> class ArrayProxy : public Array<T> {
protected:
// deallocate the memory
- void deallocate() override final {}
+ void deallocate() final {}
// allocate the memory
- void allocate(UInt /*size*/, UInt /*nb_component*/) override final {}
+ void allocate(UInt /*size*/, UInt /*nb_component*/) final {}
// allocate and initialize the memory
void allocate(UInt /*size*/, UInt /*nb_component*/,
- const T & /*value*/) override final {}
+ const T & /*value*/) final {}
public:
ArrayProxy(T * data, UInt size, UInt nb_component) {
this->values = data;
this->size_ = size;
this->nb_component = nb_component;
}
ArrayProxy(const Array<T> & src) {
this->values = src.storage();
this->size_ = src.size();
this->nb_component = src.getNbComponent();
}
- ~ArrayProxy() { this->values = nullptr; }
+ ~ArrayProxy() override { this->values = nullptr; }
- void resize(UInt size, const T & /*val*/) final {
- if (size != this->size())
- AKANTU_EXCEPTION("Cannot resize a temporary array, from "
- << this->size() << " to " << size);
- // std::fill(this->begin(), this->end(), val);
+ void resize(UInt size, const T & val) final {
+ if (size != this->size()) {
+ AKANTU_EXCEPTION("cannot resize a temporary array");
+ }
+ //std::fill(this->begin(), this->end(), val);
}
void resize(UInt new_size) final {
- if (new_size != this->size())
- AKANTU_EXCEPTION("Cannot resize a temporary array, from "
- << this->size() << " to " << new_size);
+ if (new_size != this->size()) {
+ AKANTU_EXCEPTION("cannot resize a temporary array");
+ }
}
void reserve(UInt /*size*/, UInt /*new_size*/) final {
AKANTU_EXCEPTION("cannot resize a temporary array");
}
};
/* ------------------------------------------------------------------------ */
template <typename T> struct ProxyType {};
template <typename T> struct ProxyType<Vector<T>> { using type = Vector<T>; };
template <typename T> struct ProxyType<Matrix<T>> { using type = Matrix<T>; };
template <typename T> struct ProxyType<Array<T>> {
using type = ArrayProxy<T>;
};
template <typename array> using ProxyType_t = typename ProxyType<array>::type;
} // namespace detail
} // namespace akantu
namespace pybind11 {
namespace detail {
template <typename T> struct AkaArrayType {
using type =
array_t<typename T::value_type, array::c_style | array::forcecast>;
};
template <typename T> struct AkaArrayType<_aka::Vector<T>> {
using type = array_t<T, array::f_style | array::forcecast>;
};
template <typename T> struct AkaArrayType<_aka::Matrix<T>> {
using type = array_t<T, array::f_style | array::forcecast>;
};
template <typename U> using array_type_t = typename AkaArrayType<U>::type;
/* ------------------------------------------------------------------------ */
template <typename T>
decltype(auto) create_proxy(array_type_t<_aka::Vector<T>> & ref,
- const _aka::Vector<T> *) {
+ const _aka::Vector<T> * /*unused*/) {
return std::make_unique<_aka::detail::ProxyType_t<_aka::Vector<T>>>(
ref.mutable_data(), ref.shape(0));
}
template <typename T>
decltype(auto) create_proxy(array_type_t<_aka::Matrix<T>> & ref,
- const _aka::Matrix<T> *) {
+ const _aka::Matrix<T> * /*unused*/) {
return std::make_unique<_aka::detail::ProxyType_t<_aka::Matrix<T>>>(
ref.mutable_data(), ref.shape(0), ref.shape(1));
}
template <typename T>
decltype(auto) create_proxy(array_type_t<_aka::Array<T>> & ref,
- const _aka::Array<T> *) {
+ const _aka::Array<T> * /*unused*/) {
return std::make_unique<_aka::detail::ProxyType_t<_aka::Array<T>>>(
ref.mutable_data(), ref.shape(0), ref.shape(1));
}
/* ------------------------------------------------------------------------ */
template <typename T>
py::handle aka_array_cast(const _aka::Array<T> & src,
py::handle base = handle(), bool writeable = true) {
array a;
a = array_type_t<_aka::Array<T>>({src.size(), src.getNbComponent()},
src.storage(), base);
- if (not writeable)
+ if (not writeable) {
array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_;
+ }
return a.release();
}
template <typename T>
py::handle aka_array_cast(const _aka::Vector<T> & src,
py::handle base = handle(), bool writeable = true) {
array a;
a = array_type_t<_aka::Vector<T>>({src.size()}, src.storage(), base);
- if (not writeable)
+ if (not writeable) {
array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_;
+ }
return a.release();
}
template <typename T>
py::handle aka_array_cast(const _aka::Matrix<T> & src,
py::handle base = handle(), bool writeable = true) {
array a;
a = array_type_t<_aka::Matrix<T>>({src.size(0), src.size(1)}, src.storage(),
base);
- if (not writeable)
+ if (not writeable) {
array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_;
+ }
return a.release();
}
/* ------------------------------------------------------------------------ */
template <typename AkaArrayType>
class type_caster<
AkaArrayType,
std::enable_if_t<_aka::detail::is_array_type<AkaArrayType>::value>> {
protected:
using T = typename AkaArrayType::value_type;
using type = AkaArrayType;
using proxy_type = _aka::detail::ProxyType_t<AkaArrayType>;
using array_type = array_type_t<AkaArrayType>;
std::unique_ptr<proxy_type> array_proxy;
array_type_t<AkaArrayType> copy_or_ref;
public:
#if PYBIND11_VERSION_MAJOR >= 2 && PYBIND11_VERSION_MINOR >= 3
static constexpr auto name = _("AkaArray");
operator type &&() && { return std::move(*array_proxy); }
template <typename T_>
using cast_op_type = pybind11::detail::movable_cast_op_type<T_>;
#else
static PYBIND11_DESCR name() { return type_descr(_("AkaArray")); };
template <typename _T>
using cast_op_type = pybind11::detail::cast_op_type<_T>;
#endif
operator type *() { return array_proxy.get(); }
operator type &() { return *array_proxy; }
/**
* Conversion part 1 (Python->C++)
*/
bool load(handle src, bool convert) {
bool need_copy = not isinstance<array_type>(src);
auto && fits = [&](auto && aref) {
auto && dims = aref.ndim();
- if (dims < 1 || dims > 2)
+ if (dims < 1 || dims > 2) {
return false;
+ }
return true;
};
if (not need_copy) {
// We don't need a converting copy, but we also need to check whether
// the strides are compatible with the Ref's stride requirements
auto aref = py::cast<array_type>(src);
if (not fits(aref)) {
return false;
}
copy_or_ref = std::move(aref);
} else {
if (not convert) {
return false;
}
auto copy = array_type::ensure(src);
if (not copy) {
return false;
}
if (not fits(copy)) {
return false;
}
copy_or_ref = std::move(array_type::ensure(src));
loader_life_support::add_patient(copy_or_ref);
}
AkaArrayType * dispatch = nullptr; // cannot detect T from the expression
array_proxy = create_proxy(copy_or_ref, dispatch);
return true;
}
/**
* Conversion part 2 (C++ -> Python)
*/
static handle cast(const type & src, return_value_policy policy,
handle parent) {
switch (policy) {
case return_value_policy::copy:
return aka_array_cast<T>(src);
case return_value_policy::reference_internal:
return aka_array_cast<T>(src, parent);
case return_value_policy::reference:
case return_value_policy::automatic:
case return_value_policy::automatic_reference:
return aka_array_cast<T>(src, none());
default:
pybind11_fail("Invalid return_value_policy for ArrayProxy type");
}
}
};
} // namespace detail
} // namespace pybind11
diff --git a/python/py_aka_common.hh b/python/py_aka_common.hh
index fdcfe4749..b0bdb21f3 100644
--- a/python/py_aka_common.hh
+++ b/python/py_aka_common.hh
@@ -1,14 +1,14 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_AKA_COMMON_HH__
-#define __AKANTU_PY_AKA_COMMON_HH__
+#ifndef AKANTU_PY_AKA_COMMON_HH_
+#define AKANTU_PY_AKA_COMMON_HH_
namespace akantu {
void register_enums(pybind11::module & mod);
void register_initialize(pybind11::module & mod);
void register_functions(pybind11::module & mod);
} // namespace akantu
#endif
diff --git a/python/py_aka_error.hh b/python/py_aka_error.hh
index 16b0f9ac5..269bd5c4b 100644
--- a/python/py_aka_error.hh
+++ b/python/py_aka_error.hh
@@ -1,12 +1,12 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_AKA_ERROR_HH__
-#define __AKANTU_PY_AKA_ERROR_HH__
+#ifndef AKANTU_PY_AKA_ERROR_HH_
+#define AKANTU_PY_AKA_ERROR_HH_
namespace akantu {
void register_error(pybind11::module & mod);
}
#endif
diff --git a/python/py_akantu.cc b/python/py_akantu.cc
index f0400e047..08f9d8eda 100644
--- a/python/py_akantu.cc
+++ b/python/py_akantu.cc
@@ -1,101 +1,103 @@
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "py_aka_common.hh"
#include "py_aka_error.hh"
#include "py_boundary_conditions.hh"
#include "py_fe_engine.hh"
#include "py_group_manager.hh"
#include "py_mesh.hh"
#include "py_model.hh"
#include "py_parser.hh"
#if defined(AKANTU_USE_IOHELPER)
#include "py_dumpable.hh"
#endif
#if defined(AKANTU_SOLID_MECHANICS)
#include "py_material.hh"
#include "py_solid_mechanics_model.hh"
#endif
#if defined(AKANTU_HEAT_TRANSFER)
#include "py_heat_transfer_model.hh"
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "py_solid_mechanics_model_cohesive.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <aka_error.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
namespace akantu {
void register_all(pybind11::module & mod) {
register_initialize(mod);
register_enums(mod);
register_error(mod);
register_functions(mod);
register_parser(mod);
register_group_manager(mod);
#if defined(AKANTU_USE_IOHELPER)
register_dumpable(mod);
#endif
register_mesh(mod);
register_fe_engine(mod);
register_boundary_conditions(mod);
register_model(mod);
#if defined(AKANTU_HEAT_TRANSFER)
register_heat_transfer_model(mod);
#endif
#if defined(AKANTU_SOLID_MECHANICS)
register_solid_mechanics_model(mod);
register_material(mod);
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
register_solid_mechanics_model_cohesive(mod);
#endif
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
PYBIND11_MODULE(py11_akantu, mod) {
mod.doc() = "Akantu python interface";
static py::exception<akantu::debug::Exception>
akantu_exception(mod, "Exception");
py::register_exception_translator([](std::exception_ptr ptr) {
try {
- if (ptr)
+ if (ptr) {
std::rethrow_exception(ptr);
+ }
} catch (akantu::debug::Exception & e) {
- if (akantu::debug::debugger.printBacktrace())
+ if (akantu::debug::debugger.printBacktrace()) {
akantu::debug::printBacktrace(15);
+ }
akantu_exception(e.info().c_str());
}
});
akantu::register_all(mod);
mod.def("has_mpi", []() {
#if defined(AKANTU_USE_MPI)
return true;
#else
return false;
#endif
});
} // Module akantu
diff --git a/python/py_akantu.hh b/python/py_akantu.hh
index 7b489b29f..73a65c297 100644
--- a/python/py_akantu.hh
+++ b/python/py_akantu.hh
@@ -1,14 +1,14 @@
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
-#ifndef __PY_AKANTU_HH__
-#define __PY_AKANTU_HH__
+#ifndef PY_AKANTU_HH_
+#define PY_AKANTU_HH_
namespace akantu {
void register_all(pybind11::module & mod);
}
-#endif /* __PY_AKANTU_HH__ */
+#endif /* PY_AKANTU_HH_ */
diff --git a/python/py_boundary_conditions.hh b/python/py_boundary_conditions.hh
index ee69706d9..a5fee7649 100644
--- a/python/py_boundary_conditions.hh
+++ b/python/py_boundary_conditions.hh
@@ -1,12 +1,12 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_BOUNDARY_CONDITIONS_HH__
-#define __AKANTU_PY_BOUNDARY_CONDITIONS_HH__
+#ifndef AKANTU_PY_BOUNDARY_CONDITIONS_HH_
+#define AKANTU_PY_BOUNDARY_CONDITIONS_HH_
namespace akantu {
void register_boundary_conditions(pybind11::module & mod);
} // namespace akantu
-#endif // __AKANTU_PY_BOUNDARY_CONDITIONS_HH__
+#endif // AKANTU_PY_BOUNDARY_CONDITIONS_HH_
diff --git a/python/py_dumpable.hh b/python/py_dumpable.hh
index 28dc04c29..df09c66ac 100644
--- a/python/py_dumpable.hh
+++ b/python/py_dumpable.hh
@@ -1,12 +1,12 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_DUMPABLE_HH__
-#define __AKANTU_PY_DUMPABLE_HH__
+#ifndef AKANTU_PY_DUMPABLE_HH_
+#define AKANTU_PY_DUMPABLE_HH_
namespace akantu {
void register_dumpable(pybind11::module & mod);
} // namespace akantu
-#endif /* __AKANTU_PY_DUMPABLE_HH__ */
+#endif /* AKANTU_PY_DUMPABLE_HH_ */
diff --git a/python/py_fe_engine.cc b/python/py_fe_engine.cc
index be868f7c2..70955c252 100644
--- a/python/py_fe_engine.cc
+++ b/python/py_fe_engine.cc
@@ -1,112 +1,110 @@
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
#include "py_aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <fe_engine.hh>
#include <integration_point.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/functional.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
__attribute__((visibility("default"))) void
register_fe_engine(py::module & mod) {
py::class_<Element>(mod, "Element");
py::class_<FEEngine>(mod, "FEEngine")
.def(
"getNbIntegrationPoints",
[](FEEngine & fem, const ElementType & type,
const GhostType & ghost_type) {
return fem.getNbIntegrationPoints(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def(
"gradientOnIntegrationPoints",
[](FEEngine & fem, const Array<Real> & u, Array<Real> & nablauq,
- const UInt nb_degree_of_freedom, const ElementType & type,
- const GhostType & ghost_type,
- const Array<UInt> * filter_elements) {
+ UInt nb_degree_of_freedom, ElementType type,
+ GhostType ghost_type, const Array<UInt> * filter_elements) {
if (filter_elements == nullptr) {
// This is due to the ArrayProxy that looses the
// empty_filter information
filter_elements = &empty_filter;
}
fem.gradientOnIntegrationPoints(u, nablauq, nb_degree_of_freedom,
type, ghost_type, *filter_elements);
},
py::arg("u"), py::arg("nablauq"), py::arg("nb_degree_of_freedom"),
py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::arg("filter_elements") = nullptr)
.def(
"interpolateOnIntegrationPoints",
[](FEEngine & self, const Array<Real> & u, Array<Real> & uq,
- UInt nb_degree_of_freedom, const ElementType & type,
- const GhostType & ghost_type,
- const Array<UInt> * filter_elements) {
+ UInt nb_degree_of_freedom, ElementType type,
+ GhostType ghost_type, const Array<UInt> * filter_elements) {
if (filter_elements == nullptr) {
// This is due to the ArrayProxy that looses the
// empty_filter information
filter_elements = &empty_filter;
}
self.interpolateOnIntegrationPoints(u, uq, nb_degree_of_freedom,
type, ghost_type,
*filter_elements);
},
py::arg("u"), py::arg("uq"), py::arg("nb_degree_of_freedom"),
py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::arg("filter_elements") = nullptr)
.def(
"interpolateOnIntegrationPoints",
[](FEEngine & self, const Array<Real> & u,
ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements) {
self.interpolateOnIntegrationPoints(u, uq, filter_elements);
},
py::arg("u"), py::arg("uq"), py::arg("filter_elements") = nullptr)
.def(
"computeIntegrationPointsCoordinates",
[](FEEngine & self, ElementTypeMapArray<Real> & coordinates,
const ElementTypeMapArray<UInt> * filter_elements)
-> decltype(auto) {
return self.computeIntegrationPointsCoordinates(coordinates,
filter_elements);
},
py::arg("coordinates"), py::arg("filter_elements") = nullptr)
.def(
"assembleFieldLumped",
[](FEEngine & fem,
const std::function<void(Matrix<Real> &, const Element &)> &
field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- ElementType type, const GhostType & ghost_type) {
+ ElementType type, GhostType ghost_type) {
fem.assembleFieldLumped(field_funct, matrix_id, dof_id, dof_manager,
type, ghost_type);
},
py::arg("field_funct"), py::arg("matrix_id"), py::arg("dof_id"),
py::arg("dof_manager"), py::arg("type"),
py::arg("ghost_type") = _not_ghost)
.def(
"assembleFieldMatrix",
[](FEEngine & fem,
const std::function<void(Matrix<Real> &, const Element &)> &
field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- ElementType type, const GhostType & ghost_type = _not_ghost) {
+ ElementType type, GhostType ghost_type = _not_ghost) {
fem.assembleFieldMatrix(field_funct, matrix_id, dof_id, dof_manager,
type, ghost_type);
},
py::arg("field_funct"), py::arg("matrix_id"), py::arg("dof_id"),
py::arg("dof_manager"), py::arg("type"),
py::arg("ghost_type") = _not_ghost);
py::class_<IntegrationPoint>(mod, "IntegrationPoint");
}
} // namespace akantu
diff --git a/python/py_fe_engine.hh b/python/py_fe_engine.hh
index a86871a68..feaafd1a1 100644
--- a/python/py_fe_engine.hh
+++ b/python/py_fe_engine.hh
@@ -1,12 +1,12 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_FE_ENGINE_HH__
-#define __AKANTU_PY_FE_ENGINE_HH__
+#ifndef AKANTU_PY_FE_ENGINE_HH_
+#define AKANTU_PY_FE_ENGINE_HH_
namespace akantu {
void register_fe_engine(pybind11::module & mod);
} // namespace akantu
-#endif // __AKANTU_PY_FE_ENGINE_HH__
+#endif // AKANTU_PY_FE_ENGINE_HH_
diff --git a/python/py_group_manager.hh b/python/py_group_manager.hh
index cd54359a7..9b1917b6d 100644
--- a/python/py_group_manager.hh
+++ b/python/py_group_manager.hh
@@ -1,10 +1,10 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_GROUP_MANAGER_HH__
-#define __AKANTU_PY_GROUP_MANAGER_HH__
+#ifndef AKANTU_PY_GROUP_MANAGER_HH_
+#define AKANTU_PY_GROUP_MANAGER_HH_
namespace akantu {
void register_group_manager(pybind11::module & mod);
} // namespace akantu
-#endif /* __AKANTU_PY_GROUP_MANAGER_HH__ */
+#endif /* AKANTU_PY_GROUP_MANAGER_HH_ */
diff --git a/python/py_heat_transfer_model.hh b/python/py_heat_transfer_model.hh
index c53659f4e..634c15f8a 100644
--- a/python/py_heat_transfer_model.hh
+++ b/python/py_heat_transfer_model.hh
@@ -1,12 +1,12 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_HEAT_TRANSFERT_MODEL_HH__
-#define __AKANTU_PY_HEAT_TRANSFERT_MODEL_HH__
+#ifndef AKANTU_PY_HEAT_TRANSFERT_MODEL_HH_
+#define AKANTU_PY_HEAT_TRANSFERT_MODEL_HH_
namespace akantu {
void register_heat_transfer_model(pybind11::module & mod);
} // namespace akantu
-#endif // __AKANTU_PY_HEAT_TRANSFERT_MODEL_HH__
+#endif // AKANTU_PY_HEAT_TRANSFERT_MODEL_HH_
diff --git a/python/py_material.cc b/python/py_material.cc
index 129874818..7d95389ac 100644
--- a/python/py_material.cc
+++ b/python/py_material.cc
@@ -1,223 +1,224 @@
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <solid_mechanics_model.hh>
#if defined(AKANTU_COHESIVE_ELEMENT)
#include <solid_mechanics_model_cohesive.hh>
#endif
/* -------------------------------------------------------------------------- */
#include <pybind11/operators.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
template <typename _Material> class PyMaterial : public _Material {
public:
/* Inherit the constructors */
using _Material::_Material;
- virtual ~PyMaterial(){};
+ ~PyMaterial() override{};
void initMaterial() override {
PYBIND11_OVERLOAD(void, _Material, initMaterial);
};
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override {
PYBIND11_OVERLOAD_PURE(void, _Material, computeStress, el_type, ghost_type);
}
- void computeTangentModuli(const ElementType & el_type,
+ void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override {
PYBIND11_OVERLOAD(void, _Material, computeTangentModuli, el_type,
tangent_matrix, ghost_type);
}
void computePotentialEnergy(ElementType el_type) override {
PYBIND11_OVERLOAD(void, _Material, computePotentialEnergy, el_type);
}
Real getPushWaveSpeed(const Element & element) const override {
PYBIND11_OVERLOAD(Real, _Material, getPushWaveSpeed, element);
}
Real getShearWaveSpeed(const Element & element) const override {
PYBIND11_OVERLOAD(Real, _Material, getShearWaveSpeed, element);
}
void registerInternal(const std::string & name, UInt nb_component) {
this->internals[name] = std::make_shared<InternalField<Real>>(name, *this);
AKANTU_DEBUG_INFO("alloc internal " << name << " "
<< &this->internals[name]);
this->internals[name]->initialize(nb_component);
}
auto & getInternals() { return this->internals; }
protected:
std::map<std::string, std::shared_ptr<InternalField<Real>>> internals;
};
/* -------------------------------------------------------------------------- */
template <typename T>
void register_element_type_map_array(py::module & mod,
const std::string & name) {
py::class_<ElementTypeMapArray<T>, std::shared_ptr<ElementTypeMapArray<T>>>(
mod, ("ElementTypeMapArray" + name).c_str())
.def(
"__call__",
- [](ElementTypeMapArray<T> & self, ElementType & type,
- const GhostType & ghost_type) -> decltype(auto) {
+ [](ElementTypeMapArray<T> & self, ElementType type,
+ GhostType ghost_type) -> decltype(auto) {
return self(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def(
"elementTypes",
[](ElementTypeMapArray<T> & self, UInt _dim, GhostType _ghost_type,
ElementKind _kind) -> decltype(auto) {
auto types = self.elementTypes(_dim, _ghost_type, _kind);
std::vector<ElementType> _types;
for (auto && t : types) {
_types.push_back(t);
}
return _types;
},
py::arg("dim") = _all_dimensions, py::arg("ghost_type") = _not_ghost,
py::arg("kind") = _ek_regular);
py::class_<InternalField<T>, ElementTypeMapArray<T>,
std::shared_ptr<InternalField<T>>>(
mod, ("InternalField" + name).c_str());
}
/* -------------------------------------------------------------------------- */
template <typename _Material>
void define_material(py::module & mod, const std::string & name) {
py::class_<_Material, PyMaterial<_Material>, Parsable>(
mod, name.c_str(), py::multiple_inheritance())
.def(py::init<SolidMechanicsModel &, const ID &>())
.def(
"getGradU",
[](Material & self, ElementType el_type,
GhostType ghost_type = _not_ghost) -> decltype(auto) {
return self.getGradU(el_type, ghost_type);
},
py::arg("el_type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def(
"getStress",
[](Material & self, ElementType el_type,
GhostType ghost_type = _not_ghost) -> decltype(auto) {
return self.getStress(el_type, ghost_type);
},
py::arg("el_type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def(
"getPotentialEnergy",
[](Material & self, ElementType el_type) -> decltype(auto) {
return self.getPotentialEnergy(el_type);
},
py::return_value_policy::reference)
.def("initMaterial", &Material::initMaterial)
.def("getModel", &Material::getModel)
.def("registerInternal",
[](Material & self, const std::string & name, UInt nb_component) {
return dynamic_cast<PyMaterial<Material> &>(self).registerInternal(
name, nb_component);
})
.def(
"getInternalFieldReal",
[](Material & self, const ID & id, const ElementType & type,
const GhostType & ghost_type) -> Array<Real> & {
return self.getArray<Real>(id, type, ghost_type);
},
py::arg("id"), py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def(
"getInternalFieldUInt",
[](Material & self, const ID & id, const ElementType & type,
const GhostType & ghost_type) -> Array<UInt> & {
return self.getArray<UInt>(id, type, ghost_type);
},
py::arg("id"), py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def(
"getElementFilter",
[](Material & self, const ElementType & type,
const GhostType & ghost_type) -> const Array<UInt> & {
return self.getElementFilter()(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost);
}
/* -------------------------------------------------------------------------- */
void register_material(py::module & mod) {
py::class_<MaterialFactory>(mod, "MaterialFactory")
.def_static(
"getInstance",
[]() -> MaterialFactory & { return Material::getFactory(); },
py::return_value_policy::reference)
.def("registerAllocator",
[](MaterialFactory & self, const std::string id, py::function func) {
self.registerAllocator(
id,
- [func, id](UInt dim, const ID &, SolidMechanicsModel & model,
+ [func, id](UInt dim, const ID & /*unused*/,
+ SolidMechanicsModel & model,
const ID & option) -> std::unique_ptr<Material> {
py::object obj = func(dim, id, model, option);
auto & ptr = py::cast<Material &>(obj);
obj.release();
return std::unique_ptr<Material>(&ptr);
});
});
register_element_type_map_array<Real>(mod, "Real");
register_element_type_map_array<UInt>(mod, "UInt");
define_material<Material>(mod, "Material");
py::class_<MaterialSelector, std::shared_ptr<MaterialSelector>>(
mod, "MaterialSelector")
.def("setFallback",
[](MaterialSelector & self, UInt f) { self.setFallback(f); })
.def("setFallback",
[](MaterialSelector & self,
const std::shared_ptr<MaterialSelector> & fallback_selector) {
self.setFallback(fallback_selector);
})
.def("setFallback",
[](MaterialSelector & self, MaterialSelector & fallback_selector) {
self.setFallback(fallback_selector);
});
py::class_<MeshDataMaterialSelector<std::string>, MaterialSelector,
std::shared_ptr<MeshDataMaterialSelector<std::string>>>(
mod, "MeshDataMaterialSelectorString")
.def(py::init<const std::string &, const SolidMechanicsModel &, UInt>(),
py::arg("name"), py::arg("model"), py::arg("first_index") = 1);
#if defined(AKANTU_COHESIVE_ELEMENT)
py::class_<DefaultMaterialCohesiveSelector, MaterialSelector,
std::shared_ptr<DefaultMaterialCohesiveSelector>>(
mod, "DefaultMaterialCohesiveSelector")
.def(py::init<const SolidMechanicsModelCohesive &>());
py::class_<MeshDataMaterialCohesiveSelector, MaterialSelector,
std::shared_ptr<MeshDataMaterialCohesiveSelector>>(
mod, "MeshDataMaterialCohesiveSelector")
.def(py::init<const SolidMechanicsModelCohesive &>());
py::class_<MaterialCohesiveRulesSelector, MaterialSelector,
std::shared_ptr<MaterialCohesiveRulesSelector>>(
mod, "MaterialCohesiveRulesSelector")
.def(py::init<const SolidMechanicsModelCohesive &,
const MaterialCohesiveRules &, const ID &>(),
py::arg("model"), py::arg("rules"),
py::arg("mesh_data_id") = "physical_names");
#endif
}
} // namespace akantu
diff --git a/python/py_material.hh b/python/py_material.hh
index 404b4a7ac..186538181 100644
--- a/python/py_material.hh
+++ b/python/py_material.hh
@@ -1,12 +1,12 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_MATERIAL_HH__
-#define __AKANTU_PY_MATERIAL_HH__
+#ifndef AKANTU_PY_MATERIAL_HH_
+#define AKANTU_PY_MATERIAL_HH_
namespace akantu {
void register_material(pybind11::module & mod);
} // namespace akantu
-#endif // __AKANTU_PY_MATERIAL_HH__
+#endif // AKANTU_PY_MATERIAL_HH_
diff --git a/python/py_mesh.cc b/python/py_mesh.cc
index 7a3ff9783..4b3750a69 100644
--- a/python/py_mesh.cc
+++ b/python/py_mesh.cc
@@ -1,72 +1,72 @@
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <mesh.hh>
#include <mesh_utils.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void register_mesh(py::module & mod) {
py::class_<MeshData>(mod, "MeshData")
.def(
"getElementalDataUInt",
[](MeshData & _this, const ID & name) -> ElementTypeMapArray<UInt> & {
return _this.getElementalData<UInt>(name);
},
py::return_value_policy::reference);
py::class_<Mesh, GroupManager, Dumpable, MeshData>(mod, "Mesh",
py::multiple_inheritance())
.def(py::init<UInt, const ID &, const MemoryID &>(),
py::arg("spatial_dimension"), py::arg("id") = "mesh",
py::arg("memory_id") = 0)
.def("read", &Mesh::read, py::arg("filename"),
py::arg("mesh_io_type") = _miot_auto, "read the mesh from a file")
.def(
"getNodes",
[](Mesh & self) -> decltype(auto) { return self.getNodes(); },
py::return_value_policy::reference)
.def("getNbNodes", &Mesh::getNbNodes)
.def(
"getConnectivity",
- [](Mesh & self, const ElementType & type) -> decltype(auto) {
+ [](Mesh & self, ElementType type) -> decltype(auto) {
return self.getConnectivity(type);
},
py::return_value_policy::reference)
.def("distribute", [](Mesh & self) { self.distribute(); })
.def("makePeriodic",
[](Mesh & self, const SpatialDirection & direction) {
self.makePeriodic(direction);
})
.def(
"getNbElement",
[](Mesh & self, const UInt spatial_dimension,
- const GhostType & ghost_type, const ElementKind & kind) {
+ GhostType ghost_type, ElementKind kind) {
return self.getNbElement(spatial_dimension, ghost_type, kind);
},
py::arg("spatial_dimension") = _all_dimensions,
py::arg("ghost_type") = _not_ghost, py::arg("kind") = _ek_not_defined)
.def(
"getNbElement",
- [](Mesh & self, const ElementType & type,
- const GhostType & ghost_type) {
+ [](Mesh & self, ElementType type,
+ GhostType ghost_type) {
return self.getNbElement(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def_static("getSpatialDimension", [](ElementType & type) {
return Mesh::getSpatialDimension(type);
});
/* ------------------------------------------------------------------------ */
py::class_<MeshUtils>(mod, "MeshUtils")
.def_static("buildFacets", &MeshUtils::buildFacets);
}
} // namespace akantu
diff --git a/python/py_mesh.hh b/python/py_mesh.hh
index 2a3924854..2efe88e06 100644
--- a/python/py_mesh.hh
+++ b/python/py_mesh.hh
@@ -1,10 +1,10 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_MESH_HH__
-#define __AKANTU_PY_MESH_HH__
+#ifndef AKANTU_PY_MESH_HH_
+#define AKANTU_PY_MESH_HH_
namespace akantu {
void register_mesh(pybind11::module & mod);
} // namespace akantu
-#endif // __AKANTU_PY_MESH_HH__
+#endif // AKANTU_PY_MESH_HH_
diff --git a/python/py_model.cc b/python/py_model.cc
index 32f1a5bbf..32682d8a3 100644
--- a/python/py_model.cc
+++ b/python/py_model.cc
@@ -1,105 +1,80 @@
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <model.hh>
#include <non_linear_solver.hh>
#include <sparse_matrix_aij.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/operators.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void register_model(py::module & mod) {
- py::class_<SparseMatrix>(mod, "SparseMatrix")
- .def("getMatrixType", &SparseMatrix::getMatrixType)
- .def("size", &SparseMatrix::size)
- .def("clear", &SparseMatrix::clear)
- .def("saveProfile", &SparseMatrix::saveProfile)
- .def("saveMatrix", &SparseMatrix::saveMatrix)
- .def(
- "add", [](SparseMatrix & self, UInt i, UInt j) { self.add(i, j); },
- "Add entry in the profile")
- .def(
- "add",
- [](SparseMatrix & self, UInt i, UInt j, Real value) {
- self.add(i, j, value);
- },
- "Add the value to the matrix")
- .def("__call__", [](const SparseMatrix & self, UInt i, UInt j) {
- return self(i, j);
- });
-
- py::class_<SparseMatrixAIJ, SparseMatrix>(mod, "SparseMatrixAIJ")
- .def("getIRN", &SparseMatrixAIJ::getIRN)
- .def("getJCN", &SparseMatrixAIJ::getJCN)
- .def("getA", &SparseMatrixAIJ::getA);
-
- py::class_<SolverVector>(mod, "SolverVector");
-
py::class_<DOFManager>(mod, "DOFManager")
.def("getMatrix", &DOFManager::getMatrix,
py::return_value_policy::reference)
.def(
"getNewMatrix",
[](DOFManager & self, const std::string & name,
const std::string & matrix_to_copy_id) -> decltype(auto) {
return self.getNewMatrix(name, matrix_to_copy_id);
},
py::return_value_policy::reference)
.def(
"getResidual",
[](DOFManager & self) -> decltype(auto) {
return self.getResidual();
},
py::return_value_policy::reference)
.def("getArrayPerDOFs", &DOFManager::getArrayPerDOFs)
.def("assembleToResidual", &DOFManager::assembleToResidual);
py::class_<NonLinearSolver>(mod, "NonLinearSolver")
.def(
"set",
[](NonLinearSolver & self, const std::string & id, const Real & val) {
- if (id == "max_iterations")
+ if (id == "max_iterations") {
self.set(id, int(val));
- else
+ } else {
self.set(id, val);
+ }
})
.def("set",
[](NonLinearSolver & self, const std::string & id,
const SolveConvergenceCriteria & val) { self.set(id, val); });
py::class_<ModelSolver, Parsable>(mod, "ModelSolver",
py::multiple_inheritance())
.def("getNonLinearSolver",
(NonLinearSolver & (ModelSolver::*)(const ID &)) &
ModelSolver::getNonLinearSolver,
py::arg("solver_id") = "", py::return_value_policy::reference)
.def("solveStep", [](ModelSolver & self) { self.solveStep(); })
.def("solveStep", [](ModelSolver & self, const ID & solver_id) {
self.solveStep(solver_id);
});
py::class_<Model, ModelSolver>(mod, "Model", py::multiple_inheritance())
.def("setBaseName", &Model::setBaseName)
.def("getFEEngine", &Model::getFEEngine, py::arg("name") = "",
py::return_value_policy::reference)
.def("getFEEngineBoundary", &Model::getFEEngine, py::arg("name") = "",
py::return_value_policy::reference)
.def("addDumpFieldVector", &Model::addDumpFieldVector)
.def("addDumpField", &Model::addDumpField)
.def("setBaseNameToDumper", &Model::setBaseNameToDumper)
.def("addDumpFieldVectorToDumper", &Model::addDumpFieldVectorToDumper)
.def("addDumpFieldToDumper", &Model::addDumpFieldToDumper)
.def("dump", &Model::dump)
.def("initNewSolver", &Model::initNewSolver)
.def("getDOFManager", &Model::getDOFManager,
py::return_value_policy::reference);
}
} // namespace akantu
diff --git a/python/py_model.hh b/python/py_model.hh
index e355e4962..11e329094 100644
--- a/python/py_model.hh
+++ b/python/py_model.hh
@@ -1,12 +1,12 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_AKA_MODEL_HH__
-#define __AKANTU_PY_AKA_MODEL_HH__
+#ifndef AKANTU_PY_AKA_MODEL_HH_
+#define AKANTU_PY_AKA_MODEL_HH_
namespace akantu {
void register_model(pybind11::module & mod);
}
#endif
diff --git a/python/py_parser.hh b/python/py_parser.hh
index 5c99a213d..66fec2b42 100644
--- a/python/py_parser.hh
+++ b/python/py_parser.hh
@@ -1,12 +1,12 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_AKA_PARSER_HH__
-#define __AKANTU_PY_AKA_PARSER_HH__
+#ifndef AKANTU_PY_AKA_PARSER_HH_
+#define AKANTU_PY_AKA_PARSER_HH_
namespace akantu {
void register_parser(pybind11::module & mod);
}
#endif
diff --git a/python/py_solid_mechanics_model.hh b/python/py_solid_mechanics_model.hh
index 4d5c7883f..e344e65f1 100644
--- a/python/py_solid_mechanics_model.hh
+++ b/python/py_solid_mechanics_model.hh
@@ -1,13 +1,13 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_SOLID_MECHANICS_MODEL_HH__
-#define __AKANTU_PY_SOLID_MECHANICS_MODEL_HH__
+#ifndef AKANTU_PY_SOLID_MECHANICS_MODEL_HH_
+#define AKANTU_PY_SOLID_MECHANICS_MODEL_HH_
namespace akantu {
void register_solid_mechanics_model(pybind11::module & mod);
} // namespace akantu
-#endif // __AKANTU_PY_SOLID_MECHANICS_MODEL_HH__
+#endif // AKANTU_PY_SOLID_MECHANICS_MODEL_HH_
diff --git a/python/py_solid_mechanics_model_cohesive.hh b/python/py_solid_mechanics_model_cohesive.hh
index b8d28995c..c0c883d61 100644
--- a/python/py_solid_mechanics_model_cohesive.hh
+++ b/python/py_solid_mechanics_model_cohesive.hh
@@ -1,13 +1,13 @@
#include <pybind11/pybind11.h>
-#ifndef __AKANTU_PY_SOLID_MECHANICS_MODEL_COHESIVE_HH__
-#define __AKANTU_PY_SOLID_MECHANICS_MODEL_COHESIVE_HH__
+#ifndef AKANTU_PY_SOLID_MECHANICS_MODEL_COHESIVE_HH_
+#define AKANTU_PY_SOLID_MECHANICS_MODEL_COHESIVE_HH_
namespace akantu {
void register_solid_mechanics_model_cohesive(pybind11::module & mod);
} // namespace akantu
-#endif // __AKANTU_PY_SOLID_MECHANICS_MODEL_COHESIVE_HH__
+#endif // AKANTU_PY_SOLID_MECHANICS_MODEL_COHESIVE_HH_
diff --git a/python/py_solver.cc b/python/py_solver.cc
new file mode 100644
index 000000000..6e292867d
--- /dev/null
+++ b/python/py_solver.cc
@@ -0,0 +1,45 @@
+/* -------------------------------------------------------------------------- */
+#include "py_aka_array.hh"
+/* -------------------------------------------------------------------------- */
+#include "py_solver.h"
+/* -------------------------------------------------------------------------- */#include <model.hh>
+#include <non_linear_solver.hh>
+#include <sparse_matrix_aij.hh>
+/* -------------------------------------------------------------------------- */
+#include <pybind11/operators.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+/* -------------------------------------------------------------------------- */
+namespace py = pybind11;
+/* -------------------------------------------------------------------------- */
+
+namespace akantu {
+
+/* -------------------------------------------------------------------------- */
+void register_solver(py::module & mod) {
+ py::class_<SparseMatrix>(mod, "SparseMatrix")
+ .def("getMatrixType", &SparseMatrix::getMatrixType)
+ .def("size", &SparseMatrix::size)
+ .def("zero", &SparseMatrix::zero)
+ .def("saveProfile", &SparseMatrix::saveProfile)
+ .def("saveMatrix", &SparseMatrix::saveMatrix)
+ .def(
+ "add", [](SparseMatrix & self, UInt i, UInt j) { self.add(i, j); },
+ "Add entry in the profile")
+ .def(
+ "add",
+ [](SparseMatrix & self, UInt i, UInt j, Real value) {
+ self.add(i, j, value);
+ },
+ "Add the value to the matrix")
+ .def("__call__", [](const SparseMatrix & self, UInt i, UInt j) {
+ return self(i, j);
+ });
+
+ py::class_<SparseMatrixAIJ, SparseMatrix>(mod, "SparseMatrixAIJ")
+ .def("getIRN", &SparseMatrixAIJ::getIRN)
+ .def("getJCN", &SparseMatrixAIJ::getJCN)
+ .def("getA", &SparseMatrixAIJ::getA);
+
+ py::class_<SolverVector>(mod, "SolverVector");
+}
diff --git a/python/py_solver.hh b/python/py_solver.hh
new file mode 100644
index 000000000..892606998
--- /dev/null
+++ b/python/py_solver.hh
@@ -0,0 +1,12 @@
+#include <pybind11/pybind11.h>
+
+#ifndef AKANTU_PY_AKA_SOLVER_HH_
+#define AKANTU_PY_AKA_SOLVER_HH_
+
+namespace akantu {
+
+void register_solver(pybind11::module & mod);
+
+}
+
+#endif
diff --git a/src/common/aka_array.cc b/src/common/aka_array.cc
index 52739c70f..48d7bda57 100644
--- a/src/common/aka_array.cc
+++ b/src/common/aka_array.cc
@@ -1,97 +1,96 @@
/**
* @file aka_array.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of akantu::Array
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <memory>
#include <utility>
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Functions ArrayBase */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <> UInt Array<Real>::find(const Real & elem) const {
AKANTU_DEBUG_IN();
Real epsilon = std::numeric_limits<Real>::epsilon();
auto it = std::find_if(begin(), end(), [&elem, &epsilon](auto && a) {
return std::abs(a - elem) <= epsilon;
});
AKANTU_DEBUG_OUT();
return (it != end()) ? end() - it : UInt(-1);
}
/* -------------------------------------------------------------------------- */
template <>
Array<ElementType> &
-Array<ElementType>::operator*=(const ElementType & /*alpha*/) {
+Array<ElementType>::operator*=(const ElementType &/*alpha*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<ElementType> &
-Array<ElementType>::operator-=(__attribute__((unused))
- const Array<ElementType> & /*vect*/) {
+Array<ElementType>::operator-=(const Array<ElementType> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<ElementType> &
Array<ElementType>::operator+=(const Array<ElementType> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <> Array<char> & Array<char>::operator*=(const char & /*alpha*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator-=(const Array<char> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator+=(const Array<char> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
} // namespace akantu
diff --git a/src/common/aka_array.hh b/src/common/aka_array.hh
index f9821b47e..00a92ab8d 100644
--- a/src/common/aka_array.hh
+++ b/src/common/aka_array.hh
@@ -1,434 +1,439 @@
/**
* @file aka_array.hh
*
* @author Till Junge <till.junge@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Jan 16 2018
*
* @brief Array container for Akantu
* This container differs from the std::vector from the fact it as 2 dimensions
* a main dimension and the size stored per entries
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#include <typeinfo>
#include <vector>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ARRAY_HH__
-#define __AKANTU_ARRAY_HH__
+#ifndef AKANTU_ARRAY_HH_
+#define AKANTU_ARRAY_HH_
namespace akantu {
/// class that afford to store vectors in static memory
+// NOLINTNEXTLINE(cppcoreguidelines-special-member-functions)
class ArrayBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- explicit ArrayBase(ID id = "") : id(std::move(id)) {}
+ explicit ArrayBase(const ID &id = "") : id(id) {}
ArrayBase(const ArrayBase & other, const ID & id = "") {
- this->id = (id == "") ? other.id : id;
+ this->id = (id.empty()) ? other.id : id;
}
ArrayBase(ArrayBase && other) = default;
ArrayBase & operator=(const ArrayBase & other) = default;
// ArrayBase & operator=(ArrayBase && other) = default;
virtual ~ArrayBase() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the amount of space allocated in bytes
virtual UInt getMemorySize() const = 0;
- /// set the size to zero without freeing the allocated space
- inline void empty();
+ // changed empty to match std::vector empty
+ inline bool empty() const __attribute__((warn_unused_result)) {
+ return size_ == 0;
+ }
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the Size of the Array
UInt size() const { return size_; }
/// Get the number of components
AKANTU_GET_MACRO(NbComponent, nb_component, UInt);
/// Get the name of th array
AKANTU_GET_MACRO(ID, id, const ID &);
/// Set the name of th array
AKANTU_SET_MACRO(ID, id, const ID &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the vector
- ID id{""};
+ ID id;
/// the size used
UInt size_{0};
/// number of components
UInt nb_component{1};
};
/* -------------------------------------------------------------------------- */
namespace {
template <std::size_t dim, typename T> struct IteratorHelper {};
template <typename T> struct IteratorHelper<0, T> { using type = T; };
template <typename T> struct IteratorHelper<1, T> { using type = Vector<T>; };
template <typename T> struct IteratorHelper<2, T> { using type = Matrix<T>; };
template <typename T> struct IteratorHelper<3, T> {
using type = Tensor3<T>;
};
template <std::size_t dim, typename T>
using IteratorHelper_t = typename IteratorHelper<dim, T>::type;
} // namespace
/* -------------------------------------------------------------------------- */
/* Memory handling layer */
/* -------------------------------------------------------------------------- */
enum class ArrayAllocationType {
_default,
_pod,
};
template <typename T>
struct ArrayAllocationTrait
: public std::conditional_t<
std::is_scalar<T>::value,
std::integral_constant<ArrayAllocationType,
ArrayAllocationType::_pod>,
std::integral_constant<ArrayAllocationType,
ArrayAllocationType::_default>> {};
/* -------------------------------------------------------------------------- */
template <typename T,
ArrayAllocationType allocation_trait = ArrayAllocationTrait<T>::value>
class ArrayDataLayer : public ArrayBase {
public:
using value_type = T;
using reference = value_type &;
using pointer_type = value_type *;
using const_reference = const value_type &;
public:
- virtual ~ArrayDataLayer() = default;
+ ~ArrayDataLayer() override = default;
/// Allocation of a new vector
explicit ArrayDataLayer(UInt size = 0, UInt nb_component = 1,
const ID & id = "");
/// Allocation of a new vector with a default value
ArrayDataLayer(UInt size, UInt nb_component, const_reference value,
const ID & id = "");
/// Copy constructor (deep copy)
ArrayDataLayer(const ArrayDataLayer & vect, const ID & id = "");
/// Copy constructor (deep copy)
explicit ArrayDataLayer(const std::vector<value_type> & vect);
// copy operator
ArrayDataLayer & operator=(const ArrayDataLayer & other);
// move constructor
- ArrayDataLayer(ArrayDataLayer && other);
+ ArrayDataLayer(ArrayDataLayer && other) noexcept;
// move assign
- ArrayDataLayer & operator=(ArrayDataLayer && other);
+ ArrayDataLayer & operator=(ArrayDataLayer && other) noexcept;
protected:
// deallocate the memory
virtual void deallocate() {}
// allocate the memory
virtual void allocate(UInt size, UInt nb_component);
// allocate and initialize the memory
virtual void allocate(UInt size, UInt nb_component, const T & value);
public:
/// append a tuple of size nb_component containing value
inline void push_back(const_reference value);
/// append a vector
// inline void push_back(const value_type new_elem[]);
/// append a Vector or a Matrix
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline void push_back(const C<T> & new_elem);
/// changes the allocated size but not the size, if new_size = 0, the size is
/// set to min(current_size and reserve size)
virtual void reserve(UInt size, UInt new_size = UInt(-1));
/// change the size of the Array
virtual void resize(UInt size);
/// change the size of the Array and initialize the values
virtual void resize(UInt size, const T & val);
/// get the amount of space allocated in bytes
inline UInt getMemorySize() const override;
/// Get the real size allocated in memory
inline UInt getAllocatedSize() const;
/// give the address of the memory allocated for this vector
T * storage() const { return values; };
protected:
/// allocation type agnostic data access
T * values{nullptr};
/// data storage
std::vector<T> data_storage;
};
/* -------------------------------------------------------------------------- */
/* Actual Array */
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal> class Array : public ArrayDataLayer<T> {
private:
using parent = ArrayDataLayer<T>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using value_type = typename parent::value_type;
using reference = typename parent::reference;
using pointer_type = typename parent::pointer_type;
using const_reference = typename parent::const_reference;
~Array() override;
Array() : Array(0){};
/// Allocation of a new vector
explicit Array(UInt size, UInt nb_component = 1, const ID & id = "");
/// Allocation of a new vector with a default value
explicit Array(UInt size, UInt nb_component, const_reference value,
const ID & id = "");
/// Copy constructor
Array(const Array & vect, const ID & id = "");
/// Copy constructor (deep copy)
explicit Array(const std::vector<T> & vect);
// copy operator
Array & operator=(const Array & other);
// move constructor
- Array(Array && other) = default;
+ Array(Array && other) noexcept = default;
// move assign
- Array & operator=(Array && other) = default;
+ Array & operator=(Array && other) noexcept = default;
/* ------------------------------------------------------------------------ */
/* Iterator */
/* ------------------------------------------------------------------------ */
/// \todo protected: does not compile with intel check why
public:
template <class R, class it, class IR = R,
bool is_tensor_ = aka::is_tensor<std::decay_t<R>>::value>
class iterator_internal;
public:
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
template <typename R = T> class const_iterator;
template <typename R = T> class iterator;
/* ------------------------------------------------------------------------ */
/// iterator for Array of nb_component = 1
using scalar_iterator = iterator<T>;
/// const_iterator for Array of nb_component = 1
using const_scalar_iterator = const_iterator<T>;
/// iterator returning Vectors of size n on entries of Array with
/// nb_component = n
using vector_iterator = iterator<Vector<T>>;
/// const_iterator returning Vectors of n size on entries of Array with
/// nb_component = n
using const_vector_iterator = const_iterator<Vector<T>>;
/// iterator returning Matrices of size (m, n) on entries of Array with
/// nb_component = m*n
using matrix_iterator = iterator<Matrix<T>>;
/// const iterator returning Matrices of size (m, n) on entries of Array with
/// nb_component = m*n
using const_matrix_iterator = const_iterator<Matrix<T>>;
/// iterator returning Tensor3 of size (m, n, k) on entries of Array with
/// nb_component = m*n*k
using tensor3_iterator = iterator<Tensor3<T>>;
/// const iterator returning Tensor3 of size (m, n, k) on entries of Array
/// with nb_component = m*n*k
using const_tensor3_iterator = const_iterator<Tensor3<T>>;
/* ------------------------------------------------------------------------ */
template <typename... Ns> inline decltype(auto) begin(Ns &&... n);
template <typename... Ns> inline decltype(auto) end(Ns &&... n);
template <typename... Ns> inline decltype(auto) begin(Ns &&... n) const;
template <typename... Ns> inline decltype(auto) end(Ns &&... n) const;
template <typename... Ns> inline decltype(auto) begin_reinterpret(Ns &&... n);
template <typename... Ns> inline decltype(auto) end_reinterpret(Ns &&... n);
template <typename... Ns>
inline decltype(auto) begin_reinterpret(Ns &&... n) const;
template <typename... Ns>
inline decltype(auto) end_reinterpret(Ns &&... n) const;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// search elem in the vector, return the position of the first occurrence or
/// -1 if not found
UInt find(const_reference elem) const;
/// @see Array::find(const_reference elem) const
- UInt find(T elem[]) const;
+// UInt find(T elem[]) const;
inline void push_back(const_reference value) { parent::push_back(value); }
/// append a Vector or a Matrix
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline void push_back(const C<T> & new_elem) {
parent::push_back(new_elem);
}
template <typename Ret> inline void push_back(const iterator<Ret> & it) {
push_back(*it);
}
/// erase the value at position i
inline void erase(UInt i);
/// ask Nico, clarify
template <typename R> inline iterator<R> erase(const iterator<R> & it);
/// @see Array::find(const_reference elem) const
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline UInt find(const C<T> & elem);
/// set all entries of the array to the value t
/// @param t value to fill the array with
inline void set(T t) {
std::fill_n(this->values, this->size_ * this->nb_component, t);
}
- /// set all entries of the array to 0
- inline void clear() { set(T()); }
+ inline void zero() { this->set({}); }
+
+ /// resize the array to 0
+ inline void clear() { this->resize(0); }
/// set all tuples of the array to a given vector or matrix
/// @param vm Matrix or Vector to fill the array with
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline void set(const C<T> & vm);
/// Append the content of the other array to the current one
void append(const Array<T> & other);
/// copy another Array in the current Array, the no_sanity_check allows you to
/// force the copy in cases where you know what you do with two non matching
/// Arrays in terms of n
void copy(const Array<T, is_scal> & other, bool no_sanity_check = false);
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
/// substraction entry-wise
Array<T, is_scal> & operator-=(const Array<T, is_scal> & other);
/// addition entry-wise
Array<T, is_scal> & operator+=(const Array<T, is_scal> & other);
/// multiply evry entry by alpha
Array<T, is_scal> & operator*=(const T & alpha);
/// check if the array are identical entry-wise
bool operator==(const Array<T, is_scal> & other) const;
/// @see Array::operator==(const Array<T, is_scal> & other) const
bool operator!=(const Array<T, is_scal> & other) const;
/// return a reference to the j-th entry of the i-th tuple
inline reference operator()(UInt i, UInt j = 0);
/// return a const reference to the j-th entry of the i-th tuple
inline const_reference operator()(UInt i, UInt j = 0) const;
/// return a reference to the ith component of the 1D array
inline reference operator[](UInt i);
/// return a const reference to the ith component of the 1D array
inline const_reference operator[](UInt i) const;
};
/* -------------------------------------------------------------------------- */
/* Inline Functions Array<T, is_scal> */
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal>
inline std::ostream & operator<<(std::ostream & stream,
const Array<T, is_scal> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
/* Inline Functions ArrayBase */
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream,
const ArrayBase & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "aka_array_tmpl.hh"
-#endif /* __AKANTU_ARRAY_HH__ */
+#endif /* AKANTU_ARRAY_HH_ */
diff --git a/src/common/aka_array_printer.hh b/src/common/aka_array_printer.hh
index bc6e0f8ed..cd0030613 100644
--- a/src/common/aka_array_printer.hh
+++ b/src/common/aka_array_printer.hh
@@ -1,100 +1,100 @@
/**
* @file aka_array_printer.hh
*
* @author Nicolas Richart
*
* @date creation mer jun 19 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_ARRAY_PRINTER_HH__
-#define __AKANTU_AKA_ARRAY_PRINTER_HH__
+#ifndef AKANTU_AKA_ARRAY_PRINTER_HH_
+#define AKANTU_AKA_ARRAY_PRINTER_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class container, bool no_explicit = true> class ArrayPrinter {
public:
ArrayPrinter(const container & cont) : cont(cont) {}
void printself(std::ostream & stream, int indent = 0) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "{";
for (UInt i = 0; i < this->cont.size(); ++i) {
stream << this->cont[i];
if (i != this->cont.size() - 1)
stream << ", ";
}
stream << "}";
}
private:
const container & cont;
};
/* -------------------------------------------------------------------------- */
template <class T> class ArrayPrinter<Array<T>> {
public:
ArrayPrinter(const Array<T> & cont) : cont(cont) {}
void printself(std::ostream & stream, int indent = 0) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "{";
for (UInt i = 0; i < this->cont.size(); ++i) {
stream << "{";
for (UInt j = 0; j < this->cont.getNbComponent(); ++j) {
stream << this->cont(i, j);
if (j != this->cont.getNbComponent() - 1)
stream << ", ";
}
stream << "}";
if (i != this->cont.size() - 1)
stream << ", ";
}
stream << "}";
}
private:
const Array<T> & cont;
};
template <class container>
decltype(auto) make_printer(const container & array) {
return ArrayPrinter<container>(array);
}
/* -------------------------------------------------------------------------- */
template <class T>
inline std::ostream & operator<<(std::ostream & stream,
const ArrayPrinter<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AKANTU_AKA_ARRAY_PRINTER_HH__ */
+#endif /* AKANTU_AKA_ARRAY_PRINTER_HH_ */
diff --git a/src/common/aka_array_tmpl.hh b/src/common/aka_array_tmpl.hh
index 9fa9e9a02..be45fe482 100644
--- a/src/common/aka_array_tmpl.hh
+++ b/src/common/aka_array_tmpl.hh
@@ -1,1373 +1,1335 @@
/**
* @file aka_array_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Inline functions of the classes Array<T> and ArrayBase
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* Inline Functions Array<T> */
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_static_memory.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_ARRAY_TMPL_HH__
-#define __AKANTU_AKA_ARRAY_TMPL_HH__
+#ifndef AKANTU_AKA_ARRAY_TMPL_HH_
+#define AKANTU_AKA_ARRAY_TMPL_HH_
namespace akantu {
namespace debug {
struct ArrayException : public Exception {};
} // namespace debug
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(UInt size,
UInt nb_component,
const ID & id)
: ArrayBase(id) {
allocate(size, nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(UInt size,
UInt nb_component,
const_reference value,
const ID & id)
: ArrayBase(id) {
allocate(size, nb_component, value);
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(const ArrayDataLayer & vect,
const ID & id)
: ArrayBase(vect, id) {
this->data_storage = vect.data_storage;
this->size_ = vect.size_;
this->nb_component = vect.nb_component;
this->values = this->data_storage.data();
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(
const std::vector<value_type> & vect) {
this->data_storage = vect;
this->size_ = vect.size();
this->nb_component = 1;
this->values = this->data_storage.data();
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
-ArrayDataLayer<T, allocation_trait> & ArrayDataLayer<T, allocation_trait>::
-operator=(const ArrayDataLayer & other) {
+ArrayDataLayer<T, allocation_trait> &
+ArrayDataLayer<T, allocation_trait>::operator=(const ArrayDataLayer & other) {
if (this != &other) {
this->data_storage = other.data_storage;
this->nb_component = other.nb_component;
this->size_ = other.size_;
this->values = this->data_storage.data();
}
return *this;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
-ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(ArrayDataLayer && other) =
- default;
+ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(
+ ArrayDataLayer && other) noexcept = default;
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
-ArrayDataLayer<T, allocation_trait> & ArrayDataLayer<T, allocation_trait>::
-operator=(ArrayDataLayer && other) = default;
+ArrayDataLayer<T, allocation_trait> &
+ArrayDataLayer<T, allocation_trait>::operator=(
+ ArrayDataLayer && other) noexcept = default;
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::allocate(UInt new_size,
UInt nb_component) {
this->nb_component = nb_component;
this->resize(new_size);
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::allocate(UInt new_size,
UInt nb_component,
const T & val) {
this->nb_component = nb_component;
this->resize(new_size, val);
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::resize(UInt new_size) {
this->data_storage.resize(new_size * this->nb_component);
this->values = this->data_storage.data();
this->size_ = new_size;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::resize(UInt new_size,
const T & value) {
this->data_storage.resize(new_size * this->nb_component, value);
this->values = this->data_storage.data();
this->size_ = new_size;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::reserve(UInt size, UInt new_size) {
if (new_size != UInt(-1)) {
this->data_storage.resize(new_size * this->nb_component);
}
this->data_storage.reserve(size * this->nb_component);
this->values = this->data_storage.data();
}
/* -------------------------------------------------------------------------- */
/**
* append a tuple to the array with the value value for all components
* @param value the new last tuple or the array will contain nb_component copies
* of value
*/
template <typename T, ArrayAllocationType allocation_trait>
inline void ArrayDataLayer<T, allocation_trait>::push_back(const T & value) {
this->data_storage.push_back(value);
this->values = this->data_storage.data();
this->size_ += 1;
}
/* -------------------------------------------------------------------------- */
/**
* append a matrix or a vector to the array
* @param new_elem a reference to a Matrix<T> or Vector<T> */
template <typename T, ArrayAllocationType allocation_trait>
template <template <typename> class C, typename>
inline void
ArrayDataLayer<T, allocation_trait>::push_back(const C<T> & new_elem) {
AKANTU_DEBUG_ASSERT(
nb_component == new_elem.size(),
"The vector("
<< new_elem.size()
<< ") as not a size compatible with the Array (nb_component="
<< nb_component << ").");
for (UInt i = 0; i < new_elem.size(); ++i) {
this->data_storage.push_back(new_elem[i]);
}
this->values = this->data_storage.data();
this->size_ += 1;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
inline UInt ArrayDataLayer<T, allocation_trait>::getAllocatedSize() const {
return this->data_storage.capacity() / this->nb_component;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
inline UInt ArrayDataLayer<T, allocation_trait>::getMemorySize() const {
return this->data_storage.capacity() * sizeof(T);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename T>
class ArrayDataLayer<T, ArrayAllocationType::_pod> : public ArrayBase {
public:
using value_type = T;
using reference = value_type &;
using pointer_type = value_type *;
using const_reference = const value_type &;
public:
- virtual ~ArrayDataLayer() { deallocate(); }
+ ~ArrayDataLayer() override { deallocate(); }
/// Allocation of a new vector
ArrayDataLayer(UInt size = 0, UInt nb_component = 1, const ID & id = "")
: ArrayBase(id) {
allocate(size, nb_component);
}
/// Allocation of a new vector with a default value
ArrayDataLayer(UInt size, UInt nb_component, const_reference value,
const ID & id = "")
: ArrayBase(id) {
allocate(size, nb_component, value);
}
/// Copy constructor (deep copy)
ArrayDataLayer(const ArrayDataLayer & vect, const ID & id = "")
: ArrayBase(vect, id) {
allocate(vect.size(), vect.getNbComponent());
std::copy_n(vect.storage(), this->size_ * this->nb_component, values);
}
/// Copy constructor (deep copy)
explicit ArrayDataLayer(const std::vector<value_type> & vect) {
allocate(vect.size(), 1);
std::copy_n(vect.data(), this->size_ * this->nb_component, values);
}
// copy operator
inline ArrayDataLayer & operator=(const ArrayDataLayer & other) {
if (this != &other) {
allocate(other.size(), other.getNbComponent());
std::copy_n(other.storage(), this->size_ * this->nb_component, values);
}
return *this;
}
// move constructor
- inline ArrayDataLayer(ArrayDataLayer && other) = default;
+ inline ArrayDataLayer(ArrayDataLayer && other) noexcept = default;
// move assign
- inline ArrayDataLayer & operator=(ArrayDataLayer && other) = default;
+ inline ArrayDataLayer & operator=(ArrayDataLayer && other) noexcept = default;
protected:
// deallocate the memory
- virtual void deallocate() { free(this->values); }
+ virtual void deallocate() {
+ // NOLINTNEXTLINE(cppcoreguidelines-owning-memory,
+ // cppcoreguidelines-no-malloc)
+ free(this->values);
+ }
// allocate the memory
virtual inline void allocate(UInt size, UInt nb_component) {
if (size != 0) { // malloc can return a non NULL pointer in case size is 0
- this->values =
- static_cast<T *>(std::malloc(nb_component * size * sizeof(T)));
+ this->values = static_cast<T *>( // NOLINT
+ std::malloc(nb_component * size * sizeof(T))); // NOLINT
}
if (this->values == nullptr and size != 0) {
throw std::bad_alloc();
}
this->nb_component = nb_component;
this->allocated_size = this->size_ = size;
}
// allocate and initialize the memory
virtual inline void allocate(UInt size, UInt nb_component, const T & value) {
allocate(size, nb_component);
std::fill_n(values, size * nb_component, value);
}
public:
/// append a tuple of size nb_component containing value
inline void push_back(const_reference value) {
resize(this->size_ + 1, value);
}
/// append a Vector or a Matrix
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline void push_back(const C<T> & new_elem) {
AKANTU_DEBUG_ASSERT(
nb_component == new_elem.size(),
"The vector("
<< new_elem.size()
<< ") as not a size compatible with the Array (nb_component="
<< nb_component << ").");
this->resize(this->size_ + 1);
std::copy_n(new_elem.storage(), new_elem.size(),
values + this->nb_component * (this->size_ - 1));
}
/// changes the allocated size but not the size
virtual void reserve(UInt size, UInt new_size = UInt(-1)) {
UInt tmp_size = this->size_;
- if (new_size != UInt(-1))
+ if (new_size != UInt(-1)) {
tmp_size = new_size;
+ }
this->resize(size);
this->size_ = std::min(this->size_, tmp_size);
}
/// change the size of the Array
virtual void resize(UInt size) {
if (size * this->nb_component == 0) {
- free(values);
+ free(values); // NOLINT: cppcoreguidelines-no-malloc
values = nullptr;
this->allocated_size = 0;
} else {
if (this->values == nullptr) {
this->allocate(size, this->nb_component);
return;
}
Int diff = size - allocated_size;
UInt size_to_allocate = (std::abs(diff) > AKANTU_MIN_ALLOCATION)
? size
: (diff > 0)
? allocated_size + AKANTU_MIN_ALLOCATION
: allocated_size;
-
- auto * tmp_ptr = reinterpret_cast<T *>(realloc(
- this->values, size_to_allocate * this->nb_component * sizeof(T)));
+ auto * tmp_ptr = reinterpret_cast<T *>( // NOLINT
+ realloc(this->values,
+ size_to_allocate * this->nb_component * sizeof(T))); // NOLINT
if (tmp_ptr == nullptr) {
StaticMemory::getStaticMemory().printself(std::cerr);
throw std::bad_alloc();
}
this->values = tmp_ptr;
this->allocated_size = size_to_allocate;
}
this->size_ = size;
}
/// change the size of the Array and initialize the values
virtual void resize(UInt size, const T & val) {
UInt tmp_size = this->size_;
this->resize(size);
if (size > tmp_size) {
+ // NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
std::fill_n(values + this->nb_component * tmp_size,
(size - tmp_size) * this->nb_component, val);
}
}
/// get the amount of space allocated in bytes
- inline UInt getMemorySize() const override final {
+ inline UInt getMemorySize() const final {
return this->allocated_size * this->nb_component * sizeof(T);
}
/// Get the real size allocated in memory
inline UInt getAllocatedSize() const { return this->allocated_size; }
/// give the address of the memory allocated for this vector
T * storage() const { return values; };
protected:
/// allocation type agnostic data access
T * values{nullptr};
UInt allocated_size{0};
};
-/* -------------------------------------------------------------------------- */
-
-/* -------------------------------------------------------------------------- */
-/* template <class T> class AllocatorMalloc : public Allocator<T> {
-public:
- T * allocate(UInt size, UInt nb_component) override final {
- auto * ptr = reinterpret_cast<T *>(malloc(nb_component * size * sizeof(T)));
-
- if (ptr == nullptr and size != 0) {
- throw std::bad_alloc();
- }
- return ptr;
- }
-
- void deallocate(T * ptr, UInt size, UInt ,
- UInt nb_component) override final {
- if (ptr) {
- if (not is_scalar<T>::value) {
- for (UInt i = 0; i < size * nb_component; ++i) {
- (ptr + i)->~T();
- }
- }
- free(ptr);
- }
- }
-
- std::tuple<T *, UInt> resize(UInt new_size, UInt size, UInt allocated_size,
- UInt nb_component, T * ptr) override final {
- UInt size_to_alloc = 0;
-
- if (not is_scalar<T>::value and (new_size < size)) {
- for (UInt i = new_size * nb_component; i < size * nb_component; ++i) {
- (ptr + i)->~T();
- }
- }
-
- // free some memory
- if (new_size == 0) {
- free(ptr);
- return std::make_tuple(nullptr, 0);
- }
-
- if (new_size <= allocated_size) {
- if (allocated_size - new_size > AKANTU_MIN_ALLOCATION) {
- size_to_alloc = new_size;
- } else {
- return std::make_tuple(ptr, allocated_size);
- }
- } else {
- // allocate more memory
- size_to_alloc = (new_size - allocated_size < AKANTU_MIN_ALLOCATION)
- ? allocated_size + AKANTU_MIN_ALLOCATION
- : new_size;
- }
-
- auto * tmp_ptr = reinterpret_cast<T *>(
- realloc(ptr, size_to_alloc * nb_component * sizeof(T)));
- if (tmp_ptr == nullptr) {
- throw std::bad_alloc();
- }
-
- return std::make_tuple(tmp_ptr, size_to_alloc);
- }
-};
-*/
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline auto Array<T, is_scal>::operator()(UInt i, UInt j) -> reference {
AKANTU_DEBUG_ASSERT(this->size_ > 0,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < this->size_) && (j < this->nb_component),
"The value at position ["
<< i << "," << j << "] is out of range in array \""
<< this->id << "\"");
return this->values[i * this->nb_component + j];
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline auto Array<T, is_scal>::operator()(UInt i, UInt j) const
-> const_reference {
AKANTU_DEBUG_ASSERT(this->size_ > 0,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < this->size_) && (j < this->nb_component),
"The value at position ["
<< i << "," << j << "] is out of range in array \""
<< this->id << "\"");
+ // NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
return this->values[i * this->nb_component + j];
}
template <class T, bool is_scal>
inline auto Array<T, is_scal>::operator[](UInt i) -> reference {
AKANTU_DEBUG_ASSERT(this->size_ > 0,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < this->size_ * this->nb_component),
"The value at position ["
<< i << "] is out of range in array \"" << this->id
<< "\"");
return this->values[i];
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline auto Array<T, is_scal>::operator[](UInt i) const -> const_reference {
AKANTU_DEBUG_ASSERT(this->size_ > 0,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < this->size_ * this->nb_component),
"The value at position ["
<< i << "] is out of range in array \"" << this->id
<< "\"");
return this->values[i];
}
/* -------------------------------------------------------------------------- */
/**
* erase an element. If the erased element is not the last of the array, the
* last element is moved into the hole in order to maintain contiguity. This
* may invalidate existing iterators (For instance an iterator obtained by
* Array::end() is no longer correct) and will change the order of the
* elements.
* @param i index of element to erase
*/
template <class T, bool is_scal> inline void Array<T, is_scal>::erase(UInt i) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT((this->size_ > 0), "The array is empty");
AKANTU_DEBUG_ASSERT((i < this->size_), "The element at position ["
<< i << "] is out of range (" << i
<< ">=" << this->size_ << ")");
if (i != (this->size_ - 1)) {
for (UInt j = 0; j < this->nb_component; ++j) {
+ // NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
this->values[i * this->nb_component + j] =
this->values[(this->size_ - 1) * this->nb_component + j];
}
}
this->resize(this->size_ - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Subtract another array entry by entry from this array in place. Both arrays
* must
* have the same size and nb_component. If the arrays have different shapes,
* code compiled in debug mode will throw an expeption and optimised code
* will behave in an unpredicted manner
* @param other array to subtract from this
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> &
-Array<T, is_scal>::operator-=(const Array<T, is_scal> &other) {
+Array<T, is_scal>::operator-=(const Array<T, is_scal> & other) {
AKANTU_DEBUG_ASSERT((this->size_ == other.size_) &&
(this->nb_component == other.nb_component),
"The too array don't have the same sizes");
T * a = this->values;
- T *b = other.storage();
+ T * b = other.storage();
for (UInt i = 0; i < this->size_ * this->nb_component; ++i) {
*a -= *b;
++a;
++b;
}
return *this;
}
/* -------------------------------------------------------------------------- */
/**
* Add another array entry by entry to this array in place. Both arrays must
* have the same size and nb_component. If the arrays have different shapes,
* code compiled in debug mode will throw an expeption and optimised code
* will behave in an unpredicted manner
* @param other array to add to this
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> &
Array<T, is_scal>::operator+=(const Array<T, is_scal> & other) {
AKANTU_DEBUG_ASSERT((this->size_ == other.size()) &&
(this->nb_component == other.nb_component),
"The too array don't have the same sizes");
T * a = this->values;
- T *b = other.storage();
+ T * b = other.storage();
for (UInt i = 0; i < this->size_ * this->nb_component; ++i) {
*a++ += *b++;
}
return *this;
}
/* -------------------------------------------------------------------------- */
/**
* Multiply all entries of this array by a scalar in place
* @param alpha scalar multiplicant
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> & Array<T, is_scal>::operator*=(const T & alpha) {
T * a = this->values;
for (UInt i = 0; i < this->size_ * this->nb_component; ++i) {
*a++ *= alpha;
}
return *this;
}
/* -------------------------------------------------------------------------- */
/**
* Compare this array element by element to another.
* @param other array to compare to
* @return true it all element are equal and arrays have the same shape, else
* false
*/
template <class T, bool is_scal>
-bool Array<T, is_scal>::operator==(const Array<T, is_scal> &other) const {
+bool Array<T, is_scal>::operator==(const Array<T, is_scal> & other) const {
bool equal = this->nb_component == other.nb_component &&
this->size_ == other.size_ && this->id == other.id;
- if (!equal)
+ if (not equal) {
return false;
-
- if (this->values == other.storage())
+ }
+ if (this->values == other.storage()) {
return true;
- else
- return std::equal(this->values,
- this->values + this->size_ * this->nb_component,
- other.storage());
+ }
+
+ // NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
+ return std::equal(this->values,
+ this->values + this->size_ * this->nb_component,
+ other.storage());
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
-bool Array<T, is_scal>::operator!=(const Array<T, is_scal> & array) const {
- return !operator==(array);
+bool Array<T, is_scal>::operator!=(const Array<T, is_scal> & other) const {
+ return !operator==(other);
}
/* -------------------------------------------------------------------------- */
/**
* set all tuples of the array to a given vector or matrix
* @param vm Matrix or Vector to fill the array with
*/
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline void Array<T, is_scal>::set(const C<T> & vm) {
AKANTU_DEBUG_ASSERT(
this->nb_component == vm.size(),
"The size of the object does not match the number of components");
for (T * it = this->values;
it < this->values + this->nb_component * this->size_;
it += this->nb_component) {
std::copy_n(vm.storage(), this->nb_component, it);
}
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
void Array<T, is_scal>::append(const Array<T> & other) {
AKANTU_DEBUG_ASSERT(
this->nb_component == other.nb_component,
"Cannot append an array with a different number of component");
UInt old_size = this->size_;
this->resize(this->size_ + other.size());
T * tmp = this->values + this->nb_component * old_size;
std::copy_n(other.storage(), other.size() * this->nb_component, tmp);
}
/* -------------------------------------------------------------------------- */
/* Functions Array<T, is_scal> */
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const ID & id)
: parent(size, nb_component, id) {}
template <>
inline Array<std::string, false>::Array(UInt size, UInt nb_component,
const ID & id)
: parent(size, nb_component, "", id) {}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const_reference value,
const ID & id)
: parent(size, nb_component, value, id) {}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(const Array & vect, const ID & id)
: parent(vect, id) {}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
-Array<T, is_scal> & Array<T, is_scal>::
-operator=(const Array<T, is_scal> & other) {
+Array<T, is_scal> &
+Array<T, is_scal>::operator=(const Array<T, is_scal> & other) {
AKANTU_DEBUG_WARNING("You are copying the array "
<< this->id << " are you sure it is on purpose");
- if (&other == this)
+ if (&other == this) {
return *this;
+ }
parent::operator=(other);
-
return *this;
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(const std::vector<T> & vect) : parent(vect) {}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal> Array<T, is_scal>::~Array() = default;
/* -------------------------------------------------------------------------- */
/**
* search elem in the array, return the position of the first occurrence or
* -1 if not found
* @param elem the element to look for
* @return index of the first occurrence of elem or -1 if elem is not present
*/
template <class T, bool is_scal>
UInt Array<T, is_scal>::find(const_reference elem) const {
AKANTU_DEBUG_IN();
auto begin = this->begin();
auto end = this->end();
auto it = std::find(begin, end, elem);
AKANTU_DEBUG_OUT();
return (it != end) ? it - begin : UInt(-1);
}
/* -------------------------------------------------------------------------- */
-template <class T, bool is_scal> UInt Array<T, is_scal>::find(T elem[]) const {
- AKANTU_DEBUG_IN();
- T * it = this->values;
- UInt i = 0;
- for (; i < this->size_; ++i) {
- if (*it == elem[0]) {
- T * cit = it;
- UInt c = 0;
- for (; (c < this->nb_component) && (*cit == elem[c]); ++c, ++cit)
- ;
- if (c == this->nb_component) {
- AKANTU_DEBUG_OUT();
- return i;
- }
- }
- it += this->nb_component;
- }
- return UInt(-1);
-}
+// template <class T, bool is_scal> UInt Array<T, is_scal>::find(T elem[]) const
+// {
+// AKANTU_DEBUG_IN();
+// T * it = this->values;
+// UInt i = 0;
+// for (; i < this->size_; ++i) {
+// if (*it == elem[0]) {
+// T * cit = it;
+// UInt c = 0;
+// for (; (c < this->nb_component) && (*cit == elem[c]); ++c, ++cit)
+// ;
+// if (c == this->nb_component) {
+// AKANTU_DEBUG_OUT();
+// return i;
+// }
+// }
+// it += this->nb_component;
+// }
+// return UInt(-1);
+// }
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline UInt Array<T, is_scal>::find(const C<T> & elem) {
AKANTU_DEBUG_ASSERT(elem.size() == this->nb_component,
"Cannot find an element with a wrong size ("
<< elem.size() << ") != " << this->nb_component);
- return this->find(elem.storage());
+ return this->find(*elem.storage());
}
/* -------------------------------------------------------------------------- */
/**
* copy the content of another array. This overwrites the current content.
* @param other Array to copy into this array. It has to have the same
* nb_component as this. If compiled in debug mode, an incorrect other will
* result in an exception being thrown. Optimised code may result in
* unpredicted behaviour.
* @param no_sanity_check turns off all checkes
*/
template <class T, bool is_scal>
-void Array<T, is_scal>::copy(const Array<T, is_scal> &other,
+void Array<T, is_scal>::copy(const Array<T, is_scal> & other,
bool no_sanity_check) {
AKANTU_DEBUG_IN();
- if (not no_sanity_check)
- if (other.nb_component != this->nb_component)
- AKANTU_ERROR("The two arrays do not have the same number of components");
+ if (not no_sanity_check and (other.nb_component != this->nb_component)) {
+ AKANTU_ERROR("The two arrays do not have the same number of components");
+ }
this->resize((other.size_ * other.nb_component) / this->nb_component);
std::copy_n(other.storage(), this->size_ * this->nb_component, this->values);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool is_scal> class ArrayPrintHelper {
public:
template <typename T>
static void print_content(const Array<T> & vect, std::ostream & stream,
int indent) {
std::string space(indent, AKANTU_INDENT);
stream << space << " + values : {";
for (UInt i = 0; i < vect.size(); ++i) {
stream << "{";
for (UInt j = 0; j < vect.getNbComponent(); ++j) {
stream << vect(i, j);
- if (j != vect.getNbComponent() - 1)
+ if (j != vect.getNbComponent() - 1) {
stream << ", ";
+ }
}
stream << "}";
- if (i != vect.size() - 1)
+ if (i != vect.size() - 1) {
stream << ", ";
+ }
}
stream << "}" << std::endl;
}
};
template <> class ArrayPrintHelper<false> {
public:
template <typename T>
static void print_content(__attribute__((unused)) const Array<T> & vect,
__attribute__((unused)) std::ostream & stream,
__attribute__((unused)) int indent) {}
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
void Array<T, is_scal>::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
std::streamsize prec = stream.precision();
std::ios_base::fmtflags ff = stream.flags();
stream.setf(std::ios_base::showbase);
stream.precision(2);
stream << space << "Array<" << debug::demangle(typeid(T).name()) << "> ["
<< std::endl;
stream << space << " + id : " << this->id << std::endl;
stream << space << " + size : " << this->size_ << std::endl;
stream << space << " + nb_component : " << this->nb_component << std::endl;
stream << space << " + allocated size : " << this->getAllocatedSize()
<< std::endl;
stream << space
<< " + memory size : " << printMemorySize<T>(this->getMemorySize())
<< std::endl;
- if (!AKANTU_DEBUG_LEVEL_IS_TEST())
+ if (not AKANTU_DEBUG_LEVEL_IS_TEST()) {
stream << space << " + address : " << std::hex << this->values
<< std::dec << std::endl;
+ }
stream.precision(prec);
stream.flags(ff);
if (AKANTU_DEBUG_TEST(dblDump) || AKANTU_DEBUG_LEVEL_IS_TEST()) {
ArrayPrintHelper<is_scal or std::is_enum<T>::value>::print_content(
*this, stream, indent);
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/* Inline Functions ArrayBase */
/* -------------------------------------------------------------------------- */
-inline void ArrayBase::empty() { this->size_ = 0; }
+//inline bool ArrayBase::empty() { return (this->size_ == 0); }
/* -------------------------------------------------------------------------- */
/* Iterators */
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <class R, class daughter, class IR, bool is_tensor>
class Array<T, is_scal>::iterator_internal {
public:
using value_type = R;
using pointer = R *;
using reference = R &;
using const_reference = const R &;
using internal_value_type = IR;
using internal_pointer = IR *;
using difference_type = std::ptrdiff_t;
using iterator_category = std::random_access_iterator_tag;
static_assert(not is_tensor, "Cannot handle tensors");
public:
iterator_internal(pointer data = nullptr) : ret(data), initial(data){};
iterator_internal(const iterator_internal & it) = default;
- iterator_internal(iterator_internal && it) = default;
+ iterator_internal(iterator_internal && it) noexcept = default;
virtual ~iterator_internal() = default;
inline iterator_internal & operator=(const iterator_internal & it) = default;
+ inline iterator_internal &
+ operator=(iterator_internal && it) noexcept = default;
UInt getCurrentIndex() { return (this->ret - this->initial); };
inline reference operator*() { return *ret; };
inline const_reference operator*() const { return *ret; };
inline pointer operator->() { return ret; };
inline daughter & operator++() {
++ret;
return static_cast<daughter &>(*this);
};
inline daughter & operator--() {
--ret;
return static_cast<daughter &>(*this);
};
inline daughter & operator+=(const UInt n) {
ret += n;
return static_cast<daughter &>(*this);
}
inline daughter & operator-=(const UInt n) {
ret -= n;
return static_cast<daughter &>(*this);
}
inline reference operator[](const UInt n) { return ret[n]; }
inline bool operator==(const iterator_internal & other) const {
return ret == other.ret;
}
inline bool operator!=(const iterator_internal & other) const {
return ret != other.ret;
}
inline bool operator<(const iterator_internal & other) const {
return ret < other.ret;
}
inline bool operator<=(const iterator_internal & other) const {
return ret <= other.ret;
}
inline bool operator>(const iterator_internal & other) const {
return ret > other.ret;
}
inline bool operator>=(const iterator_internal & other) const {
return ret >= other.ret;
}
inline daughter operator-(difference_type n) { return daughter(ret - n); }
inline daughter operator+(difference_type n) { return daughter(ret + n); }
inline difference_type operator-(const iterator_internal & b) {
return ret - b.ret;
}
inline pointer data() const { return ret; }
protected:
pointer ret{nullptr};
pointer initial{nullptr};
};
/* -------------------------------------------------------------------------- */
/**
* Specialization for scalar types
*/
template <class T, bool is_scal>
template <class R, class daughter, class IR>
class Array<T, is_scal>::iterator_internal<R, daughter, IR, true> {
public:
using value_type = R;
using pointer = R *;
using reference = R &;
using proxy = typename R::proxy;
using const_proxy = const typename R::proxy;
using const_reference = const R &;
using internal_value_type = IR;
using internal_pointer = IR *;
using difference_type = std::ptrdiff_t;
using iterator_category = std::random_access_iterator_tag;
using pointer_type = typename Array<T, is_scal>::pointer_type;
public:
iterator_internal() = default;
iterator_internal(pointer_type data, UInt _offset)
: _offset(_offset), initial(data), ret(nullptr), ret_ptr(data) {
AKANTU_ERROR(
"The constructor should never be called it is just an ugly trick...");
}
iterator_internal(std::unique_ptr<internal_value_type> && wrapped)
: _offset(wrapped->size()), initial(wrapped->storage()),
ret(std::move(wrapped)), ret_ptr(ret->storage()) {}
iterator_internal(const iterator_internal & it) {
if (this != &it) {
this->_offset = it._offset;
this->initial = it.initial;
this->ret_ptr = it.ret_ptr;
this->ret = std::make_unique<internal_value_type>(*it.ret, false);
}
}
- iterator_internal(iterator_internal && it) = default;
+ iterator_internal(iterator_internal && it) noexcept = default;
virtual ~iterator_internal() = default;
inline iterator_internal & operator=(const iterator_internal & it) {
if (this != &it) {
this->_offset = it._offset;
this->initial = it.initial;
this->ret_ptr = it.ret_ptr;
- if (this->ret)
+ if (this->ret) {
this->ret->shallowCopy(*it.ret);
- else
+ } else {
this->ret = std::make_unique<internal_value_type>(*it.ret, false);
+ }
}
return *this;
}
+ inline iterator_internal &
+ operator=(iterator_internal && it) noexcept = default;
+
UInt getCurrentIndex() {
return (this->ret_ptr - this->initial) / this->_offset;
};
inline reference operator*() {
ret->values = ret_ptr;
return *ret;
};
inline const_reference operator*() const {
ret->values = ret_ptr;
return *ret;
};
inline pointer operator->() {
ret->values = ret_ptr;
return ret.get();
};
inline daughter & operator++() {
ret_ptr += _offset;
return static_cast<daughter &>(*this);
};
inline daughter & operator--() {
ret_ptr -= _offset;
return static_cast<daughter &>(*this);
};
inline daughter & operator+=(const UInt n) {
ret_ptr += _offset * n;
return static_cast<daughter &>(*this);
}
inline daughter & operator-=(const UInt n) {
ret_ptr -= _offset * n;
return static_cast<daughter &>(*this);
}
inline proxy operator[](const UInt n) {
ret->values = ret_ptr + n * _offset;
return proxy(*ret);
}
- inline const_proxy operator[](const UInt n) const {
+ inline const_proxy operator[](const UInt n) const { // NOLINT
ret->values = ret_ptr + n * _offset;
return const_proxy(*ret);
}
inline bool operator==(const iterator_internal & other) const {
return this->ret_ptr == other.ret_ptr;
}
inline bool operator!=(const iterator_internal & other) const {
return this->ret_ptr != other.ret_ptr;
}
inline bool operator<(const iterator_internal & other) const {
return this->ret_ptr < other.ret_ptr;
}
inline bool operator<=(const iterator_internal & other) const {
return this->ret_ptr <= other.ret_ptr;
}
inline bool operator>(const iterator_internal & other) const {
return this->ret_ptr > other.ret_ptr;
}
inline bool operator>=(const iterator_internal & other) const {
return this->ret_ptr >= other.ret_ptr;
}
inline daughter operator+(difference_type n) {
daughter tmp(static_cast<daughter &>(*this));
tmp += n;
return tmp;
}
inline daughter operator-(difference_type n) {
daughter tmp(static_cast<daughter &>(*this));
tmp -= n;
return tmp;
}
inline difference_type operator-(const iterator_internal & b) {
return (this->ret_ptr - b.ret_ptr) / _offset;
}
inline pointer_type data() const { return ret_ptr; }
inline difference_type offset() const { return _offset; }
protected:
UInt _offset{0};
pointer_type initial{nullptr};
std::unique_ptr<internal_value_type> ret{nullptr};
pointer_type ret_ptr{nullptr};
};
/* -------------------------------------------------------------------------- */
/* Iterators */
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename R>
class Array<T, is_scal>::const_iterator
: public iterator_internal<const R, Array<T, is_scal>::const_iterator<R>,
R> {
public:
using parent = iterator_internal<const R, const_iterator, R>;
using value_type = typename parent::value_type;
using pointer = typename parent::pointer;
using reference = typename parent::reference;
using difference_type = typename parent::difference_type;
using iterator_category = typename parent::iterator_category;
public:
- const_iterator() : parent(){};
- // const_iterator(pointer_type data, UInt offset) : parent(data, offset) {}
- // const_iterator(pointer warped) : parent(warped) {}
- // const_iterator(const parent & it) : parent(it) {}
+ ~const_iterator() override = default;
+ const_iterator() = default;
const_iterator(const const_iterator & it) = default;
- const_iterator(const_iterator && it) = default;
+ const_iterator(const_iterator && it) noexcept = default;
+
+ const_iterator & operator=(const const_iterator & it) = default;
+ const_iterator & operator=(const_iterator && it) noexcept = default;
template <typename P,
typename = std::enable_if_t<not aka::is_tensor<P>::value>>
const_iterator(P * data) : parent(data) {}
template <typename UP_P, typename = std::enable_if_t<aka::is_tensor<
typename UP_P::element_type>::value>>
const_iterator(UP_P && tensor) : parent(std::forward<UP_P>(tensor)) {}
-
- const_iterator & operator=(const const_iterator & it) = default;
};
/* -------------------------------------------------------------------------- */
template <class T, class R, bool is_tensor_ = aka::is_tensor<R>::value>
struct ConstConverterIteratorHelper {
using const_iterator = typename Array<T>::template const_iterator<R>;
using iterator = typename Array<T>::template iterator<R>;
static inline const_iterator convert(const iterator & it) {
return const_iterator(std::unique_ptr<R>(new R(*it, false)));
}
};
template <class T, class R> struct ConstConverterIteratorHelper<T, R, false> {
using const_iterator = typename Array<T>::template const_iterator<R>;
using iterator = typename Array<T>::template iterator<R>;
static inline const_iterator convert(const iterator & it) {
return const_iterator(it.data());
}
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename R>
class Array<T, is_scal>::iterator
: public iterator_internal<R, Array<T, is_scal>::iterator<R>> {
public:
using parent = iterator_internal<R, iterator>;
using value_type = typename parent::value_type;
using pointer = typename parent::pointer;
using reference = typename parent::reference;
using difference_type = typename parent::difference_type;
using iterator_category = typename parent::iterator_category;
public:
- iterator() : parent(){};
+ ~iterator() override = default;
+ iterator() = default;
iterator(const iterator & it) = default;
- iterator(iterator && it) = default;
+ iterator(iterator && it) noexcept = default;
+ iterator & operator=(const iterator & it) = default;
+ iterator & operator=(iterator && it) noexcept = default;
template <typename P,
typename = std::enable_if_t<not aka::is_tensor<P>::value>>
iterator(P * data) : parent(data) {}
template <typename UP_P, typename = std::enable_if_t<aka::is_tensor<
typename UP_P::element_type>::value>>
iterator(UP_P && tensor) : parent(std::forward<UP_P>(tensor)) {}
- iterator & operator=(const iterator & it) = default;
-
operator const_iterator<R>() {
return ConstConverterIteratorHelper<T, R>::convert(*this);
}
};
/* -------------------------------------------------------------------------- */
/* Begin/End functions implementation */
/* -------------------------------------------------------------------------- */
namespace detail {
template <class Tuple, size_t... Is>
- constexpr auto take_front_impl(Tuple && t, std::index_sequence<Is...>) {
+ constexpr auto take_front_impl(Tuple && t,
+ std::index_sequence<Is...> /*idxs*/) {
return std::make_tuple(std::get<Is>(std::forward<Tuple>(t))...);
}
template <size_t N, class Tuple> constexpr auto take_front(Tuple && t) {
return take_front_impl(std::forward<Tuple>(t),
std::make_index_sequence<N>{});
}
template <typename... V> constexpr auto product_all(V &&... v) {
std::common_type_t<int, V...> result = 1;
(void)std::initializer_list<int>{(result *= v, 0)...};
return result;
}
template <typename... T> std::string to_string_all(T &&... t) {
- if (sizeof...(T) == 0)
+ if (sizeof...(T) == 0) {
return "";
+ }
std::stringstream ss;
bool noComma = true;
ss << "(";
(void)std::initializer_list<bool>{
(ss << (noComma ? "" : ", ") << t, noComma = false)...};
ss << ")";
return ss.str();
}
template <std::size_t N> struct InstantiationHelper {
template <typename type, typename T, typename... Ns>
static auto instantiate(T && data, Ns... ns) {
return std::make_unique<type>(data, ns...);
}
};
template <> struct InstantiationHelper<0> {
template <typename type, typename T> static auto instantiate(T && data) {
return data;
}
};
template <typename Arr, typename T, typename... Ns>
decltype(auto) get_iterator(Arr && array, T * data, Ns &&... ns) {
using type = IteratorHelper_t<sizeof...(Ns) - 1, T>;
using array_type = std::decay_t<Arr>;
using iterator =
std::conditional_t<std::is_const<std::remove_reference_t<Arr>>::value,
typename array_type::template const_iterator<type>,
typename array_type::template iterator<type>>;
static_assert(sizeof...(Ns), "You should provide a least one size");
if (array.getNbComponent() * array.size() !=
product_all(std::forward<Ns>(ns)...)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::ArrayException(),
"The iterator on "
<< debug::demangle(typeid(Arr).name())
<< to_string_all(array.size(), array.getNbComponent())
<< "is not compatible with the type "
<< debug::demangle(typeid(type).name()) << to_string_all(ns...));
}
auto && wrapped = aka::apply(
[&](auto... n) {
return InstantiationHelper<sizeof...(n)>::template instantiate<type>(
data, n...);
},
take_front<sizeof...(Ns) - 1>(std::make_tuple(ns...)));
return iterator(std::move(wrapped));
}
} // namespace detail
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin(Ns &&... ns) {
return detail::get_iterator(*this, this->values, std::forward<Ns>(ns)...,
this->size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end(Ns &&... ns) {
return detail::get_iterator(*this,
this->values + this->nb_component * this->size_,
std::forward<Ns>(ns)..., this->size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin(Ns &&... ns) const {
return detail::get_iterator(*this, this->values, std::forward<Ns>(ns)...,
this->size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end(Ns &&... ns) const {
return detail::get_iterator(*this,
this->values + this->nb_component * this->size_,
std::forward<Ns>(ns)..., this->size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin_reinterpret(Ns &&... ns) {
return detail::get_iterator(*this, this->values, std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end_reinterpret(Ns &&... ns) {
return detail::get_iterator(
*this, this->values + detail::product_all(std::forward<Ns>(ns)...),
std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin_reinterpret(Ns &&... ns) const {
return detail::get_iterator(*this, this->values, std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end_reinterpret(Ns &&... ns) const {
return detail::get_iterator(
*this, this->values + detail::product_all(std::forward<Ns>(ns)...),
std::forward<Ns>(ns)...);
}
/* -------------------------------------------------------------------------- */
/* Views */
/* -------------------------------------------------------------------------- */
namespace detail {
template <typename Array, typename... Ns> class ArrayView {
using tuple = std::tuple<Ns...>;
public:
- ArrayView(Array && array, Ns... ns)
+ ~ArrayView() = default;
+ ArrayView(Array && array, Ns... ns) noexcept
: array(array), sizes(std::move(ns)...) {}
- ArrayView(ArrayView && array_view) = default;
-
+ ArrayView(const ArrayView & array_view) = default;
ArrayView & operator=(const ArrayView & array_view) = default;
- ArrayView & operator=(ArrayView && array_view) = default;
+
+ ArrayView(ArrayView && array_view) noexcept = default;
+ ArrayView & operator=(ArrayView && array_view) noexcept = default;
decltype(auto) begin() {
return aka::apply(
[&](auto &&... ns) { return array.get().begin_reinterpret(ns...); },
sizes);
}
decltype(auto) begin() const {
return aka::apply(
[&](auto &&... ns) { return array.get().begin_reinterpret(ns...); },
sizes);
}
decltype(auto) end() {
return aka::apply(
[&](auto &&... ns) { return array.get().end_reinterpret(ns...); },
sizes);
}
decltype(auto) end() const {
return aka::apply(
[&](auto &&... ns) { return array.get().end_reinterpret(ns...); },
sizes);
}
decltype(auto) size() const {
return std::get<std::tuple_size<tuple>::value - 1>(sizes);
}
decltype(auto) dims() const { return std::tuple_size<tuple>::value - 1; }
private:
std::reference_wrapper<std::remove_reference_t<Array>> array;
tuple sizes;
};
} // namespace detail
/* -------------------------------------------------------------------------- */
template <typename Array, typename... Ns>
-decltype(auto) make_view(Array && array, Ns... ns) {
+decltype(auto) make_view(Array && array, const Ns... ns) {
static_assert(aka::conjunction<std::is_integral<std::decay_t<Ns>>...>::value,
"Ns should be integral types");
+ AKANTU_DEBUG_ASSERT((detail::product_all(ns...) != 0),
+ "You must specify non zero dimensions");
auto size = std::forward<decltype(array)>(array).size() *
std::forward<decltype(array)>(array).getNbComponent() /
detail::product_all(ns...);
return detail::ArrayView<Array, std::common_type_t<size_t, Ns>...,
std::common_type_t<size_t, decltype(size)>>(
std::forward<Array>(array), std::move(ns)..., size);
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename R>
inline typename Array<T, is_scal>::template iterator<R>
Array<T, is_scal>::erase(const iterator<R> & it) {
T * curr = it.data();
UInt pos = (curr - this->values) / this->nb_component;
erase(pos);
iterator<R> rit = it;
return --rit;
}
} // namespace akantu
-#endif /* __AKANTU_AKA_ARRAY_TMPL_HH__ */
+#endif /* AKANTU_AKA_ARRAY_TMPL_HH_ */
diff --git a/src/common/aka_bbox.hh b/src/common/aka_bbox.hh
index 97c0709a4..12682854b 100644
--- a/src/common/aka_bbox.hh
+++ b/src/common/aka_bbox.hh
@@ -1,264 +1,266 @@
/**
* @file aka_bbox.hh
*
* @author Nicolas Richart
*
* @date creation Mon Feb 12 2018
*
* @brief A simple bounding box class
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "aka_types.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_BBOX_HH__
-#define __AKANTU_AKA_BBOX_HH__
+#ifndef AKANTU_AKA_BBOX_HH_
+#define AKANTU_AKA_BBOX_HH_
namespace akantu {
class BBox {
public:
BBox() = default;
BBox(UInt spatial_dimension)
: dim(spatial_dimension),
lower_bounds(spatial_dimension, std::numeric_limits<Real>::max()),
upper_bounds(spatial_dimension, std::numeric_limits<Real>::lowest()) {}
BBox(const BBox & other)
: dim(other.dim), empty{false}, lower_bounds(other.lower_bounds),
upper_bounds(other.upper_bounds) {}
BBox & operator=(const BBox & other) {
if (this != &other) {
this->dim = other.dim;
this->lower_bounds = other.lower_bounds;
this->upper_bounds = other.upper_bounds;
this->empty = other.empty;
}
return *this;
}
inline BBox & operator+=(const Vector<Real> & position) {
AKANTU_DEBUG_ASSERT(
this->dim == position.size(),
"You are adding a point of a wrong dimension to the bounding box");
this->empty = false;
for (auto s : arange(dim)) {
lower_bounds(s) = std::min(lower_bounds(s), position(s));
upper_bounds(s) = std::max(upper_bounds(s), position(s));
}
return *this;
}
/* ------------------------------------------------------------------------ */
inline bool intersects(const BBox & other,
const SpatialDirection & direction) const {
AKANTU_DEBUG_ASSERT(
this->dim == other.dim,
"You are intersecting bounding boxes of different dimensions");
return Math::intersects(lower_bounds(direction), upper_bounds(direction),
other.lower_bounds(direction),
other.upper_bounds(direction));
}
inline bool intersects(const BBox & other) const {
- if (this->empty or other.empty)
+ if (this->empty or other.empty) {
return false;
+ }
bool intersects_ = true;
for (auto s : arange(this->dim)) {
intersects_ &= this->intersects(other, SpatialDirection(s));
}
return intersects_;
}
/* ------------------------------------------------------------------------ */
inline BBox intersection(const BBox & other) const {
AKANTU_DEBUG_ASSERT(
this->dim == other.dim,
"You are intersecting bounding boxes of different dimensions");
BBox intersection_(this->dim);
intersection_.empty = not this->intersects(other);
- if (intersection_.empty)
+ if (intersection_.empty) {
return intersection_;
+ }
for (auto s : arange(this->dim)) {
// is lower point in range ?
bool point1 = Math::is_in_range(other.lower_bounds(s), lower_bounds(s),
upper_bounds(s));
// is upper point in range ?
bool point2 = Math::is_in_range(other.upper_bounds(s), lower_bounds(s),
upper_bounds(s));
if (point1 and not point2) {
// |-----------| this (i)
// |-----------| other(i)
// 1 2
intersection_.lower_bounds(s) = other.lower_bounds(s);
intersection_.upper_bounds(s) = upper_bounds(s);
} else if (point1 && point2) {
// |-----------------| this (i)
// |-----------| other(i)
// 1 2
intersection_.lower_bounds(s) = other.lower_bounds(s);
intersection_.upper_bounds(s) = other.upper_bounds(s);
} else if (!point1 && point2) {
// |-----------| this (i)
// |-----------| other(i)
// 1 2
intersection_.lower_bounds(s) = this->lower_bounds(s);
intersection_.upper_bounds(s) = other.upper_bounds(s);
} else {
// |-----------| this (i)
// |-----------------| other(i)
// 1 2
intersection_.lower_bounds(s) = this->lower_bounds(s);
intersection_.upper_bounds(s) = this->upper_bounds(s);
}
}
return intersection_;
}
/* ------------------------------------------------------------------------ */
inline bool contains(const Vector<Real> & point) const {
return (point >= lower_bounds) and (point <= upper_bounds);
}
/* ------------------------------------------------------------------------ */
inline void reset() {
lower_bounds.set(std::numeric_limits<Real>::max());
upper_bounds.set(std::numeric_limits<Real>::lowest());
}
/* ------------------------------------------------------------------------ */
const Vector<Real> & getLowerBounds() const { return lower_bounds; }
const Vector<Real> & getUpperBounds() const { return upper_bounds; }
Vector<Real> & getLowerBounds() { return lower_bounds; }
Vector<Real> & getUpperBounds() { return upper_bounds; }
/* ------------------------------------------------------------------------ */
inline Real size(const SpatialDirection & direction) const {
return upper_bounds(direction) - lower_bounds(direction);
}
Vector<Real> size() const {
Vector<Real> size_(dim);
for (auto s : arange(this->dim)) {
size_(s) = this->size(SpatialDirection(s));
}
return size_;
}
inline operator bool() const { return not empty; }
/* ------------------------------------------------------------------------ */
BBox allSum(const Communicator & communicator) const {
Matrix<Real> reduce_bounds(dim, 2);
Vector<Real>(reduce_bounds(0)) = lower_bounds;
Vector<Real>(reduce_bounds(1)) = Real(-1.) * upper_bounds;
communicator.allReduce(reduce_bounds, SynchronizerOperation::_min);
BBox global(dim);
global.lower_bounds = Vector<Real>(reduce_bounds(0));
global.upper_bounds = Real(-1.) * Vector<Real>(reduce_bounds(1));
global.empty = false;
return global;
}
std::vector<BBox> allGather(const Communicator & communicator) const {
auto prank = communicator.whoAmI();
auto nb_proc = communicator.getNbProc();
Array<Real> bboxes_data(nb_proc, dim * 2 + 1);
auto * base = bboxes_data.storage() + prank * (2 * dim + 1);
Vector<Real>(base + dim * 0, dim) = lower_bounds;
Vector<Real>(base + dim * 1, dim) = upper_bounds;
base[dim * 2] = empty ? 1. : 0.; // ugly trick
communicator.allGather(bboxes_data);
std::vector<BBox> bboxes;
bboxes.reserve(nb_proc);
for (auto p : arange(nb_proc)) {
bboxes.emplace_back(dim);
auto & bbox = bboxes.back();
auto * base = bboxes_data.storage() + p * (2 * dim + 1);
bbox.lower_bounds = Vector<Real>(base + dim * 0, dim);
bbox.upper_bounds = Vector<Real>(base + dim * 1, dim);
- bbox.empty = base[dim * 2] == 1. ? true : false;
+ bbox.empty = (base[dim * 2] == 1.);
}
return bboxes;
}
std::map<UInt, BBox> intersection(const BBox & other,
- const Communicator & communicator) {
+ const Communicator & communicator) const {
// todo: change for a custom reduction algorithm
auto other_bboxes = other.allGather(communicator);
std::map<UInt, BBox> intersections;
for (const auto & bbox : enumerate(other_bboxes)) {
auto && tmp = this->intersection(std::get<1>(bbox));
if (tmp) {
intersections[std::get<0>(bbox)] = tmp;
}
}
return intersections;
}
void printself(std::ostream & stream) const {
stream << "BBox[";
if (not empty) {
stream << lower_bounds << " - " << upper_bounds;
}
stream << "]";
}
protected:
UInt dim{0};
bool empty{true};
Vector<Real> lower_bounds;
Vector<Real> upper_bounds;
};
inline std::ostream & operator<<(std::ostream & stream, const BBox & bbox) {
bbox.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AKANTU_AKA_BBOX_HH__ */
+#endif /* AKANTU_AKA_BBOX_HH_ */
diff --git a/src/common/aka_blas_lapack.hh b/src/common/aka_blas_lapack.hh
index 4795a28dd..57c199263 100644
--- a/src/common/aka_blas_lapack.hh
+++ b/src/common/aka_blas_lapack.hh
@@ -1,343 +1,343 @@
/**
* @file aka_blas_lapack.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 06 2013
* @date last modification: Tue Feb 20 2018
*
* @brief Interface of the Fortran BLAS/LAPACK libraries
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_error.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_BLAS_LAPACK_HH__
-#define __AKANTU_AKA_BLAS_LAPACK_HH__
+#ifndef AKANTU_AKA_BLAS_LAPACK_HH_
+#define AKANTU_AKA_BLAS_LAPACK_HH_
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_BLAS
#include "aka_fortran_mangling.hh"
extern "C" {
/* ------------------------------------------------------------------------ */
/* Double precision */
/* ------------------------------------------------------------------------ */
// LEVEL 1
double AKA_FC_GLOBAL(ddot, DDOT)(int *, double *, int *, double *, int *);
void AKA_FC_GLOBAL(daxpy, DAXPY)(int *, double *, double *, int *, double *,
int *);
// LEVEL 2
void AKA_FC_GLOBAL(dgemv, DGEMV)(char *, int *, int *, double *, double *,
int *, double *, int *, double *, double *,
int *);
// LEVEL 3
void AKA_FC_GLOBAL(dgemm, DGEMM)(char *, char *, int *, int *, int *, double *,
double *, int *, double *, int *, double *,
double *, int *);
/* ------------------------------------------------------------------------ */
/* Simple precision */
/* ------------------------------------------------------------------------ */
// LEVEL 1
float AKA_FC_GLOBAL(sdot, SDOT)(int *, float *, int *, float *, int *);
void AKA_FC_GLOBAL(saxpy, SAXPY)(int *, float *, float *, int *, float *,
int *);
// LEVEL 2
void AKA_FC_GLOBAL(sgemv, SGEMV)(char *, int *, int *, float *, float *, int *,
float *, int *, float *, float *, int *);
// LEVEL 3
void AKA_FC_GLOBAL(sgemm, SGEMM)(char *, char *, int *, int *, int *, float *,
float *, int *, float *, int *, float *,
float *, int *);
}
#endif
namespace akantu {
#define AKANTU_WARNING_IGNORE_UNUSED_PARAMETER
#include "aka_warning.hh"
/// Wrapper around the S/DDOT BLAS function that returns the dot product of two
/// vectors
template <typename T>
inline T aka_dot(int * n, T * x, int * incx, T * y, int * incy) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DAXPY BLAS function that computes \f$y := \alpha x +
/// y\f$
template <typename T>
inline void aka_axpy(int * n, T * alpha, T * x, int * incx, T * y, int * incy) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DGEMV BLAS function that computes matrix-vector product
/// \f$y := \alpha A^{(T)}x + \beta y \f$
template <typename T>
inline void aka_gemv(char * trans, int * m, int * n, T * alpha, T * a,
int * lda, T * x, int * incx, T * beta, T * y,
int * incy) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DGEMM BLAS function that computes the product of two
/// matrices \f$C := \alpha A^{(T)} B^{(T)} + \beta C \f$
template <typename T>
inline void aka_gemm(char * transa, char * transb, int * m, int * n, int * k,
T * alpha, T * a, int * lda, T * b, int * ldb, T * beta,
T * c, int * ldc) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
#if defined(AKANTU_USE_BLAS)
template <>
inline double aka_dot<double>(int * n, double * x, int * incx, double * y,
int * incy) {
return AKA_FC_GLOBAL(ddot, DDOT)(n, x, incx, y, incy);
}
template <>
inline void aka_axpy(int * n, double * alpha, double * x, int * incx,
double * y, int * incy) {
return AKA_FC_GLOBAL(daxpy, DAXPY)(n, alpha, x, incx, y, incy);
}
template <>
inline void aka_gemv<double>(char * trans, int * m, int * n, double * alpha,
double * a, int * lda, double * x, int * incx,
double * beta, double * y, int * incy) {
return AKA_FC_GLOBAL(dgemv, DGEMV)(trans, m, n, alpha, a, lda, x, incx, beta,
y, incy);
}
template <>
inline void aka_gemm<double>(char * transa, char * transb, int * m, int * n,
int * k, double * alpha, double * a, int * lda,
double * b, int * ldb, double * beta, double * c,
int * ldc) {
AKA_FC_GLOBAL(dgemm, DGEMM)
(transa, transb, m, n, k, alpha, a, lda, b, ldb, beta, c, ldc);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <>
inline float aka_dot<float>(int * n, float * x, int * incx, float * y,
int * incy) {
return AKA_FC_GLOBAL(sdot, SDOT)(n, x, incx, y, incy);
}
template <>
inline void aka_axpy(int * n, float * alpha, float * x, int * incx, float * y,
int * incy) {
return AKA_FC_GLOBAL(daxpy, DAXPY)(n, alpha, x, incx, y, incy);
}
template <>
inline void aka_gemv<float>(char * trans, int * m, int * n, float * alpha,
float * a, int * lda, float * x, int * incx,
float * beta, float * y, int * incy) {
AKA_FC_GLOBAL(sgemv, SGEMV)
(trans, m, n, alpha, a, lda, x, incx, beta, y, incy);
}
template <>
inline void aka_gemm<float>(char * transa, char * transb, int * m, int * n,
int * k, float * alpha, float * a, int * lda,
float * b, int * ldb, float * beta, float * c,
int * ldc) {
AKA_FC_GLOBAL(sgemm, SGEMM)
(transa, transb, m, n, k, alpha, a, lda, b, ldb, beta, c, ldc);
}
#endif
} // namespace akantu
#ifdef AKANTU_USE_LAPACK
#include "aka_fortran_mangling.hh"
extern "C" {
/* ------------------------------------------------------------------------ */
/* Double general matrix */
/* ------------------------------------------------------------------------ */
/// compute the eigenvalues/vectors
void AKA_FC_GLOBAL(dgeev, DGEEV)(char * jobvl, char * jobvr, int * n,
double * a, int * lda, double * wr,
double * wi, double * vl, int * ldvl,
double * vr, int * ldvr, double * work,
int * lwork, int * info);
/// LU decomposition of a general matrix
void AKA_FC_GLOBAL(dgetrf, DGETRF)(int * m, int * n, double * a, int * lda,
int * ipiv, int * info);
/// generate inverse of a matrix given its LU decomposition
void AKA_FC_GLOBAL(dgetri, DGETRI)(int * n, double * a, int * lda, int * ipiv,
double * work, int * lwork, int * info);
/// solving A x = b using a LU factorization
void AKA_FC_GLOBAL(dgetrs, DGETRS)(char * trans, int * n, int * nrhs,
double * A, int * lda, int * ipiv,
double * b, int * ldb, int * info);
/* ------------------------------------------------------------------------ */
/* Simple general matrix */
/* ------------------------------------------------------------------------ */
/// compute the eigenvalues/vectors
void AKA_FC_GLOBAL(sgeev, SGEEV)(char * jobvl, char * jobvr, int * n, float * a,
int * lda, float * wr, float * wi, float * vl,
int * ldvl, float * vr, int * ldvr,
float * work, int * lwork, int * info);
/// LU decomposition of a general matrix
void AKA_FC_GLOBAL(sgetrf, SGETRF)(int * m, int * n, float * a, int * lda,
int * ipiv, int * info);
/// generate inverse of a matrix given its LU decomposition
void AKA_FC_GLOBAL(sgetri, SGETRI)(int * n, float * a, int * lda, int * ipiv,
float * work, int * lwork, int * info);
/// solving A x = b using a LU factorization
void AKA_FC_GLOBAL(sgetrs, SGETRS)(char * trans, int * n, int * nrhs, float * A,
int * lda, int * ipiv, float * b, int * ldb,
int * info);
}
#endif // AKANTU_USE_LAPACK
namespace akantu {
/// Wrapper around the S/DGEEV BLAS function that computes the eigenvalues and
/// eigenvectors of a matrix
template <typename T>
inline void aka_geev(char * jobvl, char * jobvr, int * n, T * a, int * lda,
T * wr, T * wi, T * vl, int * ldvl, T * vr, int * ldvr,
T * work, int * lwork, int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRF BLAS function that computes the LU decomposition
/// of a matrix
template <typename T>
inline void aka_getrf(int * m, int * n, T * a, int * lda, int * ipiv,
int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRI BLAS function that computes the inverse of a
/// matrix given its LU decomposition
template <typename T>
inline void aka_getri(int * n, T * a, int * lda, int * ipiv, T * work,
int * lwork, int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRS BLAS function that solves \f$A^{(T)}x = b\f$
/// using LU decomposition
template <typename T>
inline void aka_getrs(char * trans, int * n, int * nrhs, T * A, int * lda,
int * ipiv, T * b, int * ldb, int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
#include "aka_warning_restore.hh"
#ifdef AKANTU_USE_LAPACK
template <>
inline void aka_geev<double>(char * jobvl, char * jobvr, int * n, double * a,
int * lda, double * wr, double * wi, double * vl,
int * ldvl, double * vr, int * ldvr, double * work,
int * lwork, int * info) {
AKA_FC_GLOBAL(dgeev, DGEEV)
(jobvl, jobvr, n, a, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
}
template <>
inline void aka_getrf<double>(int * m, int * n, double * a, int * lda,
int * ipiv, int * info) {
AKA_FC_GLOBAL(dgetrf, DGETRF)(m, n, a, lda, ipiv, info);
}
template <>
inline void aka_getri<double>(int * n, double * a, int * lda, int * ipiv,
double * work, int * lwork, int * info) {
AKA_FC_GLOBAL(dgetri, DGETRI)(n, a, lda, ipiv, work, lwork, info);
}
template <>
inline void aka_getrs<double>(char * trans, int * n, int * nrhs, double * A,
int * lda, int * ipiv, double * b, int * ldb,
int * info) {
AKA_FC_GLOBAL(dgetrs, DGETRS)(trans, n, nrhs, A, lda, ipiv, b, ldb, info);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <>
inline void aka_geev<float>(char * jobvl, char * jobvr, int * n, float * a,
int * lda, float * wr, float * wi, float * vl,
int * ldvl, float * vr, int * ldvr, float * work,
int * lwork, int * info) {
AKA_FC_GLOBAL(sgeev, SGEEV)
(jobvl, jobvr, n, a, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
}
template <>
inline void aka_getrf<float>(int * m, int * n, float * a, int * lda, int * ipiv,
int * info) {
AKA_FC_GLOBAL(sgetrf, SGETRF)(m, n, a, lda, ipiv, info);
}
template <>
inline void aka_getri<float>(int * n, float * a, int * lda, int * ipiv,
float * work, int * lwork, int * info) {
AKA_FC_GLOBAL(sgetri, SGETRI)(n, a, lda, ipiv, work, lwork, info);
}
template <>
inline void aka_getrs<float>(char * trans, int * n, int * nrhs, float * A,
int * lda, int * ipiv, float * b, int * ldb,
int * info) {
AKA_FC_GLOBAL(sgetrs, SGETRS)(trans, n, nrhs, A, lda, ipiv, b, ldb, info);
}
#endif
} // namespace akantu
-#endif /* __AKANTU_AKA_BLAS_LAPACK_HH__ */
+#endif /* AKANTU_AKA_BLAS_LAPACK_HH_ */
diff --git a/src/common/aka_circular_array.hh b/src/common/aka_circular_array.hh
index bb8f296ef..08a391564 100644
--- a/src/common/aka_circular_array.hh
+++ b/src/common/aka_circular_array.hh
@@ -1,120 +1,120 @@
/**
* @file aka_circular_array.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Aug 13 2017
*
* @brief class of circular array
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <typeinfo>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_CIRCULAR_ARRAY_HH__
-#define __AKANTU_AKA_CIRCULAR_ARRAY_HH__
+#ifndef AKANTU_AKA_CIRCULAR_ARRAY_HH_
+#define AKANTU_AKA_CIRCULAR_ARRAY_HH_
namespace akantu {
template <class T> class CircularArray : protected Array<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef typename Array<T>::value_type value_type;
typedef typename Array<T>::reference reference;
typedef typename Array<T>::pointer_type pointer_type;
typedef typename Array<T>::const_reference const_reference;
/// Allocation of a new array with a default value
CircularArray(UInt size, UInt nb_component = 1,
const_reference value = value_type(), const ID & id = "")
: Array<T>(size, nb_component, value, id), start_position(0),
end_position(size - 1) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
virtual ~CircularArray() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
advance start and end position by one:
the first element is now at the end of the array
**/
inline void makeStep();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
private:
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
inline reference operator()(UInt i, UInt j = 0);
inline const_reference operator()(UInt i, UInt j = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
UInt size() const { return this->size_; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// indice of first element in this circular array
UInt start_position;
/// indice of last element in this circular array
UInt end_position;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const CircularArray<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "aka_circular_array_inline_impl.hh"
-#endif /* __AKANTU_AKA_CIRCULAR_ARRAY_HH__ */
+#endif /* AKANTU_AKA_CIRCULAR_ARRAY_HH_ */
diff --git a/src/common/aka_common.cc b/src/common/aka_common.cc
index 936c3ca2d..392fc587e 100644
--- a/src/common/aka_common.cc
+++ b/src/common/aka_common.cc
@@ -1,167 +1,168 @@
/**
* @file aka_common.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Mon Feb 05 2018
*
* @brief Initialization of global variables
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "aka_static_memory.hh"
#include "communicator.hh"
#include "cppargparse.hh"
#include "parser.hh"
#include "communication_tag.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <ctime>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void initialize(int & argc, char **& argv) {
AKANTU_DEBUG_IN();
initialize("", argc, argv);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void initialize(const std::string & input_file, int & argc, char **& argv) {
AKANTU_DEBUG_IN();
StaticMemory::getStaticMemory();
Communicator & comm = Communicator::getStaticCommunicator(argc, argv);
Tag::setMaxTag(comm.getMaxTag());
debug::debugger.setParallelContext(comm.whoAmI(), comm.getNbProc());
debug::setDebugLevel(dblError);
static_argparser.setParallelContext(comm.whoAmI(), comm.getNbProc());
static_argparser.setExternalExitFunction(debug::exit);
static_argparser.addArgument("--aka_input_file", "Akantu's input file", 1,
cppargparse::_string, std::string());
static_argparser.addArgument(
"--aka_debug_level",
std::string("Akantu's overall debug level") +
std::string(" (0: error, 1: exceptions, 4: warnings, 5: info, ..., "
"100: dump") +
std::string(" more info on levels can be foind in aka_error.hh)"),
1, cppargparse::_integer, (long int)(dblWarning));
static_argparser.addArgument(
"--aka_print_backtrace",
"Should Akantu print a backtrace in case of error", 0,
cppargparse::_boolean, false, true);
static_argparser.addArgument("--aka_seed", "The seed to use on prank 0", 1,
cppargparse::_integer);
static_argparser.parse(argc, argv, cppargparse::_remove_parsed);
std::string infile = static_argparser["aka_input_file"];
- if (infile == "")
+ if (infile.empty()) {
infile = input_file;
+ }
debug::debugger.printBacktrace(static_argparser["aka_print_backtrace"]);
- if ("" != infile) {
+ if (not infile.empty()) {
readInputFile(infile);
}
long int seed;
if (static_argparser.has("aka_seed")) {
seed = static_argparser["aka_seed"];
} else {
seed =
static_parser.getParameter("seed", time(nullptr), _ppsc_current_scope);
}
seed *= (comm.whoAmI() + 1);
RandomGenerator<UInt>::seed(seed);
long int dbl_level = static_argparser["aka_debug_level"];
debug::setDebugLevel(DebugLevel(dbl_level));
AKANTU_DEBUG_INFO("Random seed set to " << seed);
std::atexit(finalize);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void finalize() {
AKANTU_DEBUG_IN();
// if (StaticCommunicator::isInstantiated()) {
// StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
// delete &comm;
// }
if (StaticMemory::isInstantiated()) {
delete &(StaticMemory::getStaticMemory());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void readInputFile(const std::string & input_file) {
static_parser.parse(input_file);
}
/* -------------------------------------------------------------------------- */
cppargparse::ArgumentParser & getStaticArgumentParser() {
return static_argparser;
}
/* -------------------------------------------------------------------------- */
Parser & getStaticParser() { return static_parser; }
/* -------------------------------------------------------------------------- */
const ParserSection & getUserParser() {
return *(static_parser.getSubSections(ParserType::_user).first);
}
std::unique_ptr<Communicator> Communicator::static_communicator;
std::ostream & operator<<(std::ostream & stream, NodeFlag flag) {
using under = std::underlying_type_t<NodeFlag>;
- int digits = std::log(std::numeric_limits<under>::max() + 1) / std::log(16);
+ auto digits = static_cast<int>(std::log(std::numeric_limits<under>::max() + 1) / std::log(16));
std::ios_base::fmtflags ff;
ff = stream.flags();
auto value = static_cast<std::common_type_t<under, unsigned int>>(flag);
stream << "0x" << std::hex << std::setw(digits) << std::setfill('0') << value;
stream.flags(ff);
return stream;
}
} // namespace akantu
diff --git a/src/common/aka_common.hh b/src/common/aka_common.hh
index be2fe7c77..f7702d6e5 100644
--- a/src/common/aka_common.hh
+++ b/src/common/aka_common.hh
@@ -1,643 +1,651 @@
/**
* @file aka_common.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Mon Feb 12 2018
*
* @brief common type descriptions for akantu
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COMMON_HH__
-#define __AKANTU_COMMON_HH__
+#ifndef AKANTU_COMMON_HH_
+#define AKANTU_COMMON_HH_
#include "aka_compatibilty_with_cpp_standard.hh"
/* -------------------------------------------------------------------------- */
#if defined(WIN32)
#define __attribute__(x)
#endif
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
#include "aka_error.hh"
#include "aka_safe_enum.hh"
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
#include <limits>
#include <list>
#include <memory>
#include <string>
#include <type_traits>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Constants */
/* -------------------------------------------------------------------------- */
namespace {
[[gnu::unused]] constexpr UInt _all_dimensions{
std::numeric_limits<UInt>::max()};
#ifdef AKANTU_NDEBUG
[[gnu::unused]] constexpr Real REAL_INIT_VALUE{0.};
#else
[[gnu::unused]] constexpr Real REAL_INIT_VALUE{
std::numeric_limits<Real>::quiet_NaN()};
#endif
} // namespace
/* -------------------------------------------------------------------------- */
/* Common types */
/* -------------------------------------------------------------------------- */
using ID = std::string;
using MemoryID = UInt;
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "aka_enum_macros.hh"
/* -------------------------------------------------------------------------- */
#include "aka_element_classes_info.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Mesh/FEM/Model types */
/* -------------------------------------------------------------------------- */
/// small help to use names for directions
enum SpatialDirection { _x = 0, _y = 1, _z = 2 };
/// enum MeshIOType type of mesh reader/writer
enum MeshIOType {
_miot_auto, ///< Auto guess of the reader to use based on the extension
_miot_gmsh, ///< Gmsh files
_miot_gmsh_struct, ///< Gsmh reader with reintpretation of elements has
/// structures elements
_miot_diana, ///< TNO Diana mesh format
_miot_abaqus ///< Abaqus mesh format
};
/// enum MeshEventHandlerPriority defines relative order of execution of
/// events
enum EventHandlerPriority {
_ehp_highest = 0,
_ehp_mesh = 5,
_ehp_fe_engine = 9,
_ehp_synchronizer = 10,
_ehp_dof_manager = 20,
_ehp_model = 94,
_ehp_non_local_manager = 100,
_ehp_lowest = 100
};
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_MODEL_TYPES \
(model) \
(solid_mechanics_model) \
(solid_mechanics_model_cohesive) \
(heat_transfer_model) \
(structural_mechanics_model) \
(embedded_model)
// clang-format on
/// enum ModelType defines which type of physics is solved
AKANTU_CLASS_ENUM_DECLARE(ModelType, AKANTU_MODEL_TYPES)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(ModelType, AKANTU_MODEL_TYPES)
AKANTU_CLASS_ENUM_INPUT_STREAM(ModelType, AKANTU_MODEL_TYPES)
#else
enum class ModelType {
model,
solid_mechanics_model,
solid_mechanics_model_cohesive,
heat_transfer_model,
structural_mechanics_model,
embedded_model,
};
#endif
/// enum AnalysisMethod type of solving method used to solve the equation of
/// motion
enum AnalysisMethod {
_static = 0,
_implicit_dynamic = 1,
_explicit_lumped_mass = 2,
_explicit_lumped_capacity = 2,
_explicit_consistent_mass = 3
};
/// enum DOFSupportType defines which kind of dof that can exists
enum DOFSupportType { _dst_nodal, _dst_generic };
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_NON_LINEAR_SOLVER_TYPES \
(linear) \
(newton_raphson) \
(newton_raphson_modified) \
(lumped) \
(gmres) \
(bfgs) \
(cg) \
(auto)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(NonLinearSolverType, AKANTU_NON_LINEAR_SOLVER_TYPES)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(NonLinearSolverType,
AKANTU_NON_LINEAR_SOLVER_TYPES)
AKANTU_CLASS_ENUM_INPUT_STREAM(NonLinearSolverType,
AKANTU_NON_LINEAR_SOLVER_TYPES)
#else
/// Type of non linear resolution available in akantu
enum class NonLinearSolverType {
_linear, ///< No non linear convergence loop
_newton_raphson, ///< Regular Newton-Raphson
_newton_raphson_modified, ///< Newton-Raphson with initial tangent
_lumped, ///< Case of lumped mass or equivalent matrix
_gmres,
_bfgs,
_cg,
_auto ///< This will take a default value that make sense in case of
/// model::getNewSolver
};
#endif
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_TIME_STEP_SOLVER_TYPE \
(static) \
(dynamic) \
(dynamic_lumped) \
(not_defined)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(TimeStepSolverType, AKANTU_TIME_STEP_SOLVER_TYPE)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(TimeStepSolverType,
AKANTU_TIME_STEP_SOLVER_TYPE)
AKANTU_CLASS_ENUM_INPUT_STREAM(TimeStepSolverType, AKANTU_TIME_STEP_SOLVER_TYPE)
#else
/// Type of time stepping solver
enum class TimeStepSolverType {
_static, ///< Static solution
_dynamic, ///< Dynamic solver
_dynamic_lumped, ///< Dynamic solver with lumped mass
_not_defined, ///< For not defined cases
};
#endif
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_INTEGRATION_SCHEME_TYPE \
(pseudo_time) \
(forward_euler) \
(trapezoidal_rule_1) \
(backward_euler) \
(central_difference) \
(fox_goodwin) \
(trapezoidal_rule_2) \
(linear_acceleration) \
(newmark_beta) \
(generalized_trapezoidal)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(IntegrationSchemeType, AKANTU_INTEGRATION_SCHEME_TYPE)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(IntegrationSchemeType,
AKANTU_INTEGRATION_SCHEME_TYPE)
AKANTU_CLASS_ENUM_INPUT_STREAM(IntegrationSchemeType,
AKANTU_INTEGRATION_SCHEME_TYPE)
#else
/// Type of integration scheme
enum class IntegrationSchemeType {
_pseudo_time, ///< Pseudo Time
_forward_euler, ///< GeneralizedTrapezoidal(0)
_trapezoidal_rule_1, ///< GeneralizedTrapezoidal(1/2)
_backward_euler, ///< GeneralizedTrapezoidal(1)
_central_difference, ///< NewmarkBeta(0, 1/2)
_fox_goodwin, ///< NewmarkBeta(1/6, 1/2)
_trapezoidal_rule_2, ///< NewmarkBeta(1/2, 1/2)
_linear_acceleration, ///< NewmarkBeta(1/3, 1/2)
_newmark_beta, ///< generic NewmarkBeta with user defined
/// alpha and beta
_generalized_trapezoidal ///< generic GeneralizedTrapezoidal with user
/// defined alpha
};
#endif
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_SOLVE_CONVERGENCE_CRITERIA \
(residual) \
(solution) \
(residual_mass_wgh)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(SolveConvergenceCriteria,
AKANTU_SOLVE_CONVERGENCE_CRITERIA)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(SolveConvergenceCriteria,
AKANTU_SOLVE_CONVERGENCE_CRITERIA)
AKANTU_CLASS_ENUM_INPUT_STREAM(SolveConvergenceCriteria,
AKANTU_SOLVE_CONVERGENCE_CRITERIA)
#else
/// enum SolveConvergenceCriteria different convergence criteria
enum class SolveConvergenceCriteria {
_residual, ///< Use residual to test the convergence
_solution, ///< Use solution to test the convergence
_residual_mass_wgh ///< Use residual weighted by inv. nodal mass to
///< testb
};
#endif
/// enum CohesiveMethod type of insertion of cohesive elements
enum CohesiveMethod { _intrinsic, _extrinsic };
/// @enum MatrixType type of sparse matrix used
enum MatrixType { _unsymmetric, _symmetric, _mt_not_defined };
/* -------------------------------------------------------------------------- */
/* Ghosts handling */
/* -------------------------------------------------------------------------- */
/// @enum CommunicatorType type of communication method to use
enum CommunicatorType { _communicator_mpi, _communicator_dummy };
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_SYNCHRONIZATION_TAG \
(whatever) \
(update) \
(ask_nodes) \
(size) \
(smm_mass) \
(smm_for_gradu) \
(smm_boundary) \
(smm_uv) \
(smm_res) \
(smm_init_mat) \
(smm_stress) \
(smmc_facets) \
(smmc_facets_conn) \
(smmc_facets_stress) \
(smmc_damage) \
(giu_global_conn) \
(ce_groups) \
(gm_clusters) \
(htm_temperature) \
(htm_gradient_temperature) \
(htm_phi) \
(htm_gradient_phi) \
(mnl_for_average) \
(mnl_weight) \
(nh_criterion) \
(test) \
(user_1) \
(user_2) \
(material_id) \
(for_dump) \
(cf_nodal) \
(cf_incr) \
(solver_solution)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(SynchronizationTag, AKANTU_SYNCHRONIZATION_TAG)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(SynchronizationTag, AKANTU_SYNCHRONIZATION_TAG)
#else
/// @enum SynchronizationTag type of synchronizations
enum class SynchronizationTag {
//--- Generic tags ---
_whatever,
_update,
_ask_nodes,
_size,
//--- SolidMechanicsModel tags ---
_smm_mass, ///< synchronization of the SolidMechanicsModel.mass
_smm_for_gradu, ///< synchronization of the
/// SolidMechanicsModel.displacement
_smm_boundary, ///< synchronization of the boundary, forces, velocities
/// and displacement
_smm_uv, ///< synchronization of the nodal velocities and displacement
_smm_res, ///< synchronization of the nodal residual
_smm_init_mat, ///< synchronization of the data to initialize materials
_smm_stress, ///< synchronization of the stresses to compute the
///< internal
/// forces
_smmc_facets, ///< synchronization of facet data to setup facet synch
_smmc_facets_conn, ///< synchronization of facet global connectivity
_smmc_facets_stress, ///< synchronization of facets' stress to setup
///< facet
/// synch
_smmc_damage, ///< synchronization of damage
// --- GlobalIdsUpdater tags ---
_giu_global_conn, ///< synchronization of global connectivities
// --- CohesiveElementInserter tags ---
_ce_groups, ///< synchronization of cohesive element insertion depending
/// on facet groups
// --- GroupManager tags ---
_gm_clusters, ///< synchronization of clusters
// --- HeatTransfer tags ---
_htm_temperature, ///< synchronization of the nodal temperature
_htm_gradient_temperature, ///< synchronization of the element gradient
/// temperature
// --- LevelSet tags ---
_htm_phi, ///< synchronization of the nodal level set value phi
_htm_gradient_phi, ///< synchronization of the element gradient phi
//--- Material non local ---
_mnl_for_average, ///< synchronization of data to average in non local
/// material
_mnl_weight, ///< synchronization of data for the weight computations
// --- NeighborhoodSynchronization tags ---
_nh_criterion,
// --- General tags ---
_test, ///< Test tag
_user_1, ///< tag for user simulations
_user_2, ///< tag for user simulations
_material_id, ///< synchronization of the material ids
_for_dump, ///< everything that needs to be synch before dump
// --- Contact & Friction ---
_cf_nodal, ///< synchronization of disp, velo, and current position
_cf_incr, ///< synchronization of increment
// --- Solver tags ---
_solver_solution ///< synchronization of the solution obained with the
/// PETSc solver
};
#endif
/// @enum GhostType type of ghost
enum GhostType {
_not_ghost = 0,
_ghost = 1,
_casper // not used but a real cute ghost
};
/// Define the flag that can be set to a node
enum class NodeFlag : std::uint8_t {
_normal = 0x00,
_distributed = 0x01,
_master = 0x03,
_slave = 0x05,
_pure_ghost = 0x09,
_shared_mask = 0x0F,
_periodic = 0x10,
_periodic_master = 0x30,
_periodic_slave = 0x50,
_periodic_mask = 0xF0,
_local_master_mask = 0xCC, // ~(_master & _periodic_mask)
};
inline NodeFlag operator&(const NodeFlag & a, const NodeFlag & b) {
using under = std::underlying_type_t<NodeFlag>;
return NodeFlag(under(a) & under(b));
}
inline NodeFlag operator|(const NodeFlag & a, const NodeFlag & b) {
using under = std::underlying_type_t<NodeFlag>;
return NodeFlag(under(a) | under(b));
}
inline NodeFlag & operator|=(NodeFlag & a, const NodeFlag & b) {
a = a | b;
return a;
}
inline NodeFlag & operator&=(NodeFlag & a, const NodeFlag & b) {
a = a & b;
return a;
}
inline NodeFlag operator~(const NodeFlag & a) {
using under = std::underlying_type_t<NodeFlag>;
return NodeFlag(~under(a));
}
std::ostream & operator<<(std::ostream & stream, NodeFlag flag);
} // namespace akantu
AKANTU_ENUM_HASH(GhostType)
namespace akantu {
/* -------------------------------------------------------------------------- */
struct GhostType_def {
using type = GhostType;
static const type _begin_ = _not_ghost;
static const type _end_ = _casper;
};
using ghost_type_t = safe_enum<GhostType_def>;
namespace {
constexpr ghost_type_t ghost_types{_casper};
}
/// standard output stream operator for GhostType
// inline std::ostream & operator<<(std::ostream & stream, GhostType type);
/* -------------------------------------------------------------------------- */
/* Global defines */
/* -------------------------------------------------------------------------- */
#define AKANTU_MIN_ALLOCATION 2000
#define AKANTU_INDENT ' '
#define AKANTU_INCLUDE_INLINE_IMPL
/* -------------------------------------------------------------------------- */
#define AKANTU_SET_MACRO(name, variable, type) \
inline void set##name(type variable) { this->variable = variable; }
#define AKANTU_GET_MACRO(name, variable, type) \
inline type get##name() const { return variable; }
#define AKANTU_GET_MACRO_NOT_CONST(name, variable, type) \
inline type get##name() { return variable; }
#define AKANTU_GET_MACRO_DEREF_PTR(name, ptr) \
- inline decltype(auto) get##name() const { \
- if (not ptr) { \
+ inline const auto & get##name() const { \
+ if (not(ptr)) { \
AKANTU_EXCEPTION("The member " << #ptr << " is not initialized"); \
} \
- return (*ptr); \
+ return (*(ptr)); \
+ }
+
+#define AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(name, ptr) \
+ inline auto & get##name() { \
+ if (not(ptr)) { \
+ AKANTU_EXCEPTION("The member " << #ptr << " is not initialized"); \
+ } \
+ return (*(ptr)); \
}
#define AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, support, con) \
- inline con Array<type> & get##name( \
- const support & el_type, const GhostType & ghost_type = _not_ghost) \
- con { \
+ inline con Array<type> & get##name(const support & el_type, \
+ GhostType ghost_type = _not_ghost) \
+ con { /* NOLINT */ \
return variable(el_type, ghost_type); \
- }
+ } // NOLINT
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, )
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, const)
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, )
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, const)
/* -------------------------------------------------------------------------- */
/// initialize the static part of akantu
void initialize(int & argc, char **& argv);
/// initialize the static part of akantu and read the global input_file
void initialize(const std::string & input_file, int & argc, char **& argv);
/* -------------------------------------------------------------------------- */
/// finilize correctly akantu and clean the memory
void finalize();
/* -------------------------------------------------------------------------- */
/// Read an new input file
void readInputFile(const std::string & input_file);
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* string manipulation */
/* -------------------------------------------------------------------------- */
inline std::string to_lower(const std::string & str);
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim);
inline std::string trim(const std::string & to_trim, char c);
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/// give a string representation of the a human readable size in bit
template <typename T> std::string printMemorySize(UInt size);
/* -------------------------------------------------------------------------- */
struct TensorTrait {};
struct TensorProxyTrait {};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Type traits */
/* -------------------------------------------------------------------------- */
namespace aka {
/* ------------------------------------------------------------------------ */
template <typename T> using is_tensor = std::is_base_of<akantu::TensorTrait, T>;
template <typename T>
using is_tensor_proxy = std::is_base_of<akantu::TensorProxyTrait, T>;
/* ------------------------------------------------------------------------ */
template <typename T> using is_scalar = std::is_arithmetic<T>;
/* ------------------------------------------------------------------------ */
template <typename R, typename T,
std::enable_if_t<std::is_reference<T>::value> * = nullptr>
bool is_of_type(T && t) {
return (
dynamic_cast<std::add_pointer_t<
std::conditional_t<std::is_const<std::remove_reference_t<T>>::value,
std::add_const_t<R>, R>>>(&t) != nullptr);
}
/* -------------------------------------------------------------------------- */
template <typename R, typename T> bool is_of_type(std::unique_ptr<T> & t) {
return (
dynamic_cast<std::add_pointer_t<
std::conditional_t<std::is_const<T>::value, std::add_const_t<R>, R>>>(
t.get()) != nullptr);
}
/* ------------------------------------------------------------------------ */
template <typename R, typename T,
std::enable_if_t<std::is_reference<T>::value> * = nullptr>
decltype(auto) as_type(T && t) {
static_assert(
disjunction<
std::is_base_of<std::decay_t<T>, std::decay_t<R>>, // down-cast
std::is_base_of<std::decay_t<R>, std::decay_t<T>> // up-cast
>::value,
"Type T and R are not valid for a as_type conversion");
return dynamic_cast<std::add_lvalue_reference_t<
std::conditional_t<std::is_const<std::remove_reference_t<T>>::value,
std::add_const_t<R>, R>>>(t);
}
/* -------------------------------------------------------------------------- */
template <typename R, typename T,
std::enable_if_t<std::is_pointer<T>::value> * = nullptr>
decltype(auto) as_type(T && t) {
return &as_type<R>(*t);
}
/* -------------------------------------------------------------------------- */
template <typename R, typename T>
decltype(auto) as_type(const std::shared_ptr<T> & t) {
return std::dynamic_pointer_cast<R>(t);
}
} // namespace aka
#include "aka_common_inline_impl.hh"
#include "aka_fwd.hh"
namespace akantu {
/// get access to the internal argument parser
cppargparse::ArgumentParser & getStaticArgumentParser();
/// get access to the internal input file parser
Parser & getStaticParser();
/// get access to the user part of the internal input file parser
const ParserSection & getUserParser();
#define AKANTU_CURRENT_FUNCTION \
(std::string(__func__) + "():" + std::to_string(__LINE__))
} // namespace akantu
/* -------------------------------------------------------------------------- */
#if AKANTU_INTEGER_SIZE == 4
#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b9
#elif AKANTU_INTEGER_SIZE == 8
#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b97f4a7c13LL
#endif
namespace std {
/**
* Hashing function for pairs based on hash_combine from boost The magic
* number is coming from the golden number @f[\phi = \frac{1 + \sqrt5}{2}@f]
* @f[\frac{2^32}{\phi} = 0x9e3779b9@f]
* http://stackoverflow.com/questions/4948780/magic-number-in-boosthash-combine
* http://burtleburtle.net/bob/hash/doobs.html
*/
template <typename a, typename b> struct hash<std::pair<a, b>> {
hash() = default;
size_t operator()(const std::pair<a, b> & p) const {
size_t seed = ah(p.first);
return bh(p.second) + AKANTU_HASH_COMBINE_MAGIC_NUMBER + (seed << 6) +
(seed >> 2);
}
private:
const hash<a> ah{};
const hash<b> bh{};
};
} // namespace std
-#endif /* __AKANTU_COMMON_HH__ */
+#endif // AKANTU_COMMON_HH_
diff --git a/src/common/aka_common_inline_impl.hh b/src/common/aka_common_inline_impl.hh
index 5403ad538..64616aa1a 100644
--- a/src/common/aka_common_inline_impl.hh
+++ b/src/common/aka_common_inline_impl.hh
@@ -1,149 +1,150 @@
/**
* @file aka_common_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief inline implementations of common akantu type descriptions
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <cctype>
#include <cmath>
#include <iomanip>
#include <iostream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/// standard output stream operator for GhostType
-inline std::ostream & operator<<(std::ostream & stream, const GhostType & type) {
+inline std::ostream & operator<<(std::ostream & stream, GhostType type) {
switch (type) {
case _not_ghost:
stream << "not_ghost";
break;
case _ghost:
stream << "ghost";
break;
case _casper:
stream << "Casper the friendly ghost";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
inline std::string to_lower(const std::string & str) {
std::string lstr = str;
std::transform(lstr.begin(), lstr.end(), lstr.begin(), (int (*)(int))tolower);
return lstr;
}
namespace {
template <typename pred>
inline std::string trim_p(const std::string & to_trim, pred && p) {
std::string trimed = to_trim;
auto && not_ = [&](auto && a) { return not p(a); };
// left trim
trimed.erase(trimed.begin(),
std::find_if(trimed.begin(), trimed.end(), not_));
// right trim
trimed.erase(std::find_if(trimed.rbegin(), trimed.rend(), not_).base(),
trimed.end());
return trimed;
}
} // namespace
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim) {
return trim_p(to_trim, [&](auto && a) { return std::isspace(a); });
}
inline std::string trim(const std::string & to_trim, char c) {
return trim_p(to_trim, [&c](auto && a) { return (a == c); });
}
/* -------------------------------------------------------------------------- */
template <typename T> std::string printMemorySize(UInt size) {
Real real_size = size * sizeof(T);
UInt mult = 0;
- if (real_size != 0)
+ if (real_size != 0) {
mult = (std::log(real_size) / std::log(2)) / 10;
+ }
std::stringstream sstr;
real_size /= Real(1 << (10 * mult));
sstr << std::setprecision(2) << std::fixed << real_size;
std::string size_prefix;
switch (mult) {
case 0:
sstr << "";
break;
case 1:
sstr << "Ki";
break;
case 2:
sstr << "Mi";
break;
case 3:
sstr << "Gi";
break; // I started on this type of machines
// (32bit computers) (Nicolas)
case 4:
sstr << "Ti";
break;
case 5:
sstr << "Pi";
break;
case 6:
sstr << "Ei";
break; // theoritical limit of RAM of the current
// computers in 2014 (64bit computers) (Nicolas)
case 7:
sstr << "Zi";
break;
case 8:
sstr << "Yi";
break;
default:
AKANTU_ERROR(
"The programmer in 2014 didn't thought so far (even wikipedia does not "
"go further)."
<< " You have at least 1024 times more than a yobibit of RAM!!!"
<< " Just add the prefix corresponding in this switch case.");
}
sstr << "Byte";
return sstr.str();
}
} // namespace akantu
diff --git a/src/common/aka_config.hh.in b/src/common/aka_config.hh.in
index 2f79074cb..dfe78ea2a 100644
--- a/src/common/aka_config.hh.in
+++ b/src/common/aka_config.hh.in
@@ -1,93 +1,90 @@
/**
* @file aka_config.hh.in
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
* @date last modification: Thu Jan 25 2018
*
* @brief Compilation time configuration of Akantu
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-
-#ifndef __AKANTU_AKA_CONFIG_HH__
-#define __AKANTU_AKA_CONFIG_HH__
+#ifndef AKANTU_AKA_CONFIG_HH_
+#define AKANTU_AKA_CONFIG_HH_
#define AKANTU_VERSION_MAJOR @AKANTU_MAJOR_VERSION@
#define AKANTU_VERSION_MINOR @AKANTU_MINOR_VERSION@
#define AKANTU_VERSION_PATCH @AKANTU_PATCH_VERSION@
#define AKANTU_VERSION (AKANTU_VERSION_MAJOR * 10000 \
+ AKANTU_VERSION_MINOR * 100 \
+ AKANTU_VERSION_PATCH)
@AKANTU_TYPES_EXTRA_INCLUDES@
namespace akantu {
using Real = @AKANTU_FLOAT_TYPE@;
using Int = @AKANTU_SIGNED_INTEGER_TYPE@;
using UInt = @AKANTU_UNSIGNED_INTEGER_TYPE@;
} // akantu
#define AKANTU_INTEGER_SIZE @AKANTU_INTEGER_SIZE@
#define AKANTU_FLOAT_SIZE @AKANTU_FLOAT_SIZE@
#cmakedefine AKANTU_HAS_STRDUP
#cmakedefine AKANTU_USE_BLAS
#cmakedefine AKANTU_USE_LAPACK
#cmakedefine AKANTU_PARALLEL
#cmakedefine AKANTU_USE_MPI
#cmakedefine AKANTU_USE_SCOTCH
#cmakedefine AKANTU_USE_PTSCOTCH
#cmakedefine AKANTU_SCOTCH_NO_EXTERN
#cmakedefine AKANTU_IMPLICIT
#cmakedefine AKANTU_USE_MUMPS
#cmakedefine AKANTU_USE_PETSC
#cmakedefine AKANTU_USE_IOHELPER
#cmakedefine AKANTU_USE_QVIEW
#cmakedefine AKANTU_USE_BLACKDYNAMITE
#cmakedefine AKANTU_USE_PYBIND11
#cmakedefine AKANTU_USE_OBSOLETE_GETTIMEOFDAY
#cmakedefine AKANTU_EXTRA_MATERIALS
#cmakedefine AKANTU_STUDENTS_EXTRA_PACKAGE
#cmakedefine AKANTU_DAMAGE_NON_LOCAL
#cmakedefine AKANTU_SOLID_MECHANICS
#cmakedefine AKANTU_STRUCTURAL_MECHANICS
#cmakedefine AKANTU_HEAT_TRANSFER
#cmakedefine AKANTU_PYTHON_INTERFACE
#cmakedefine AKANTU_COHESIVE_ELEMENT
#cmakedefine AKANTU_PARALLEL_COHESIVE_ELEMENT
#cmakedefine AKANTU_IGFEM
#cmakedefine AKANTU_USE_CGAL
#cmakedefine AKANTU_EMBEDDED
// Debug tools
//#cmakedefine AKANTU_NDEBUG
#cmakedefine AKANTU_DEBUG_TOOLS
#cmakedefine READLINK_COMMAND @READLINK_COMMAND@
#cmakedefine ADDR2LINE_COMMAND @ADDR2LINE_COMMAND@
-#define __aka_inline__ inline
-
-#endif /* __AKANTU_AKA_CONFIG_HH__ */
+#endif /* AKANTU_AKA_CONFIG_HH_ */
diff --git a/src/common/aka_csr.hh b/src/common/aka_csr.hh
index 1233f8f6b..8724edca6 100644
--- a/src/common/aka_csr.hh
+++ b/src/common/aka_csr.hh
@@ -1,282 +1,285 @@
/**
* @file aka_csr.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 20 2011
* @date last modification: Sun Dec 03 2017
*
* @brief A compresed sparse row structure based on akantu Arrays
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_CSR_HH__
-#define __AKANTU_AKA_CSR_HH__
+#ifndef AKANTU_AKA_CSR_HH_
+#define AKANTU_AKA_CSR_HH_
namespace akantu {
/**
* This class can be used to store the structure of a sparse matrix or for
* vectors with variable number of component per element
*
* @param nb_rows number of rows of a matrix or size of a vector.
*/
template <typename T> class CSR {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit CSR(UInt nb_rows = 0)
: nb_rows(nb_rows), rows_offsets(nb_rows + 1, 1, "rows_offsets"),
rows(0, 1, "rows") {
- rows_offsets.clear();
+ rows_offsets.zero();
};
virtual ~CSR() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// does nothing
inline void beginInsertions(){};
/// insert a new entry val in row row
inline UInt insertInRow(UInt row, const T & val) {
UInt pos = rows_offsets(row)++;
rows(pos) = val;
return pos;
}
/// access an element of the matrix
inline const T & operator()(UInt row, UInt col) const {
AKANTU_DEBUG_ASSERT(rows_offsets(row + 1) - rows_offsets(row) > col,
"This element is not present in this CSR");
return rows(rows_offsets(row) + col);
}
/// access an element of the matrix
inline T & operator()(UInt row, UInt col) {
AKANTU_DEBUG_ASSERT(rows_offsets(row + 1) - rows_offsets(row) > col,
"This element is not present in this CSR");
return rows(rows_offsets(row) + col);
}
inline void endInsertions() {
- for (UInt i = nb_rows; i > 0; --i)
+ for (UInt i = nb_rows; i > 0; --i) {
rows_offsets(i) = rows_offsets(i - 1);
+ }
rows_offsets(0) = 0;
}
inline void countToCSR() {
- for (UInt i = 1; i < nb_rows; ++i)
+ for (UInt i = 1; i < nb_rows; ++i) {
rows_offsets(i) += rows_offsets(i - 1);
- for (UInt i = nb_rows; i >= 1; --i)
+ }
+ for (UInt i = nb_rows; i >= 1; --i) {
rows_offsets(i) = rows_offsets(i - 1);
+ }
rows_offsets(0) = 0;
}
inline void clearRows() {
- rows_offsets.clear();
+ rows_offsets.zero();
rows.resize(0);
};
inline void resizeRows(UInt nb_rows) {
this->nb_rows = nb_rows;
rows_offsets.resize(nb_rows + 1);
- rows_offsets.clear();
+ rows_offsets.zero();
}
inline void resizeCols() { rows.resize(rows_offsets(nb_rows)); }
inline void copy(Array<UInt> & offsets, Array<T> & values) {
offsets.copy(rows_offsets);
values.copy(rows);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// returns the number of rows
inline UInt getNbRows() const { return rows_offsets.size() - 1; };
/// returns the number of non-empty columns in a given row
inline UInt getNbCols(UInt row) const {
return rows_offsets(row + 1) - rows_offsets(row);
};
/// returns the offset (start of columns) for a given row
inline UInt & rowOffset(UInt row) { return rows_offsets(row); };
// /// iterator on a row
// template <class array_iterator>
// class iterator_internal
// : public std::iterator<std::bidirectional_iterator_tag, typename
// array_iterator::value_type> {
// public:
// using _parent = std::iterator<std::bidirectional_iterator_tag, R>;
// using pointer = typename _parent::pointer;
// using reference = typename _parent::reference;
// explicit iterator_internal(array_iterator ait) : pos(std::move(ait)){};
// iterator_internal(const iterator_internal & it) : pos(it.pos){};
// iterator_internal & operator++() {
// ++pos;
// return *this;
// };
// iterator_internal operator++(int) {
// iterator tmp(*this);
// operator++();
// return tmp;
// };
// iterator_internal & operator--() {
// --pos;
// return *this;
// };
// iterator_internal operator--(int) {
// iterator_internal tmp(*this);
// operator--();
// return tmp;
// };
// bool operator==(const iterator_internal & rhs) { return pos == rhs.pos;
// }; bool operator!=(const iterator_internal & rhs) { return pos !=
// rhs.pos; }; reference operator*() { return *pos; }; pointer operator->()
// const { return pos; };
// private:
// array_iterator pos;
// };
using iterator = typename Array<T>::scalar_iterator;
using const_iterator = typename Array<T>::const_scalar_iterator;
template <typename iterator_internal> class CSRRow {
public:
CSRRow(iterator_internal begin, iterator_internal end)
: begin_(std::move(begin)), end_(std::move(end)) {}
inline auto begin() const { return begin_; }
inline auto end() const { return end_; }
private:
iterator_internal begin_, end_;
};
inline iterator begin(UInt row) { return rows.begin() + rows_offsets(row); };
inline iterator end(UInt row) {
return rows.begin() + rows_offsets(row + 1);
};
inline const_iterator begin(UInt row) const {
return rows.begin() + rows_offsets(row);
};
inline const_iterator end(UInt row) const {
return rows.begin() + rows_offsets(row + 1);
};
private:
template <typename iterator_internal>
decltype(auto) make_row(iterator_internal begin, iterator_internal end) {
return CSRRow<iterator_internal>(std::move(begin), std::move(end));
}
public:
inline decltype(auto) getRow(UInt row) {
return make_row(begin(row), end(row));
}
inline decltype(auto) getRow(UInt row) const {
return make_row(begin(row), end(row));
}
inline iterator rbegin(UInt row) {
return rows.begin() + rows_offsets(row + 1) - 1;
};
inline iterator rend(UInt row) {
return rows.begin() + rows_offsets(row) - 1;
};
inline const Array<UInt> & getRowsOffset() const { return rows_offsets; };
inline const Array<T> & getRows() const { return rows; };
inline Array<T> & getRows() { return rows; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
UInt nb_rows;
/// array of size nb_rows containing the offset where the values are stored in
Array<UInt> rows_offsets;
/// compressed row values, values of row[i] are stored between rows_offsets[i]
/// and rows_offsets[i+1]
Array<T> rows;
};
/* -------------------------------------------------------------------------- */
/* Data CSR */
/* -------------------------------------------------------------------------- */
/**
* Inherits from CSR<UInt> and can contain information such as matrix values
* where the mother class would be a CSR structure for row and cols
*
* @return nb_rows
*/
template <class T> class DataCSR : public CSR<UInt> {
public:
DataCSR(UInt nb_rows = 0) : CSR<UInt>(nb_rows), data(0, 1){};
inline void resizeCols() {
CSR<UInt>::resizeCols();
data.resize(rows_offsets(nb_rows));
}
inline const Array<T> & getData() const { return data; };
private:
Array<T> data;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "aka_csr_inline_impl.hh"
/// standard output stream operator
// inline std::ostream & operator <<(std::ostream & stream, const CSR & _this)
// {
// _this.printself(stream);
// return stream;
// }
} // namespace akantu
-#endif /* __AKANTU_AKA_CSR_HH__ */
+#endif /* AKANTU_AKA_CSR_HH_ */
diff --git a/src/common/aka_element_classes_info.hh.in b/src/common/aka_element_classes_info.hh.in
index 5a7fc4a80..2b34cddb3 100644
--- a/src/common/aka_element_classes_info.hh.in
+++ b/src/common/aka_element_classes_info.hh.in
@@ -1,201 +1,209 @@
/**
* @file aka_element_classes_info.hh.in
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Jul 19 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Declaration of the enums for the element classes
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
*
- * You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_safe_enum.hh"
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_ELEMENT_CLASSES_INFO_HH__
-#define __AKANTU_AKA_ELEMENT_CLASSES_INFO_HH__
+#ifndef AKANTU_AKA_ELEMENT_CLASSES_INFO_HH_
+#define AKANTU_AKA_ELEMENT_CLASSES_INFO_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Element Types */
/* -------------------------------------------------------------------------- */
/// @enum ElementType type of elements
enum ElementType {
_not_defined,
@AKANTU_ELEMENT_TYPES_ENUM@
_max_element_type
};
@AKANTU_ELEMENT_TYPES_BOOST_SEQ@
@AKANTU_ALL_ELEMENT_BOOST_SEQ@
/* -------------------------------------------------------------------------- */
/* Element Kinds */
/* -------------------------------------------------------------------------- */
@AKANTU_ELEMENT_KINDS_BOOST_SEQ@
@AKANTU_ELEMENT_KIND_BOOST_SEQ@
enum ElementKind {
BOOST_PP_SEQ_ENUM(AKANTU_ELEMENT_KIND),
_ek_not_defined
};
/* -------------------------------------------------------------------------- */
struct ElementKind_def {
using type = ElementKind;
static const type _begin_ = BOOST_PP_SEQ_HEAD(AKANTU_ELEMENT_KIND);
static const type _end_ = _ek_not_defined;
};
using element_kind_t = safe_enum<ElementKind_def> ;
/* -------------------------------------------------------------------------- */
/// @enum GeometricalType type of element potentially contained in a Mesh
enum GeometricalType {
@AKANTU_GEOMETRICAL_TYPES_ENUM@
_gt_not_defined
};
/* -------------------------------------------------------------------------- */
/* Interpolation Types */
/* -------------------------------------------------------------------------- */
@AKANTU_INTERPOLATION_TYPES_BOOST_SEQ@
/// @enum InterpolationType type of elements
enum InterpolationType {
BOOST_PP_SEQ_ENUM(AKANTU_INTERPOLATION_TYPES),
_itp_not_defined
};
/* -------------------------------------------------------------------------- */
/* Some sub types less probable to change */
/* -------------------------------------------------------------------------- */
/// @enum GeometricalShapeType types of shapes to define the contains
/// function in the element classes
enum GeometricalShapeType {
@AKANTU_GEOMETRICAL_SHAPES_ENUM@
_gst_not_defined
};
/* -------------------------------------------------------------------------- */
/// @enum GaussIntegrationType classes of types using common
/// description of the gauss point position and weights
enum GaussIntegrationType {
@AKANTU_GAUSS_INTEGRATION_TYPES_ENUM@
_git_not_defined
};
/* -------------------------------------------------------------------------- */
/// @enum InterpolationKind the family of interpolation types
enum InterpolationKind {
@AKANTU_INTERPOLATION_KIND_ENUM@
_itk_not_defined
};
/* -------------------------------------------------------------------------- */
// BOOST PART: TOUCH ONLY IF YOU KNOW WHAT YOU ARE DOING
#define AKANTU_BOOST_CASE_MACRO(r, macro, _type) \
case _type: { \
macro(_type); \
break; \
}
#define AKANTU_BOOST_LIST_SWITCH(macro1, list1, var) \
do { \
switch (var) { \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, macro1, list1) \
default: { \
- AKANTU_ERROR("Type (" << var << ") not handled by this function"); \
+ AKANTU_ERROR("Type (" \
+ << var /* NOLINT */ << ") not handled by this function"); \
} \
} \
} while (0)
#define AKANTU_BOOST_LIST_SWITCH_NO_DEFAULT(macro1, list1, var) \
do { \
switch (var) { \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, macro1, list1) \
- case _not_defined: \
- break; \
+ case _not_defined: /* FALLTHRU */ \
case _max_element_type: \
break; \
} \
} while (0)
#define AKANTU_BOOST_ELEMENT_SWITCH(macro1, list1) \
AKANTU_BOOST_LIST_SWITCH(macro1, list1, type)
#define AKANTU_BOOST_ELEMENT_SWITCH_NO_DEFAULT(macro1, list1) \
AKANTU_BOOST_LIST_SWITCH_NO_DEFAULT(macro1, list1, type)
#define AKANTU_BOOST_ALL_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_BOOST_ALL_ELEMENT_SWITCH_NO_DEFAULT(macro) \
AKANTU_BOOST_ELEMENT_SWITCH_NO_DEFAULT(macro, AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_BOOST_LIST_MACRO(r, macro, type) macro(type)
#define AKANTU_BOOST_APPLY_ON_LIST(macro, list) \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_GET_ELEMENT_LIST(kind) AKANTU##kind##_ELEMENT_TYPE
#define AKANTU_BOOST_KIND_ELEMENT_SWITCH(macro, kind) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, AKANTU_GET_ELEMENT_LIST(kind))
// BOOST_PP_SEQ_TO_LIST does not exists in Boost < 1.49
#define AKANTU_GENERATE_KIND_LIST(seq) \
BOOST_PP_TUPLE_TO_LIST(BOOST_PP_SEQ_SIZE(seq), BOOST_PP_SEQ_TO_TUPLE(seq))
#define AKANTU_ELEMENT_KIND_BOOST_LIST \
AKANTU_GENERATE_KIND_LIST(AKANTU_ELEMENT_KIND)
#define AKANTU_BOOST_ALL_KIND_LIST(macro, list) \
BOOST_PP_LIST_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_KIND(macro) \
AKANTU_BOOST_ALL_KIND_LIST(macro, AKANTU_ELEMENT_KIND_BOOST_LIST)
#define AKANTU_BOOST_ALL_KIND_SWITCH(macro) \
AKANTU_BOOST_LIST_SWITCH(macro, AKANTU_ELEMENT_KIND, kind)
@AKANTU_ELEMENT_KINDS_BOOST_MACROS@
// /// define kept for compatibility reasons (they are most probably not needed
// /// anymore) \todo check if they can be removed
// #define AKANTU_REGULAR_ELEMENT_TYPE AKANTU_ek_regular_ELEMENT_TYPE
// #define AKANTU_COHESIVE_ELEMENT_TYPE AKANTU_ek_cohesive_ELEMENT_TYPE
// #define AKANTU_STRUCTURAL_ELEMENT_TYPE AKANTU_ek_structural_ELEMENT_TYPE
// #define AKANTU_IGFEM_ELEMENT_TYPE AKANTU_ek_igfem_ELEMENT_TYPE
/* -------------------------------------------------------------------------- */
/* Lists of interests for FEEngineTemplate functions */
/* -------------------------------------------------------------------------- */
@AKANTU_FE_ENGINE_LISTS@
} // akantu
-#endif /* __AKANTU_AKA_ELEMENT_CLASSES_INFO_HH__ */
+#endif /* AKANTU_AKA_ELEMENT_CLASSES_INFO_HH_ */
#include "aka_element_classes_info_inline_impl.hh"
diff --git a/src/common/aka_element_classes_info_inline_impl.hh b/src/common/aka_element_classes_info_inline_impl.hh
index c76fc05a4..3a05abbe8 100644
--- a/src/common/aka_element_classes_info_inline_impl.hh
+++ b/src/common/aka_element_classes_info_inline_impl.hh
@@ -1,52 +1,52 @@
/**
* @file aka_element_classes_info_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 18 2015
* @date last modification: Wed Jan 10 2018
*
* @brief Implementation of the streaming fonction for the element classes
* enums
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_HH__
-#define __AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_HH__
+#ifndef AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_HH_
+#define AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_HH_
namespace akantu {
AKANTU_ENUM_OUTPUT_STREAM(
ElementType, AKANTU_ALL_ELEMENT_TYPE(_not_defined)(_max_element_type))
AKANTU_ENUM_INPUT_STREAM(ElementType, AKANTU_ALL_ELEMENT_TYPE)
AKANTU_ENUM_OUTPUT_STREAM(InterpolationType, AKANTU_INTERPOLATION_TYPES)
AKANTU_ENUM_INPUT_STREAM(InterpolationType, AKANTU_INTERPOLATION_TYPES)
AKANTU_ENUM_OUTPUT_STREAM(ElementKind, AKANTU_ELEMENT_KIND)
AKANTU_ENUM_INPUT_STREAM(ElementKind, AKANTU_ELEMENT_KIND)
} // namespace akantu
-#endif /* __AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_HH__ */
+#endif /* AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_HH_ */
diff --git a/src/common/aka_enum_macros.hh b/src/common/aka_enum_macros.hh
index e0e82be7e..bee12f1d2 100644
--- a/src/common/aka_enum_macros.hh
+++ b/src/common/aka_enum_macros.hh
@@ -1,132 +1,133 @@
/**
* @file aka_enum_macros.hh
*
* @author Nicolas Richart
*
* @date creation Wed Oct 31 2018
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <string>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_ENUM_MACROS_HH__
-#define __AKANTU_AKA_ENUM_MACROS_HH__
+#ifndef AKANTU_AKA_ENUM_MACROS_HH_
+#define AKANTU_AKA_ENUM_MACROS_HH_
#define AKANTU_PP_ENUM(s, data, i, elem) \
BOOST_PP_TUPLE_REM() \
elem BOOST_PP_COMMA_IF(BOOST_PP_NOT_EQUAL(i, BOOST_PP_DEC(data)))
#if (defined(__GNUC__) || defined(__GNUG__))
#define AKA_GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if AKA_GCC_VERSION < 60000
#define AKANTU_ENUM_HASH(type_name) \
namespace std { \
template <> struct hash<::akantu::type_name> { \
using argument_type = ::akantu::type_name; \
size_t operator()(const argument_type & e) const noexcept { \
auto ue = underlying_type_t<argument_type>(e); \
return uh(ue); \
} \
\
private: \
const hash<underlying_type_t<argument_type>> uh{}; \
}; \
}
#else
#define AKANTU_ENUM_HASH(type_name)
#endif // AKA_GCC_VERSION
#endif // GNU
#define AKANTU_PP_CAT(s, data, elem) BOOST_PP_CAT(data, elem)
#define AKANTU_PP_TYPE_TO_STR(s, data, elem) \
({BOOST_PP_CAT(data, elem), BOOST_PP_STRINGIZE(elem)})
#define AKANTU_PP_STR_TO_TYPE(s, data, elem) \
({BOOST_PP_STRINGIZE(elem), BOOST_PP_CAT(data, elem)})
#define AKANTU_CLASS_ENUM_DECLARE(type_name, list) \
enum class type_name { \
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_CAT, _, list)) \
};
#define AKANTU_ENUM_OUTPUT_STREAM_(type_name, list, prefix) \
} \
AKANTU_ENUM_HASH(type_name) \
namespace std { \
inline string to_string(const ::akantu::type_name & type) { \
using namespace akantu; \
static unordered_map<::akantu::type_name, string> convert{ \
BOOST_PP_SEQ_FOR_EACH_I( \
AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(list), \
BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_TYPE_TO_STR, prefix, list))}; \
return convert.at(type); \
} \
} \
namespace akantu { \
inline std::ostream & operator<<(std::ostream & stream, \
const type_name & type) { \
stream << std::to_string(type); \
return stream; \
}
#define AKANTU_ENUM_INPUT_STREAM_(type_name, list, prefix) \
- inline std::istream & operator>>(std::istream & stream, type_name & type) { \
+ inline std::istream & operator>>(std::istream & stream, \
+ type_name & type) { /* NOLINT */ \
std::string str; \
- stream >> str; \
+ stream >> str; /* NOLINT */ \
static std::unordered_map<std::string, type_name> convert{ \
BOOST_PP_SEQ_FOR_EACH_I( \
AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(list), \
BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_STR_TO_TYPE, prefix, list))}; \
try { \
type = convert.at(str); \
} catch (std::out_of_range &) { \
std::ostringstream values; \
std::for_each(convert.begin(), convert.end(), [&values](auto && pair) { \
static bool first = true; \
if (not first) \
values << ", "; \
values << "\"" << pair.first << "\""; \
first = false; \
}); \
AKANTU_EXCEPTION("The value " << str << " is not a valid " \
<< BOOST_PP_STRINGIZE(type_name) \
<< " valid values are " << values.str()); \
} \
return stream; \
}
#define AKANTU_CLASS_ENUM_OUTPUT_STREAM(type_name, list) \
AKANTU_ENUM_OUTPUT_STREAM_(type_name, list, type_name::_)
#define AKANTU_ENUM_OUTPUT_STREAM(type_name, list) \
AKANTU_ENUM_OUTPUT_STREAM_(type_name, list, )
#define AKANTU_CLASS_ENUM_INPUT_STREAM(type_name, list) \
AKANTU_ENUM_INPUT_STREAM_(type_name, list, type_name::_)
#define AKANTU_ENUM_INPUT_STREAM(type_name, list) \
AKANTU_ENUM_INPUT_STREAM_(type_name, list, )
-#endif /* __AKANTU_AKA_ENUM_MACROS_HH__ */
+#endif /* AKANTU_AKA_ENUM_MACROS_HH_ */
diff --git a/src/common/aka_error.cc b/src/common/aka_error.cc
index c75d92d1d..9a3767e0c 100644
--- a/src/common/aka_error.cc
+++ b/src/common/aka_error.cc
@@ -1,363 +1,367 @@
/**
* @file aka_error.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 06 2010
* @date last modification: Sun Dec 03 2017
*
* @brief handling of errors
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_error.hh"
#include "aka_common.hh"
#include "aka_config.hh"
#include "aka_iterators.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
#include <csignal>
#include <iostream>
#include <vector>
#if (defined(READLINK_COMMAND) || defined(ADDR2LINE_COMMAND)) && \
(!defined(_WIN32))
#include <execinfo.h>
#include <sys/wait.h>
#endif
#include <chrono>
#include <cmath>
#include <cstring>
#include <cxxabi.h>
#include <fstream>
#include <iomanip>
#include <map>
#include <sys/types.h>
#include <unistd.h>
#ifdef AKANTU_USE_MPI
#include <mpi.h>
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace debug {
// static void printBacktraceAndExit(int) { std::terminate(); }
// /* ------------------------------------------------------------------------ */
// void initSignalHandler() { std::signal(SIGSEGV, &printBacktraceAndExit); }
/* ------------------------------------------------------------------------ */
std::string demangle(const char * symbol) {
int status;
std::string result;
char * demangled_name;
if ((demangled_name = abi::__cxa_demangle(symbol, nullptr, nullptr,
&status)) != nullptr) {
result = demangled_name;
free(demangled_name);
} else {
result = symbol;
}
return result;
}
/* ------------------------------------------------------------------------ */
#if (defined(READLINK_COMMAND) || defined(ADDR2LINK_COMMAND)) && \
(!defined(_WIN32))
std::string exec(const std::string & cmd) {
FILE * pipe = popen(cmd.c_str(), "r");
- if (!pipe)
+ if (pipe == nullptr) {
return "";
+ }
char buffer[1024];
- std::string result = "";
- while (!feof(pipe)) {
- if (fgets(buffer, 128, pipe) != nullptr)
+ std::string result;
+ while (feof(pipe) == 0) {
+ if (fgets(buffer, 128, pipe) != nullptr) {
result += buffer;
+ }
}
result = result.substr(0, result.size() - 1);
pclose(pipe);
return result;
}
#endif
auto getBacktrace() -> std::vector<std::string> {
std::vector<std::string> backtrace_lines;
#if not defined(_WIN32)
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
-
- std::string me = "";
+ std::string me;
char buf[1024];
/* The manpage says it won't null terminate. Let's zero the buffer. */
memset(buf, 0, sizeof(buf));
/* Note we use sizeof(buf)-1 since we may need an extra char for NUL. */
- if (readlink("/proc/self/exe", buf, sizeof(buf) - 1))
+ if (readlink("/proc/self/exe", buf, sizeof(buf) - 1) != 0) {
me = std::string(buf);
+ }
std::ifstream inmaps;
inmaps.open("/proc/self/maps");
std::map<std::string, size_t> addr_map;
std::string line;
while (inmaps.good()) {
std::getline(inmaps, line);
std::stringstream sstr(line);
size_t first = line.find('-');
std::stringstream sstra(line.substr(0, first));
size_t addr;
sstra >> std::hex >> addr;
std::string lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
- if (lib != "" && addr_map.find(lib) == addr_map.end()) {
+ if (not lib.empty() and (addr_map.find(lib) == addr_map.end())) {
addr_map[lib] = addr;
}
}
- if (me != "")
+ if (not me.empty()) {
addr_map[me] = 0;
+ }
#endif
/// \todo for windows this part could be coded using CaptureStackBackTrace
/// and SymFromAddr
const size_t max_depth = 100;
size_t stack_depth;
void * stack_addrs[max_depth];
char ** stack_strings;
size_t i;
stack_depth = backtrace(stack_addrs, max_depth);
stack_strings = backtrace_symbols(stack_addrs, stack_depth);
/// -1 to remove the call to the printBacktrace function
for (i = 1; i < stack_depth; i++) {
std::string bt_line(stack_strings[i]);
- size_t first, second;
+ size_t first;
+ size_t second;
if ((first = bt_line.find('(')) != std::string::npos &&
(second = bt_line.find('+')) != std::string::npos) {
std::string location = bt_line.substr(0, first);
#if defined(READLINK_COMMAND)
std::string location_cmd =
std::string(BOOST_PP_STRINGIZE(READLINK_COMMAND)) +
std::string(" -f ") + location;
location = exec(location_cmd);
#endif
std::string call =
demangle(bt_line.substr(first + 1, second - first - 1).c_str());
size_t f = bt_line.find('[');
size_t s = bt_line.find(']');
std::string address = bt_line.substr(f + 1, s - f - 1);
std::stringstream sstra(address);
size_t addr;
sstra >> std::hex >> addr;
std::string trace = location + " [" + call + "]";
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
auto it = addr_map.find(location);
if (it != addr_map.end()) {
std::stringstream syscom;
syscom << BOOST_PP_STRINGIZE(ADDR2LINE_COMMAND) << " 0x" << std::hex
<< (addr - it->second) << " -i -e " << location;
std::string line = exec(syscom.str());
trace += " (" + line + ")";
} else {
#endif
std::stringstream sstr_addr;
sstr_addr << std::hex << addr;
trace += " (0x" + sstr_addr.str() + ")";
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
}
#endif
backtrace_lines.push_back(trace);
} else {
backtrace_lines.push_back(bt_line);
}
}
free(stack_strings);
#endif
return backtrace_lines;
}
/* ------------------------------------------------------------------------ */
void printBacktrace(const std::vector<std::string> & backtrace) {
auto w = size_t(std::floor(std::log10(double(backtrace.size()))) + 1);
std::cerr << "BACKTRACE : " << backtrace.size() << " stack frames.\n";
for (auto && data : enumerate(backtrace))
std::cerr << " [" << std::setw(w) << (std::get<0>(data) + 1) << "] "
<< std::get<1>(data) << "\n";
std::cerr << "END BACKTRACE" << std::endl;
}
/* ------------------------------------------------------------------------ */
namespace {
void terminate_handler() {
auto eptr = std::current_exception();
- auto t = abi::__cxa_current_exception_type();
- auto name = t ? demangle(t->name()) : std::string("unknown");
+ auto *t = abi::__cxa_current_exception_type();
+ auto name = (t != nullptr) ? demangle(t->name()) : std::string("unknown");
try {
- if (eptr)
+ if (eptr) {
std::rethrow_exception(eptr);
- else {
+ } else {
printBacktrace();
std::cerr << AKANTU_LOCATION
<< "!! Execution terminated for unknown reasons !!"
<< std::endl;
}
} catch (Exception & e) {
printBacktrace(e.backtrace());
std::cerr << "!! Uncaught akantu::Exception of type " << name
<< " !!\nwhat(): \"" << e.what() << "\"" << std::endl;
} catch (std::exception & e) {
std::cerr << "!! Uncaught exception of type " << name
<< " !!\nwhat(): \"" << e.what() << "\"" << std::endl;
} catch (...) {
std::cerr << "!! Something strange of type \"" << name
<< "\" was thrown.... !!" << std::endl;
}
if (debugger.printBacktrace()) {
std::cerr << "Random generator seed: " << RandomGenerator<UInt>::seed()
<< std::endl;
printBacktrace();
}
}
} // namespace
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
- Debugger::Debugger() {
+ Debugger::Debugger() noexcept {
cout = &std::cerr;
level = dblWarning;
parallel_context = "";
file_open = false;
print_backtrace = false;
//initSignalHandler();
std::set_terminate(terminate_handler);
}
/* ------------------------------------------------------------------------ */
Debugger::~Debugger() {
if (file_open) {
dynamic_cast<std::ofstream *>(cout)->close();
delete cout;
}
}
/* ------------------------------------------------------------------------ */
void Debugger::exit(int status) {
- if (status != 0)
+ if (status != 0) {
std::terminate();
+ }
std::exit(0);
}
/*------------------------------------------------------------------------- */
void Debugger::throwException(const std::string & info,
const std::string & file, unsigned int line,
__attribute__((unused)) bool silent,
__attribute__((unused))
const std::string & location,
const std::string & module) const
noexcept(false) {
#if !defined(AKANTU_NDEBUG)
if (not silent) {
printMessage("###", dblWarning, info + " " + location, module);
}
#endif
debug::Exception ex(info, file, line);
ex.setModule(module);
throw ex;
}
/* ------------------------------------------------------------------------ */
void Debugger::printMessage(const std::string & prefix,
const DebugLevel & level,
const std::string & info,
const std::string & module) const {
if (testLevel(level, module)) {
double timestamp =
std::chrono::duration_cast<std::chrono::duration<double, std::micro>>(
std::chrono::system_clock::now().time_since_epoch())
.count();
*(cout) << parallel_context << "{" << (size_t)timestamp << "} " << prefix
<< " " << info << std::endl;
}
}
/* ------------------------------------------------------------------------ */
void Debugger::setDebugLevel(const DebugLevel & level) {
this->level = level;
}
/* ------------------------------------------------------------------------ */
const DebugLevel & Debugger::getDebugLevel() const { return this->level; }
/* ------------------------------------------------------------------------ */
void Debugger::setLogFile(const std::string & filename) {
if (file_open) {
dynamic_cast<std::ofstream *>(cout)->close();
delete cout;
}
auto * fileout = new std::ofstream(filename.c_str());
file_open = true;
cout = fileout;
}
std::ostream & Debugger::getOutputStream() { return *cout; }
/* ------------------------------------------------------------------------ */
void Debugger::setParallelContext(int rank, int size) {
std::stringstream sstr;
UInt pad = std::ceil(std::log10(size));
sstr << "<" << getpid() << ">[R" << std::setfill(' ') << std::right
<< std::setw(pad) << rank << "|S" << size << "] ";
parallel_context = sstr.str();
}
void setDebugLevel(const DebugLevel & level) {
debugger.setDebugLevel(level);
}
const DebugLevel & getDebugLevel() { return debugger.getDebugLevel(); }
- /* --------------------------------------------------------------------------
- */
- void exit(int status) { debugger.exit(status); }
+ /* ------------------------------------------------------------------------ */
+ void exit(int status) { Debugger::exit(status); }
} // namespace debug
} // namespace akantu
diff --git a/src/common/aka_error.hh b/src/common/aka_error.hh
index 3badb946f..269a7400b 100644
--- a/src/common/aka_error.hh
+++ b/src/common/aka_error.hh
@@ -1,415 +1,418 @@
/**
* @file aka_error.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Tue Feb 20 2018
*
* @brief error management and internal exceptions
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <set>
#include <sstream>
#include <typeinfo>
#include <utility>
#include <vector>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ERROR_HH__
-#define __AKANTU_ERROR_HH__
+#ifndef AKANTU_ERROR_HH_
+#define AKANTU_ERROR_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
enum DebugLevel {
dbl0 = 0,
dblError = 0,
dblAssert = 0,
dbl1 = 1,
dblException = 1,
dblCritical = 1,
dbl2 = 2,
dblMajor = 2,
dbl3 = 3,
dblCall = 3,
dblSecondary = 3,
dblHead = 3,
dbl4 = 4,
dblWarning = 4,
dbl5 = 5,
dblInfo = 5,
dbl6 = 6,
dblIn = 6,
dblOut = 6,
dbl7 = 7,
dbl8 = 8,
dblTrace = 8,
dbl9 = 9,
dblAccessory = 9,
dbl10 = 10,
dblDebug = 42,
dbl100 = 100,
dblDump = 100,
dblTest = 1337
};
/* -------------------------------------------------------------------------- */
#define AKANTU_LOCATION \
"(" << std::string(__func__) << "(): " << std::string(__FILE__) << ":" \
<< std::to_string(__LINE__) \
<< ")" // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay)
/* -------------------------------------------------------------------------- */
namespace debug {
void setDebugLevel(const DebugLevel & level);
const DebugLevel & getDebugLevel();
void initSignalHandler();
std::string demangle(const char * symbol);
template <class T> std::string demangle() {
return demangle(typeid(T).name());
}
template <class T> std::string demangle(const T & t) {
return demangle(typeid(t).name());
}
auto exec(const std::string & cmd) -> std::string;
auto getBacktrace() -> std::vector<std::string>;
void
printBacktrace(const std::vector<std::string> & backtrace = getBacktrace());
void exit(int status) __attribute__((noreturn));
/* ------------------------------------------------------------------------ */
/// exception class that can be thrown by akantu
class Exception : public std::exception {
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
protected:
- explicit Exception(std::string info = "")
- : _info(std::move(info)), _file("") {}
+ explicit Exception(std::string info = "") : _info(std::move(info)) {}
public:
//! full constructor
Exception(std::string info, std::string file, unsigned int line)
: _info(std::move(info)), _file(std::move(file)), _line(line) {}
- //! destructor
- ~Exception() noexcept override = default;
-
/* ---------------------------------------------------------------------- */
/* Methods */
/* ---------------------------------------------------------------------- */
public:
const char * what() const noexcept override { return _info.c_str(); }
- virtual const std::string info() const noexcept {
+ virtual std::string info() const noexcept {
std::stringstream stream;
stream << debug::demangle(typeid(*this).name()) << " : " << _info << " ["
<< _file << ":" << _line << "]";
return stream.str();
}
public:
void setInfo(const std::string & info) { _info = info; }
void setFile(const std::string & file) { _file = file; }
void setLine(unsigned int line) { _line = line; }
void setModule(const std::string & module) { _module = module; }
void setBacktrace(const std::vector<std::string> & backtrace) {
backtrace_ = backtrace;
}
decltype(auto) backtrace() const { return backtrace_; }
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
protected:
/// exception description and additionals
std::string _info;
private:
/// file it is thrown from
std::string _file;
/// line it is thrown from
unsigned int _line{0};
/// module in which exception was raised
std::string _module{"core"};
std::vector<std::string> backtrace_;
};
class CriticalError : public Exception {};
class AssertException : public Exception {};
class NotImplementedException : public Exception {};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Exception & _this) {
stream << _this.what();
return stream;
}
/* --------------------------------------------------------------------------
*/
class Debugger {
public:
- Debugger();
+ Debugger() noexcept;
virtual ~Debugger();
Debugger(const Debugger &) = default;
Debugger & operator=(const Debugger &) = default;
+ Debugger(Debugger &&) noexcept = default;
+ Debugger & operator=(Debugger &&) noexcept = default;
- void exit(int status) __attribute__((noreturn));
+ static void exit(int status) __attribute__((noreturn));
void throwException(const std::string & info, const std::string & file,
- unsigned int line, bool, const std::string &,
+ unsigned int line, bool /*silent*/,
+ const std::string & /*location*/,
const std::string & module) const noexcept(false)
__attribute__((noreturn));
/*----------------------------------------------------------------------- */
template <class Except>
- void throwCustomException(const Except & ex, const std::string & info,
+ void throwCustomException(Except ex, const std::string & info,
const std::string & file, unsigned int line,
const std::string & module) const noexcept(false)
__attribute__((noreturn));
/*----------------------------------------------------------------------- */
template <class Except>
- void throwCustomException(const Except & ex, const std::string & file,
+ void throwCustomException(Except ex, const std::string & file,
unsigned int line,
const std::string & module_) const noexcept(false)
__attribute__((noreturn));
void printMessage(const std::string & prefix, const DebugLevel & level,
const std::string & info,
const std::string & module_) const;
void setOutStream(std::ostream & out) { cout = &out; }
std::ostream & getOutStream() { return *cout; }
public:
void setParallelContext(int rank, int size);
void setDebugLevel(const DebugLevel & level);
const DebugLevel & getDebugLevel() const;
void setLogFile(const std::string & filename);
std::ostream & getOutputStream();
inline bool testLevel(const DebugLevel & level,
const std::string & module = "core") const {
auto level_reached = (this->level >= (level));
auto correct_module =
- (level <= dblCritical) or (modules_to_debug.size() == 0) or
+ (level <= dblCritical) or (modules_to_debug.empty()) or
(modules_to_debug.find(module) != modules_to_debug.end());
return level_reached and correct_module;
}
void printBacktrace(bool on_off) { this->print_backtrace = on_off; }
- bool printBacktrace() { return this->print_backtrace; }
+ bool printBacktrace() const { return this->print_backtrace; }
void addModuleToDebug(const std::string & id) {
modules_to_debug.insert(id);
}
void removeModuleToDebug(const std::string & id) {
auto it = modules_to_debug.find(id);
- if (it != modules_to_debug.end())
+ if (it != modules_to_debug.end()) {
modules_to_debug.erase(it);
+ }
}
void listModules() {
- for (auto & module_ : modules_to_debug) {
+ for (const auto & module_ : modules_to_debug) {
(*cout) << module_ << std::endl;
}
}
private:
std::string parallel_context;
std::ostream * cout;
bool file_open;
DebugLevel level;
bool print_backtrace;
std::set<std::string> modules_to_debug;
};
- extern Debugger debugger;
+ extern Debugger debugger; // NOLINT
} // namespace debug
/* -------------------------------------------------------------------------- */
#define AKANTU_STRINGIZE_(str) #str
#define AKANTU_STRINGIZE(str) AKANTU_STRINGIZE_(str)
/* -------------------------------------------------------------------------- */
#define AKANTU_DEBUG_MODULE AKANTU_STRINGIZE(AKANTU_MODULE)
/* -------------------------------------------------------------------------- */
#define AKANTU_STRINGSTREAM_IN(_str, _sstr) \
; \
do { \
std::stringstream _dbg_s_info; \
- _dbg_s_info << _sstr; \
- _str = _dbg_s_info.str(); \
+ _dbg_s_info << _sstr; /* NOLINT */ \
+ (_str) = _dbg_s_info.str(); \
} while (false)
/* -------------------------------------------------------------------------- */
#define AKANTU_EXCEPTION(info) AKANTU_EXCEPTION_(info, false)
#define AKANTU_SILENT_EXCEPTION(info) AKANTU_EXCEPTION_(info, true)
#define AKANTU_EXCEPTION_(info, silent) \
do { \
std::stringstream _dbg_str; \
- _dbg_str << info; \
+ _dbg_str << info; /* NOLINT */ \
std::stringstream _dbg_loc; \
_dbg_loc << AKANTU_LOCATION; \
::akantu::debug::debugger.throwException(_dbg_str.str(), __FILE__, \
__LINE__, silent, _dbg_loc.str(), \
AKANTU_DEBUG_MODULE); \
} while (false)
#define AKANTU_CUSTOM_EXCEPTION_INFO(ex, info) \
do { \
std::stringstream _dbg_str; \
- _dbg_str << info; \
+ _dbg_str << info; /* NOLINT */ \
::akantu::debug::debugger.throwCustomException( \
ex, _dbg_str.str(), __FILE__, __LINE__, AKANTU_DEBUG_MODULE); \
} while (false)
#define AKANTU_CUSTOM_EXCEPTION(ex) \
do { \
::akantu::debug::debugger.throwCustomException(ex, __FILE__, __LINE__, \
AKANTU_DEBUG_MODULE); \
} while (false)
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_NDEBUG
#define AKANTU_DEBUG_TEST(level) (false)
#define AKANTU_DEBUG_LEVEL_IS_TEST() \
(::akantu::debug::debugger.testLevel(dblTest, AKANTU_DEBUG_MODULE))
#define AKANTU_DEBUG(level, info)
#define AKANTU_DEBUG_(pref, level, info)
#define AKANTU_DEBUG_IN()
#define AKANTU_DEBUG_OUT()
#define AKANTU_DEBUG_INFO(info)
#define AKANTU_DEBUG_WARNING(info)
#define AKANTU_DEBUG_TRACE(info)
#define AKANTU_DEBUG_ASSERT(test, info)
#define AKANTU_ERROR(info) \
AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::CriticalError(), info)
/* -------------------------------------------------------------------------- */
#else
#define AKANTU_DEBUG(level, info) AKANTU_DEBUG_(" ", level, info)
#define AKANTU_DEBUG_(pref, level, info) \
do { \
std::string _dbg_str; \
- AKANTU_STRINGSTREAM_IN(_dbg_str, info << " " << AKANTU_LOCATION); \
+ AKANTU_STRINGSTREAM_IN(_dbg_str, \
+ info << " " << AKANTU_LOCATION); /* NOLINT */ \
::akantu::debug::debugger.printMessage(pref, level, _dbg_str, \
AKANTU_DEBUG_MODULE); \
} while (false)
#define AKANTU_DEBUG_TEST(level) \
(::akantu::debug::debugger.testLevel(level, AKANTU_DEBUG_MODULE))
#define AKANTU_DEBUG_LEVEL_IS_TEST() \
(::akantu::debug::debugger.testLevel(dblTest))
#define AKANTU_DEBUG_IN() \
AKANTU_DEBUG_( \
"==>", ::akantu::dblIn, \
__func__ \
- << "()") // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay)
+ << "()") // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay,
+ // bugprone-lambda-function-name)
#define AKANTU_DEBUG_OUT() \
AKANTU_DEBUG_( \
"<==", ::akantu::dblOut, \
__func__ \
- << "()") // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay)
+ << "()") // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay,
+ // bugprone-lambda-function-name)
#define AKANTU_DEBUG_INFO(info) AKANTU_DEBUG_("---", ::akantu::dblInfo, info)
#define AKANTU_DEBUG_WARNING(info) \
AKANTU_DEBUG_("/!\\", ::akantu::dblWarning, info)
#define AKANTU_DEBUG_TRACE(info) AKANTU_DEBUG_(">>>", ::akantu::dblTrace, info)
#define AKANTU_DEBUG_ASSERT(test, info) \
do { \
if (not(test)) \
AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::AssertException(), \
- "assert [" << #test << "] " << info); \
+ "assert [" << #test << "] " \
+ << info); /* NOLINT */ \
} while (false)
#define AKANTU_ERROR(info) \
do { \
AKANTU_DEBUG_("!!! ", ::akantu::dblError, info); \
- AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::CriticalError(), info); \
+ AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::CriticalError(), \
+ info); /* NOLINT */ \
} while (false)
#endif // AKANTU_NDEBUG
#define AKANTU_TO_IMPLEMENT() \
AKANTU_CUSTOM_EXCEPTION_INFO( \
::akantu::debug::NotImplementedException(), \
__func__ \
- << " : not implemented yet !") // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay)
+ << " : not implemented yet !") // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay,
+ // bugprone-lambda-function-name)
/* -------------------------------------------------------------------------- */
namespace debug {
/* ------------------------------------------------------------------------ */
template <class Except>
void
- Debugger::throwCustomException(const Except & ex, const std::string & info,
+ Debugger::throwCustomException(Except ex, const std::string & info,
const std::string & file, unsigned int line,
const std::string & module_) const
noexcept(false) {
- auto & nc_ex = const_cast<Except &>(ex);
- nc_ex.setInfo(info);
- nc_ex.setFile(file);
- nc_ex.setLine(line);
- nc_ex.setModule(module_);
- if (::akantu::debug::debugger.printBacktrace())
- nc_ex.setBacktrace(::akantu::debug::getBacktrace());
-
+ ex.setInfo(info);
+ ex.setFile(file);
+ ex.setLine(line);
+ ex.setModule(module_);
+ if (::akantu::debug::debugger.printBacktrace()) {
+ ex.setBacktrace(::akantu::debug::getBacktrace());
+ }
throw ex;
}
/* ------------------------------------------------------------------------ */
template <class Except>
- void Debugger::throwCustomException(const Except & ex,
- const std::string & file,
+ void Debugger::throwCustomException(Except ex, const std::string & file,
unsigned int line,
const std::string & module_) const
noexcept(false) {
- auto & nc_ex = const_cast<Except &>(ex);
- nc_ex.setFile(file);
- nc_ex.setLine(line);
- nc_ex.setModule(module_);
- if (::akantu::debug::debugger.printBacktrace())
- nc_ex.setBacktrace(::akantu::debug::getBacktrace());
-
+ ex.setFile(file);
+ ex.setLine(line);
+ ex.setModule(module_);
+ if (::akantu::debug::debugger.printBacktrace()) {
+ ex.setBacktrace(::akantu::debug::getBacktrace());
+ }
throw ex;
}
} // namespace debug
} // namespace akantu
-#endif /* __AKANTU_ERROR_HH__ */
+#endif /* AKANTU_ERROR_HH_ */
diff --git a/src/common/aka_event_handler_manager.hh b/src/common/aka_event_handler_manager.hh
index ea8d9f032..258f1f94f 100644
--- a/src/common/aka_event_handler_manager.hh
+++ b/src/common/aka_event_handler_manager.hh
@@ -1,124 +1,126 @@
/**
* @file aka_event_handler_manager.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Base of Event Handler classes
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_EVENT_HANDLER_MANAGER_HH__
-#define __AKANTU_AKA_EVENT_HANDLER_MANAGER_HH__
+#ifndef AKANTU_AKA_EVENT_HANDLER_MANAGER_HH_
+#define AKANTU_AKA_EVENT_HANDLER_MANAGER_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <list>
/* -------------------------------------------------------------------------- */
namespace akantu {
template <class EventHandler> class EventHandlerManager {
private:
using priority_value = std::pair<EventHandlerPriority, EventHandler *>;
using priority_list = std::list<priority_value>;
struct KeyComp {
bool operator()(const priority_value & a, const priority_value & b) const {
return (a.first < b.first);
}
bool operator()(const priority_value & a, UInt b) const {
return (a.first < b);
}
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
virtual ~EventHandlerManager() { event_handlers.clear(); }
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register a new EventHandler to the Manager. The register object
/// will then be informed about the events the manager observes.
void registerEventHandler(EventHandler & event_handler,
EventHandlerPriority priority = _ehp_highest) {
auto it = this->searchEventHandler(event_handler);
if (it != this->event_handlers.end()) {
AKANTU_EXCEPTION("This event handler was already registered (priority: "
<< priority << ")");
}
auto pos =
std::lower_bound(this->event_handlers.begin(),
this->event_handlers.end(), priority, KeyComp());
this->event_handlers.insert(pos, std::make_pair(priority, &event_handler));
}
/// unregister a EventHandler object. This object will not be
/// notified anymore about the events this manager observes.
void unregisterEventHandler(EventHandler & event_handler) {
auto it = this->searchEventHandler(event_handler);
if (it == this->event_handlers.end()) {
AKANTU_EXCEPTION("This event handler is not registered");
}
this->event_handlers.erase(it);
}
/// Notify all the registered EventHandlers about the event that just occured.
template <class Event> void sendEvent(const Event & event) {
- for (auto & pair : this->event_handlers)
+ for (auto & pair : this->event_handlers) {
pair.second->sendEvent(event);
+ }
}
private:
typename priority_list::iterator searchEventHandler(EventHandler & handler) {
auto it = this->event_handlers.begin();
auto end = this->event_handlers.end();
- for (; it != end && it->second != &handler; ++it)
+ for (; it != end && it->second != &handler; ++it) {
;
+ }
return it;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// list of the event handlers
priority_list event_handlers;
};
} // namespace akantu
-#endif /* __AKANTU_AKA_EVENT_HANDLER_MANAGER_HH__ */
+#endif /* AKANTU_AKA_EVENT_HANDLER_MANAGER_HH_ */
diff --git a/src/common/aka_extern.cc b/src/common/aka_extern.cc
index 3f38bec5c..6f35a56f9 100644
--- a/src/common/aka_extern.cc
+++ b/src/common/aka_extern.cc
@@ -1,103 +1,103 @@
/**
* @file aka_extern.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Tue Feb 20 2018
*
* @brief initialisation of all global variables
* to insure the order of creation
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_math.hh"
#include "aka_named_argument.hh"
#include "aka_random_generator.hh"
#include "communication_tag.hh"
#include "cppargparse.hh"
#include "parser.hh"
#include "solid_mechanics_model.hh"
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "solid_mechanics_model_cohesive.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
/* error.hpp variables */
/* -------------------------------------------------------------------------- */
namespace debug {
/** \todo write function to get this
* values from the environment or a config file
*/
/// standard output for debug messages
std::ostream * _akantu_debug_cout = &std::cerr;
/// standard output for normal messages
std::ostream & _akantu_cout = std::cout;
/// parallel context used in debug messages
- std::string _parallel_context = "";
+ std::string _parallel_context;
Debugger debugger;
#if defined(AKANTU_DEBUG_TOOLS)
DebugElementManager element_manager;
#endif
} // namespace debug
/* -------------------------------------------------------------------------- */
/// Paser for commandline arguments
::cppargparse::ArgumentParser static_argparser;
/// Parser containing the information parsed by the input file given to initFull
Parser static_parser;
bool Parser::permissive_parser = false;
/* -------------------------------------------------------------------------- */
Real Math::tolerance = 1e2 * std::numeric_limits<Real>::epsilon();
/* -------------------------------------------------------------------------- */
const UInt _all_dimensions [[gnu::unused]] = UInt(-1);
/* -------------------------------------------------------------------------- */
const Array<UInt> empty_filter(0, 1, "empty_filter");
/* -------------------------------------------------------------------------- */
-template <> long int RandomGenerator<UInt>::_seed = 5489u;
-template <> std::default_random_engine RandomGenerator<UInt>::generator(5489u);
+template <> long int RandomGenerator<UInt>::_seed = 5489U;
+template <> std::default_random_engine RandomGenerator<UInt>::generator(5489U);
/* -------------------------------------------------------------------------- */
int Tag::max_tag = 0;
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/common/aka_factory.hh b/src/common/aka_factory.hh
index 9034eb969..1e178991f 100644
--- a/src/common/aka_factory.hh
+++ b/src/common/aka_factory.hh
@@ -1,84 +1,86 @@
/**
* @file aka_factory.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Jul 09 2017
* @date last modification: Fri Dec 08 2017
*
* @brief This is a generic factory
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
#include <map>
#include <memory>
#include <string>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_FACTORY_HH__
-#define __AKANTU_AKA_FACTORY_HH__
+#ifndef AKANTU_AKA_FACTORY_HH_
+#define AKANTU_AKA_FACTORY_HH_
namespace akantu {
template <class Base, class T = ID, class... Args> class Factory {
using allocator_t = std::function<std::unique_ptr<Base>(Args...)>;
private:
Factory() = default;
public:
Factory(const Factory &) = delete;
Factory & operator=(const Factory &) = delete;
static Factory & getInstance() {
static Factory instance;
return instance;
}
/* ------------------------------------------------------------------------ */
bool registerAllocator(const T & id, const allocator_t & allocator) {
- if (allocators.find(id) != allocators.end())
+ if (allocators.find(id) != allocators.end()) {
AKANTU_EXCEPTION("The id "
<< " is already registered in the "
<< debug::demangle(typeid(Base).name()) << " factory");
+ }
allocators[id] = allocator;
return true;
}
template <typename... AArgs>
std::unique_ptr<Base> allocate(const T & id, AArgs &&... args) const {
- if (allocators.find(id) == allocators.end())
+ if (allocators.find(id) == allocators.end()) {
AKANTU_EXCEPTION("The id "
<< " is not registered in the "
<< debug::demangle(typeid(Base).name()) << " factory.");
+ }
return std::forward<std::unique_ptr<Base>>(
allocators.at(id)(std::forward<AArgs>(args)...));
}
private:
std::map<T, allocator_t> allocators;
};
} // namespace akantu
-#endif /* __AKANTU_AKA_FACTORY_HH__ */
+#endif /* AKANTU_AKA_FACTORY_HH_ */
diff --git a/src/common/aka_fwd.hh b/src/common/aka_fwd.hh
index bf96d9fc1..dbff6e8a1 100644
--- a/src/common/aka_fwd.hh
+++ b/src/common/aka_fwd.hh
@@ -1,70 +1,70 @@
/**
* @file aka_fwd.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Apr 13 2012
* @date last modification: Wed Oct 25 2017
*
* @brief File containing forward declarations in akantu.
* This file helps if circular #include would be needed because two classes
* refer both to each other. This file usually does not need any modification.
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_FWD_HH__
-#define __AKANTU_FWD_HH__
+#ifndef AKANTU_FWD_HH_
+#define AKANTU_FWD_HH_
namespace cppargparse {
class ArgumentParser;
}
namespace akantu {
// forward declaration
template <int dim, class model_type> struct ContactData;
template <typename T> class Matrix;
template <typename T> class Vector;
template <typename T> class Tensor3;
template <typename T, bool is_scal = aka::is_scalar<T>::value> class Array;
template <typename T, typename SupportType = ElementType>
class ElementTypeMapArray;
template <class T> class SpatialGrid;
// Model element
template <class ModelPolicy> class ModelElement;
extern const Array<UInt> empty_filter;
class Parser;
class ParserSection;
-extern Parser static_parser;
+extern Parser static_parser; // NOLINT
-extern cppargparse::ArgumentParser static_argparser;
+extern cppargparse::ArgumentParser static_argparser; // NOLINT
class Mesh;
class SparseMatrix;
} // namespace akantu
-#endif /* __AKANTU_FWD_HH__ */
+#endif /* AKANTU_FWD_HH_ */
diff --git a/src/common/aka_grid_dynamic.hh b/src/common/aka_grid_dynamic.hh
index 8d33798c7..1de09d280 100644
--- a/src/common/aka_grid_dynamic.hh
+++ b/src/common/aka_grid_dynamic.hh
@@ -1,512 +1,529 @@
/**
* @file aka_grid_dynamic.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Nov 08 2017
*
* @brief Grid that is auto balanced
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_types.hh"
#include "mesh_accessor.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_GRID_DYNAMIC_HH__
-#define __AKANTU_AKA_GRID_DYNAMIC_HH__
+#ifndef AKANTU_AKA_GRID_DYNAMIC_HH_
+#define AKANTU_AKA_GRID_DYNAMIC_HH_
namespace akantu {
class Mesh;
template <typename T> class SpatialGrid {
public:
explicit SpatialGrid(UInt dimension)
: dimension(dimension), spacing(dimension), center(dimension),
lower(dimension), upper(dimension), empty_cell() {}
SpatialGrid(UInt dimension, const Vector<Real> & spacing,
const Vector<Real> & center)
: dimension(dimension), spacing(spacing), center(center),
lower(dimension), upper(dimension), empty_cell() {
for (UInt i = 0; i < dimension; ++i) {
lower(i) = std::numeric_limits<Real>::max();
upper(i) = -std::numeric_limits<Real>::max();
}
}
virtual ~SpatialGrid() = default;
class neighbor_cells_iterator;
class cells_iterator;
class CellID {
public:
- CellID() : ids() {}
+ CellID() = default;
explicit CellID(UInt dimention) : ids(dimention) {}
void setID(UInt dir, Int id) { ids(dir) = id; }
Int getID(UInt dir) const { return ids(dir); }
bool operator<(const CellID & id) const {
return std::lexicographical_compare(
ids.storage(), ids.storage() + ids.size(), id.ids.storage(),
id.ids.storage() + id.ids.size());
}
bool operator==(const CellID & id) const {
return std::equal(ids.storage(), ids.storage() + ids.size(),
id.ids.storage());
}
bool operator!=(const CellID & id) const { return !(operator==(id)); }
class neighbor_cells_iterator
: private std::iterator<std::forward_iterator_tag, UInt> {
public:
neighbor_cells_iterator(const CellID & cell_id, bool end)
: cell_id(cell_id), position(cell_id.ids.size(), end ? 1 : -1) {
this->updateIt();
- if (end)
+ if (end) {
this->it++;
+ }
}
neighbor_cells_iterator & operator++() {
UInt i = 0;
- for (; i < position.size() && position(i) == 1; ++i)
+ for (; i < position.size() && position(i) == 1; ++i) {
;
+ }
if (i == position.size()) {
++it;
return *this;
}
- for (UInt j = 0; j < i; ++j)
+ for (UInt j = 0; j < i; ++j) {
position(j) = -1;
+ }
position(i)++;
updateIt();
return *this;
}
neighbor_cells_iterator operator++(int) {
neighbor_cells_iterator tmp(*this);
operator++();
return tmp;
};
bool operator==(const neighbor_cells_iterator & rhs) const {
return cell_id == rhs.cell_id && it == rhs.it;
};
bool operator!=(const neighbor_cells_iterator & rhs) const {
return !operator==(rhs);
};
CellID operator*() const {
CellID cur_cell_id(cell_id);
cur_cell_id.ids += position;
return cur_cell_id;
};
private:
void updateIt() {
it = 0;
- for (UInt i = 0; i < position.size(); ++i)
+ for (UInt i = 0; i < position.size(); ++i) {
it = it * 3 + (position(i) + 1);
+ }
}
private:
/// central cell id
const CellID & cell_id;
// number representing the current neighbor in base 3;
UInt it;
// current cell shift
Vector<Int> position;
};
class Neighbors {
public:
explicit Neighbors(const CellID & cell_id) : cell_id(cell_id) {}
decltype(auto) begin() { return neighbor_cells_iterator(cell_id, false); }
decltype(auto) end() { return neighbor_cells_iterator(cell_id, true); }
private:
const CellID & cell_id;
};
decltype(auto) neighbors() { return Neighbors(*this); }
private:
friend class cells_iterator;
Vector<Int> ids;
};
/* ------------------------------------------------------------------------ */
class Cell {
public:
using iterator = typename std::vector<T>::iterator;
using const_iterator = typename std::vector<T>::const_iterator;
Cell() : id(), data() {}
explicit Cell(const CellID & cell_id) : id(cell_id), data() {}
bool operator==(const Cell & cell) const { return id == cell.id; }
bool operator!=(const Cell & cell) const { return id != cell.id; }
Cell & add(const T & d) {
data.push_back(d);
return *this;
}
iterator begin() { return data.begin(); }
const_iterator begin() const { return data.begin(); }
iterator end() { return data.end(); }
const_iterator end() const { return data.end(); }
private:
CellID id;
std::vector<T> data;
};
private:
using cells_container = std::map<CellID, Cell>;
public:
const Cell & getCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
- if (it != cells.end())
+ if (it != cells.end()) {
return it->second;
+ }
return empty_cell;
}
decltype(auto) beginCell(const CellID & cell_id) {
auto it = cells.find(cell_id);
- if (it != cells.end())
+ if (it != cells.end()) {
return it->second.begin();
+ }
return empty_cell.begin();
}
decltype(auto) endCell(const CellID & cell_id) {
auto it = cells.find(cell_id);
- if (it != cells.end())
+ if (it != cells.end()) {
return it->second.end();
+ }
return empty_cell.end();
}
decltype(auto) beginCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
- if (it != cells.end())
+ if (it != cells.end()) {
return it->second.begin();
+ }
return empty_cell.begin();
}
decltype(auto) endCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
- if (it != cells.end())
+ if (it != cells.end()) {
return it->second.end();
+ }
return empty_cell.end();
}
/* ------------------------------------------------------------------------ */
class cells_iterator
: private std::iterator<std::forward_iterator_tag, CellID> {
public:
explicit cells_iterator(typename std::map<CellID, Cell>::const_iterator it)
: it(it) {}
cells_iterator & operator++() {
this->it++;
return *this;
}
cells_iterator operator++(int) {
cells_iterator tmp(*this);
operator++();
return tmp;
};
bool operator==(const cells_iterator & rhs) const { return it == rhs.it; };
bool operator!=(const cells_iterator & rhs) const {
return !operator==(rhs);
};
CellID operator*() const {
CellID cur_cell_id(this->it->first);
return cur_cell_id;
};
private:
/// map iterator
typename std::map<CellID, Cell>::const_iterator it;
};
public:
template <class vector_type>
Cell & insert(const T & d, const vector_type & position) {
auto && cell_id = getCellID(position);
auto && it = cells.find(cell_id);
if (it == cells.end()) {
Cell cell(cell_id);
auto & tmp = (cells[cell_id] = cell).add(d);
for (UInt i = 0; i < dimension; ++i) {
Real posl = center(i) + cell_id.getID(i) * spacing(i);
Real posu = posl + spacing(i);
- if (posl < lower(i))
+ if (posl < lower(i)) {
lower(i) = posl;
- if (posu > upper(i))
+ }
+ if (posu > upper(i)) {
upper(i) = posu;
+ }
}
return tmp;
- } else {
- return it->second.add(d);
}
+ return it->second.add(d);
}
/* ------------------------------------------------------------------------ */
inline decltype(auto) begin() const {
auto begin = this->cells.begin();
return cells_iterator(begin);
}
inline decltype(auto) end() const {
auto end = this->cells.end();
return cells_iterator(end);
}
template <class vector_type>
CellID getCellID(const vector_type & position) const {
CellID cell_id(dimension);
for (UInt i = 0; i < dimension; ++i) {
cell_id.setID(i, getCellID(position(i), i));
}
return cell_id;
}
void printself(std::ostream & stream, int indent = 0) const {
std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
+ for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
+ }
std::streamsize prec = stream.precision();
std::ios_base::fmtflags ff = stream.flags();
stream.setf(std::ios_base::showbase);
stream.precision(5);
stream << space << "SpatialGrid<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
stream << space << " + dimension : " << this->dimension << std::endl;
stream << space << " + lower bounds : {";
for (UInt i = 0; i < lower.size(); ++i) {
- if (i != 0)
+ if (i != 0) {
stream << ", ";
+ }
stream << lower(i);
};
stream << "}" << std::endl;
stream << space << " + upper bounds : {";
for (UInt i = 0; i < upper.size(); ++i) {
- if (i != 0)
+ if (i != 0) {
stream << ", ";
+ }
stream << upper(i);
};
stream << "}" << std::endl;
stream << space << " + spacing : {";
for (UInt i = 0; i < spacing.size(); ++i) {
- if (i != 0)
+ if (i != 0) {
stream << ", ";
+ }
stream << spacing(i);
};
stream << "}" << std::endl;
stream << space << " + center : {";
for (UInt i = 0; i < center.size(); ++i) {
- if (i != 0)
+ if (i != 0) {
stream << ", ";
+ }
stream << center(i);
};
stream << "}" << std::endl;
stream << space << " + nb_cells : " << this->cells.size() << "/";
Vector<Real> dist(this->dimension);
dist = upper;
dist -= lower;
for (UInt i = 0; i < this->dimension; ++i) {
dist(i) /= spacing(i);
}
UInt nb_cells = std::ceil(dist(0));
for (UInt i = 1; i < this->dimension; ++i) {
nb_cells *= std::ceil(dist(i));
}
stream << nb_cells << std::endl;
stream << space << "]" << std::endl;
stream.precision(prec);
stream.flags(ff);
}
void saveAsMesh(Mesh & mesh) const;
private:
/* --------------------------------------------------------------------------
*/
inline UInt getCellID(Real position, UInt direction) const {
AKANTU_DEBUG_ASSERT(direction < center.size(), "The direction asked ("
<< direction
<< ") is out of range "
<< center.size());
Real dist_center = position - center(direction);
Int id = std::floor(dist_center / spacing(direction));
// if(dist_center < 0) id--;
return id;
}
friend class GridSynchronizer;
public:
AKANTU_GET_MACRO(LowerBounds, lower, const Vector<Real> &);
AKANTU_GET_MACRO(UpperBounds, upper, const Vector<Real> &);
AKANTU_GET_MACRO(Spacing, spacing, const Vector<Real> &);
protected:
UInt dimension;
cells_container cells;
Vector<Real> spacing;
Vector<Real> center;
Vector<Real> lower;
Vector<Real> upper;
Cell empty_cell;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const SpatialGrid<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "mesh.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> void SpatialGrid<T>::saveAsMesh(Mesh & mesh) const {
-
+
ElementType type = _not_defined;
switch (dimension) {
case 1:
type = _segment_2;
break;
case 2:
type = _quadrangle_4;
break;
case 3:
type = _hexahedron_8;
break;
}
MeshAccessor mesh_accessor(mesh);
auto & connectivity = mesh_accessor.getConnectivity(type);
auto & nodes = mesh_accessor.getNodes();
auto & uint_data = mesh.getDataPointer<UInt>("tag_1", type);
Vector<Real> pos(dimension);
UInt global_id = 0;
for (auto & cell_pair : cells) {
UInt cur_node = nodes.size();
UInt cur_elem = connectivity.size();
const CellID & cell_id = cell_pair.first;
- for (UInt i = 0; i < dimension; ++i)
+ for (UInt i = 0; i < dimension; ++i) {
pos(i) = center(i) + cell_id.getID(i) * spacing(i);
+ }
nodes.push_back(pos);
- for (UInt i = 0; i < dimension; ++i)
+ for (UInt i = 0; i < dimension; ++i) {
pos(i) += spacing(i);
+ }
nodes.push_back(pos);
connectivity.push_back(cur_node);
switch (dimension) {
case 1:
connectivity(cur_elem, 1) = cur_node + 1;
break;
case 2:
pos(0) -= spacing(0);
nodes.push_back(pos);
pos(0) += spacing(0);
pos(1) -= spacing(1);
nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 3;
connectivity(cur_elem, 2) = cur_node + 1;
connectivity(cur_elem, 3) = cur_node + 2;
break;
case 3:
pos(1) -= spacing(1);
pos(2) -= spacing(2);
nodes.push_back(pos);
pos(1) += spacing(1);
nodes.push_back(pos);
pos(0) -= spacing(0);
nodes.push_back(pos);
pos(1) -= spacing(1);
pos(2) += spacing(2);
nodes.push_back(pos);
pos(0) += spacing(0);
nodes.push_back(pos);
pos(0) -= spacing(0);
pos(1) += spacing(1);
nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 2;
connectivity(cur_elem, 2) = cur_node + 3;
connectivity(cur_elem, 3) = cur_node + 4;
connectivity(cur_elem, 4) = cur_node + 5;
connectivity(cur_elem, 5) = cur_node + 6;
connectivity(cur_elem, 6) = cur_node + 1;
connectivity(cur_elem, 7) = cur_node + 7;
break;
}
uint_data.push_back(global_id);
++global_id;
}
}
} // namespace akantu
-#endif /* __AKANTU_AKA_GRID_DYNAMIC_HH__ */
+#endif /* AKANTU_AKA_GRID_DYNAMIC_HH_ */
diff --git a/src/common/aka_math.cc b/src/common/aka_math.cc
index bb86ba2c9..58f554e73 100644
--- a/src/common/aka_math.cc
+++ b/src/common/aka_math.cc
@@ -1,252 +1,269 @@
/**
* @file aka_math.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Sun Aug 13 2017
*
* @brief Implementation of the math toolbox
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_math.hh"
#include "aka_array.hh"
-
+#include "aka_iterators.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
+namespace Math {
+ /* --------------------------------------------------------------------------
+ */
+ void matrix_vector(UInt m, UInt n, const Array<Real> & A,
+ const Array<Real> & x, Array<Real> & y, Real alpha) {
+ AKANTU_DEBUG_IN();
+
+ AKANTU_DEBUG_ASSERT(A.size() == x.size(),
+ "The vector A(" << A.getID() << ") and the vector x("
+ << x.getID()
+ << ") must have the same size");
+
+ AKANTU_DEBUG_ASSERT(
+ A.getNbComponent() == m * n,
+ "The vector A(" << A.getID() << ") has the good number of component.");
+
+ AKANTU_DEBUG_ASSERT(x.getNbComponent() == n,
+ "The vector x("
+ << x.getID()
+ << ") do not the good number of component.");
+
+ AKANTU_DEBUG_ASSERT(y.getNbComponent() == n,
+ "The vector y("
+ << y.getID()
+ << ") do not the good number of component.");
+
+ UInt nb_element = A.size();
+ UInt offset_A = A.getNbComponent();
+ UInt offset_x = x.getNbComponent();
+
+ y.resize(nb_element);
+
+ Real * A_val = A.storage();
+ Real * x_val = x.storage();
+ Real * y_val = y.storage();
+
+ for (UInt el = 0; el < nb_element; ++el) {
+ matrix_vector(m, n, A_val, x_val, y_val, alpha);
+
+ A_val += offset_A;
+ x_val += offset_x;
+ y_val += offset_x;
+ }
-/* -------------------------------------------------------------------------- */
-void Math::matrix_vector(UInt m, UInt n, const Array<Real> & A,
- const Array<Real> & x, Array<Real> & y, Real alpha) {
- AKANTU_DEBUG_IN();
-
- AKANTU_DEBUG_ASSERT(A.size() == x.size(),
- "The vector A(" << A.getID() << ") and the vector x("
- << x.getID()
- << ") must have the same size");
-
- AKANTU_DEBUG_ASSERT(A.getNbComponent() == m * n,
- "The vector A(" << A.getID()
- << ") has the good number of component.");
-
- AKANTU_DEBUG_ASSERT(
- x.getNbComponent() == n,
- "The vector x(" << x.getID() << ") do not the good number of component.");
-
- AKANTU_DEBUG_ASSERT(
- y.getNbComponent() == n,
- "The vector y(" << y.getID() << ") do not the good number of component.");
-
- UInt nb_element = A.size();
- UInt offset_A = A.getNbComponent();
- UInt offset_x = x.getNbComponent();
-
- y.resize(nb_element);
-
- Real * A_val = A.storage();
- Real * x_val = x.storage();
- Real * y_val = y.storage();
-
- for (UInt el = 0; el < nb_element; ++el) {
- matrix_vector(m, n, A_val, x_val, y_val, alpha);
-
- A_val += offset_A;
- x_val += offset_x;
- y_val += offset_x;
+ AKANTU_DEBUG_OUT();
}
- AKANTU_DEBUG_OUT();
-}
+ /* --------------------------------------------------------------------------
+ */
+ void matrix_matrix(UInt m, UInt n, UInt k, const Array<Real> & A,
+ const Array<Real> & B, Array<Real> & C, Real alpha) {
+ AKANTU_DEBUG_IN();
-/* -------------------------------------------------------------------------- */
-void Math::matrix_matrix(UInt m, UInt n, UInt k, const Array<Real> & A,
- const Array<Real> & B, Array<Real> & C, Real alpha) {
- AKANTU_DEBUG_IN();
+ AKANTU_DEBUG_ASSERT(A.size() == B.size(),
+ "The vector A(" << A.getID() << ") and the vector B("
+ << B.getID()
+ << ") must have the same size");
- AKANTU_DEBUG_ASSERT(A.size() == B.size(),
- "The vector A(" << A.getID() << ") and the vector B("
- << B.getID()
- << ") must have the same size");
+ AKANTU_DEBUG_ASSERT(
+ A.getNbComponent() == m * k,
+ "The vector A(" << A.getID() << ") has the good number of component.");
- AKANTU_DEBUG_ASSERT(A.getNbComponent() == m * k,
- "The vector A(" << A.getID()
- << ") has the good number of component.");
+ AKANTU_DEBUG_ASSERT(B.getNbComponent() == k * n,
+ "The vector B("
+ << B.getID()
+ << ") do not the good number of component.");
- AKANTU_DEBUG_ASSERT(
- B.getNbComponent() == k * n,
- "The vector B(" << B.getID() << ") do not the good number of component.");
+ AKANTU_DEBUG_ASSERT(C.getNbComponent() == m * n,
+ "The vector C("
+ << C.getID()
+ << ") do not the good number of component.");
- AKANTU_DEBUG_ASSERT(
- C.getNbComponent() == m * n,
- "The vector C(" << C.getID() << ") do not the good number of component.");
+ UInt nb_element = A.size();
+ UInt offset_A = A.getNbComponent();
+ UInt offset_B = B.getNbComponent();
+ UInt offset_C = C.getNbComponent();
- UInt nb_element = A.size();
- UInt offset_A = A.getNbComponent();
- UInt offset_B = B.getNbComponent();
- UInt offset_C = C.getNbComponent();
+ C.resize(nb_element);
- C.resize(nb_element);
+ Real * A_val = A.storage();
+ Real * B_val = B.storage();
+ Real * C_val = C.storage();
- Real * A_val = A.storage();
- Real * B_val = B.storage();
- Real * C_val = C.storage();
+ for (UInt el = 0; el < nb_element; ++el) {
+ matrix_matrix(m, n, k, A_val, B_val, C_val, alpha);
- for (UInt el = 0; el < nb_element; ++el) {
- matrix_matrix(m, n, k, A_val, B_val, C_val, alpha);
+ A_val += offset_A;
+ B_val += offset_B;
+ C_val += offset_C;
+ }
- A_val += offset_A;
- B_val += offset_B;
- C_val += offset_C;
+ AKANTU_DEBUG_OUT();
}
- AKANTU_DEBUG_OUT();
-}
+ /* --------------------------------------------------------------------------
+ */
+ void matrix_matrixt(UInt m, UInt n, UInt k, const Array<Real> & A,
+ const Array<Real> & B, Array<Real> & C, Real alpha) {
+ AKANTU_DEBUG_IN();
-/* -------------------------------------------------------------------------- */
-void Math::matrix_matrixt(UInt m, UInt n, UInt k, const Array<Real> & A,
- const Array<Real> & B, Array<Real> & C, Real alpha) {
- AKANTU_DEBUG_IN();
+ AKANTU_DEBUG_ASSERT(A.size() == B.size(),
+ "The vector A(" << A.getID() << ") and the vector B("
+ << B.getID()
+ << ") must have the same size");
- AKANTU_DEBUG_ASSERT(A.size() == B.size(),
- "The vector A(" << A.getID() << ") and the vector B("
- << B.getID()
- << ") must have the same size");
+ AKANTU_DEBUG_ASSERT(
+ A.getNbComponent() == m * k,
+ "The vector A(" << A.getID() << ") has the good number of component.");
- AKANTU_DEBUG_ASSERT(A.getNbComponent() == m * k,
- "The vector A(" << A.getID()
- << ") has the good number of component.");
+ AKANTU_DEBUG_ASSERT(B.getNbComponent() == k * n,
+ "The vector B("
+ << B.getID()
+ << ") do not the good number of component.");
- AKANTU_DEBUG_ASSERT(
- B.getNbComponent() == k * n,
- "The vector B(" << B.getID() << ") do not the good number of component.");
+ AKANTU_DEBUG_ASSERT(C.getNbComponent() == m * n,
+ "The vector C("
+ << C.getID()
+ << ") do not the good number of component.");
- AKANTU_DEBUG_ASSERT(
- C.getNbComponent() == m * n,
- "The vector C(" << C.getID() << ") do not the good number of component.");
+ UInt nb_element = A.size();
+ UInt offset_A = A.getNbComponent();
+ UInt offset_B = B.getNbComponent();
+ UInt offset_C = C.getNbComponent();
- UInt nb_element = A.size();
- UInt offset_A = A.getNbComponent();
- UInt offset_B = B.getNbComponent();
- UInt offset_C = C.getNbComponent();
+ C.resize(nb_element);
- C.resize(nb_element);
+ Real * A_val = A.storage();
+ Real * B_val = B.storage();
+ Real * C_val = C.storage();
- Real * A_val = A.storage();
- Real * B_val = B.storage();
- Real * C_val = C.storage();
+ for (UInt el = 0; el < nb_element; ++el) {
+ matrix_matrixt(m, n, k, A_val, B_val, C_val, alpha);
- for (UInt el = 0; el < nb_element; ++el) {
- matrix_matrixt(m, n, k, A_val, B_val, C_val, alpha);
+ A_val += offset_A;
+ B_val += offset_B;
+ C_val += offset_C;
+ }
- A_val += offset_A;
- B_val += offset_B;
- C_val += offset_C;
+ AKANTU_DEBUG_OUT();
}
- AKANTU_DEBUG_OUT();
-}
-
-/* -------------------------------------------------------------------------- */
-void Math::compute_tangents(const Array<Real> & normals,
- Array<Real> & tangents) {
- AKANTU_DEBUG_IN();
+ /* --------------------------------------------------------------------------
+ */
+ void compute_tangents(const Array<Real> & normals, Array<Real> & tangents) {
+ AKANTU_DEBUG_IN();
- UInt spatial_dimension = normals.getNbComponent();
- UInt tangent_components = spatial_dimension * (spatial_dimension - 1);
-
- if (tangent_components == 0)
- return;
+ if (normals.empty()) {
+ return;
+ }
- AKANTU_DEBUG_ASSERT(
- tangent_components == tangents.getNbComponent(),
- "Cannot compute the tangents, the storage array for tangents"
- << " does not have the good amount of components.");
+ auto spatial_dimension = normals.getNbComponent();
+ auto tangent_components = spatial_dimension * (spatial_dimension - 1);
- UInt nb_normals = normals.size();
- tangents.resize(nb_normals, 0.);
+ if (tangent_components == 0) {
+ return;
+ }
- Real * normal_it = normals.storage();
- Real * tangent_it = tangents.storage();
+ AKANTU_DEBUG_ASSERT(
+ tangent_components == tangents.getNbComponent(),
+ "Cannot compute the tangents, the storage array for tangents"
+ << " does not have the good amount of components.");
+
+ auto nb_normals = normals.size();
+ tangents.resize(nb_normals);
+ tangents.zero();
+
+ /// compute first tangent
+ for (auto && data : zip(make_view(normals, spatial_dimension),
+ make_view(tangents, tangent_components))) {
+ const auto & normal = std::get<0>(data);
+ auto & tangent = std::get<1>(data);
+
+ if (are_float_equal(norm2(normal.storage()), 0.)) {
+ tangent(0) = 1.;
+ } else {
+ normal2(normal.storage(), tangent.storage());
+ }
+ }
- /// compute first tangent
- for (UInt q = 0; q < nb_normals; ++q) {
- /// if normal is orthogonal to xy plane, arbitrarly define tangent
- if (Math::are_float_equal(Math::norm2(normal_it), 0))
- tangent_it[0] = 1;
- else
- Math::normal2(normal_it, tangent_it);
+ /// compute second tangent (3D case)
+ if (spatial_dimension == 3) {
+ for (auto && data : zip(make_view(normals, spatial_dimension),
+ make_view(tangents, tangent_components))) {
+ const auto & normal = std::get<0>(data);
+ auto & tangent = std::get<1>(data);
- normal_it += spatial_dimension;
- tangent_it += tangent_components;
- }
+ normal3(normal.storage(), tangent.storage(),
+ tangent.storage() + spatial_dimension);
+ }
+ }
- /// compute second tangent (3D case)
- if (spatial_dimension == 3) {
- normal_it = normals.storage();
- tangent_it = tangents.storage();
+ AKANTU_DEBUG_OUT();
+ } // namespace akantu
- for (UInt q = 0; q < nb_normals; ++q) {
- Math::normal3(normal_it, tangent_it, tangent_it + spatial_dimension);
- normal_it += spatial_dimension;
- tangent_it += tangent_components;
+ /* --------------------------------------------------------------------------
+ */
+ Real reduce(Array<Real> & array) {
+ UInt nb_values = array.size();
+ if (nb_values == 0) {
+ return 0.;
}
- }
- AKANTU_DEBUG_OUT();
-}
+ UInt nb_values_to_sum = nb_values >> 1;
-/* -------------------------------------------------------------------------- */
-Real Math::reduce(Array<Real> & array) {
- UInt nb_values = array.size();
- if (nb_values == 0)
- return 0.;
-
- UInt nb_values_to_sum = nb_values >> 1;
+ std::sort(array.begin(), array.end());
- std::sort(array.begin(), array.end());
+ // as long as the half is not empty
+ while (nb_values_to_sum != 0U) {
+ UInt remaining = (nb_values - 2 * nb_values_to_sum);
+ if (remaining != 0U) {
+ array(nb_values - 2) += array(nb_values - 1);
+ }
- // as long as the half is not empty
- while (nb_values_to_sum) {
- UInt remaining = (nb_values - 2 * nb_values_to_sum);
- if (remaining)
- array(nb_values - 2) += array(nb_values - 1);
+ // sum to consecutive values and store the sum in the first half
+ for (UInt i = 0; i < nb_values_to_sum; ++i) {
+ array(i) = array(2 * i) + array(2 * i + 1);
+ }
- // sum to consecutive values and store the sum in the first half
- for (UInt i = 0; i < nb_values_to_sum; ++i) {
- array(i) = array(2 * i) + array(2 * i + 1);
+ nb_values = nb_values_to_sum;
+ nb_values_to_sum >>= 1;
}
- nb_values = nb_values_to_sum;
- nb_values_to_sum >>= 1;
+ return array(0);
}
- return array(0);
-}
-
+} // namespace Math
} // namespace akantu
diff --git a/src/common/aka_math.hh b/src/common/aka_math.hh
index 19430897b..f288c9657 100644
--- a/src/common/aka_math.hh
+++ b/src/common/aka_math.hh
@@ -1,286 +1,283 @@
/**
* @file aka_math.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Mon Sep 11 2017
*
* @brief mathematical operations
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <utility>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_MATH_H__
-#define __AKANTU_AKA_MATH_H__
+#ifndef AKANTU_AKA_MATH_H_
+#define AKANTU_AKA_MATH_H_
namespace akantu {
/* -------------------------------------------------------------------------- */
+namespace Math {
+ /// tolerance for functions that need one
+ extern Real tolerance; // NOLINT
-class Math {
- /* ------------------------------------------------------------------------ */
- /* Methods */
- /* ------------------------------------------------------------------------ */
-public:
/* ------------------------------------------------------------------------ */
/* Matrix algebra */
/* ------------------------------------------------------------------------ */
/// @f$ y = A*x @f$
- static void matrix_vector(UInt m, UInt n, const Array<Real> & A,
- const Array<Real> & x, Array<Real> & y,
- Real alpha = 1.);
+ void matrix_vector(UInt m, UInt n, const Array<Real> & A,
+ const Array<Real> & x, Array<Real> & y, Real alpha = 1.);
/// @f$ y = A*x @f$
- static inline void matrix_vector(UInt m, UInt n, Real * A, Real * x, Real * y,
- Real alpha = 1.);
+ inline void matrix_vector(UInt m, UInt n, Real * A, Real * x, Real * y,
+ Real alpha = 1.);
/// @f$ y = A^t*x @f$
- static inline void matrixt_vector(UInt m, UInt n, Real * A, Real * x,
- Real * y, Real alpha = 1.);
+ inline void matrixt_vector(UInt m, UInt n, Real * A, Real * x, Real * y,
+ Real alpha = 1.);
/// @f$ C = A*B @f$
- static void matrix_matrix(UInt m, UInt n, UInt k, const Array<Real> & A,
- const Array<Real> & B, Array<Real> & C,
- Real alpha = 1.);
+ void matrix_matrix(UInt m, UInt n, UInt k, const Array<Real> & A,
+ const Array<Real> & B, Array<Real> & C, Real alpha = 1.);
/// @f$ C = A*B^t @f$
- static void matrix_matrixt(UInt m, UInt n, UInt k,
- const Array<Real> & A,
- const Array<Real> & B, Array<Real> & C,
- Real alpha = 1.);
+ void matrix_matrixt(UInt m, UInt n, UInt k, const Array<Real> & A,
+ const Array<Real> & B, Array<Real> & C, Real alpha = 1.);
/// @f$ C = A*B @f$
- static inline void matrix_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
- Real * C, Real alpha = 1.);
+ inline void matrix_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
+ Real * C, Real alpha = 1.);
/// @f$ C = A^t*B @f$
- static inline void matrixt_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
- Real * C, Real alpha = 1.);
+ inline void matrixt_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
+ Real * C, Real alpha = 1.);
/// @f$ C = A*B^t @f$
- static inline void matrix_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
- Real * C, Real alpha = 1.);
+ inline void matrix_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
+ Real * C, Real alpha = 1.);
/// @f$ C = A^t*B^t @f$
- static inline void matrixt_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
- Real * C, Real alpha = 1.);
+ inline void matrixt_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
+ Real * C, Real alpha = 1.);
template <bool tr_A, bool tr_B>
- static inline void matMul(UInt m, UInt n, UInt k, Real alpha, Real * A,
- Real * B, Real beta, Real * C);
+ inline void matMul(UInt m, UInt n, UInt k, Real alpha, Real * A, Real * B,
+ Real beta, Real * C);
template <bool tr_A>
- static inline void matVectMul(UInt m, UInt n, Real alpha, Real * A, Real * x,
- Real beta, Real * y);
+ inline void matVectMul(UInt m, UInt n, Real alpha, Real * A, Real * x,
+ Real beta, Real * y);
- static inline void aXplusY(UInt n, Real alpha, Real * x, Real * y);
+ inline void aXplusY(UInt n, Real alpha, Real * x, Real * y);
- static inline void matrix33_eigenvalues(Real * A, Real * Adiag);
+ inline void matrix33_eigenvalues(Real * A, Real * Adiag);
- static inline void matrix22_eigenvalues(Real * A, Real * Adiag);
- template <UInt dim> static inline void eigenvalues(Real * A, Real * d);
+ inline void matrix22_eigenvalues(Real * A, Real * Adiag);
+ template <UInt dim> inline void eigenvalues(Real * A, Real * d);
/// solve @f$ A x = \Lambda x @f$ and return d and V such as @f$ A V[i:] =
/// d[i] V[i:]@f$
- template <typename T>
- static void matrixEig(UInt n, T * A, T * d, T * V = nullptr);
+ template <typename T> void matrixEig(UInt n, T * A, T * d, T * V = nullptr);
/// determinent of a 2x2 matrix
- static inline Real det2(const Real * mat);
+ Real det2(const Real * mat);
/// determinent of a 3x3 matrix
- static inline Real det3(const Real * mat);
+ Real det3(const Real * mat);
/// determinent of a nxn matrix
- template <UInt n> static inline Real det(const Real * mat);
+ template <UInt n> Real det(const Real * mat);
/// determinent of a nxn matrix
- template <typename T> static inline T det(UInt n, const T * mat);
+ template <typename T> T det(UInt n, const T * A);
/// inverse a nxn matrix
- template <UInt n> static inline void inv(const Real * mat, Real * inv);
+ template <UInt n> inline void inv(const Real * A, Real * inv);
/// inverse a nxn matrix
- template <typename T> static inline void inv(UInt n, const T * mat, T * inv);
+ template <typename T> inline void inv(UInt n, const T * A, T * inv);
/// inverse a 3x3 matrix
- static inline void inv3(const Real * mat, Real * inv);
+ inline void inv3(const Real * mat, Real * inv);
/// inverse a 2x2 matrix
- static inline void inv2(const Real * mat, Real * inv);
+ inline void inv2(const Real * mat, Real * inv);
/// solve A x = b using a LU factorization
template <typename T>
- static inline void solve(UInt n, const T * A, T * x, const T * b);
+ inline void solve(UInt n, const T * A, T * x, const T * b);
/// return the double dot product between 2 tensors in 2d
- static inline Real matrixDoubleDot22(Real * A, Real * B);
+ inline Real matrixDoubleDot22(Real * A, Real * B);
/// return the double dot product between 2 tensors in 3d
- static inline Real matrixDoubleDot33(Real * A, Real * B);
+ inline Real matrixDoubleDot33(Real * A, Real * B);
/// extension of the double dot product to two 2nd order tensor in dimension n
- static inline Real matrixDoubleDot(UInt n, Real * A, Real * B);
+ inline Real matrixDoubleDot(UInt n, Real * A, Real * B);
/* ------------------------------------------------------------------------ */
/* Array algebra */
/* ------------------------------------------------------------------------ */
/// vector cross product
- static inline void vectorProduct3(const Real * v1, const Real * v2,
- Real * res);
+ inline void vectorProduct3(const Real * v1, const Real * v2, Real * res);
/// normalize a vector
- static inline void normalize2(Real * v);
+ inline void normalize2(Real * v);
/// normalize a vector
- static inline void normalize3(Real * v);
+ inline void normalize3(Real * v);
/// return norm of a 2-vector
- static inline Real norm2(const Real * v);
+ inline Real norm2(const Real * v);
/// return norm of a 3-vector
- static inline Real norm3(const Real * v);
+ inline Real norm3(const Real * v);
/// return norm of a vector
- static inline Real norm(UInt n, const Real * v);
+ inline Real norm(UInt n, const Real * v);
/// return the dot product between 2 vectors in 2d
- static inline Real vectorDot2(const Real * v1, const Real * v2);
+ inline Real vectorDot2(const Real * v1, const Real * v2);
/// return the dot product between 2 vectors in 3d
- static inline Real vectorDot3(const Real * v1, const Real * v2);
+ inline Real vectorDot3(const Real * v1, const Real * v2);
/// return the dot product between 2 vectors
- static inline Real vectorDot(Real * v1, Real * v2, UInt n);
+ inline Real vectorDot(Real * v1, Real * v2, UInt n);
/* ------------------------------------------------------------------------ */
/* Geometry */
/* ------------------------------------------------------------------------ */
/// compute normal a normal to a vector
- static inline void normal2(const Real * v1, Real * res);
+ inline void normal2(const Real * vec, Real * normal);
/// compute normal a normal to a vector
- static inline void normal3(const Real * v1, const Real * v2, Real * res);
+ inline void normal3(const Real * vec1, const Real * vec2, Real * normal);
/// compute the tangents to an array of normal vectors
- static void compute_tangents(const Array<Real> & normals,
- Array<Real> & tangents);
+ void compute_tangents(const Array<Real> & normals, Array<Real> & tangents);
/// distance in 2D between x and y
- static inline Real distance_2d(const Real * x, const Real * y);
+ inline Real distance_2d(const Real * x, const Real * y);
/// distance in 3D between x and y
- static inline Real distance_3d(const Real * x, const Real * y);
+ inline Real distance_3d(const Real * x, const Real * y);
/// radius of the in-circle of a triangle
- static inline Real triangle_inradius(const Real * coord1, const Real * coord2,
- const Real * coord3);
+ inline Real triangle_inradius(const Real * coord1, const Real * coord2,
+ const Real * coord3);
/// radius of the in-circle of a tetrahedron
- static inline Real tetrahedron_inradius(const Real * coord1,
- const Real * coord2,
- const Real * coord3,
- const Real * coord4);
+ inline Real tetrahedron_inradius(const Real * coord1, const Real * coord2,
+ const Real * coord3, const Real * coord4);
/// volume of a tetrahedron
- static inline Real tetrahedron_volume(const Real * coord1,
- const Real * coord2,
- const Real * coord3,
- const Real * coord4);
+ inline Real tetrahedron_volume(const Real * coord1, const Real * coord2,
+ const Real * coord3, const Real * coord4);
/// compute the barycenter of n points
- static inline void barycenter(const Real * coord, UInt nb_points,
- UInt spatial_dimension, Real * barycenter);
+ inline void barycenter(const Real * coord, UInt nb_points,
+ UInt spatial_dimension, Real * barycenter);
/// vector between x and y
- static inline void vector_2d(const Real * x, const Real * y, Real * vec);
+ inline void vector_2d(const Real * x, const Real * y, Real * res);
/// vector pointing from x to y in 3 spatial dimension
- static inline void vector_3d(const Real * x, const Real * y, Real * vec);
+ inline void vector_3d(const Real * x, const Real * y, Real * res);
/// test if two scalar are equal within a given tolerance
- static inline bool are_float_equal(Real x, Real y);
+ inline bool are_float_equal(Real x, Real y);
/// test if two vectors are equal within a given tolerance
- static inline bool are_vector_equal(UInt n, Real * x, Real * y);
+ inline bool are_vector_equal(UInt n, Real * x, Real * y);
#ifdef isnan
#error \
"You probably included <math.h> which is incompatible with aka_math please use\
<cmath> or add a \"#undef isnan\" before akantu includes"
#endif
/// test if a real is a NaN
- static inline bool isnan(Real x);
+ inline bool isnan(Real x);
/// test if the line x and y intersects each other
- static inline bool intersects(Real x_min, Real x_max, Real y_min, Real y_max);
+ inline bool intersects(Real x_min, Real x_max, Real y_min, Real y_max);
/// test if a is in the range [x_min, x_max]
- static inline bool is_in_range(Real a, Real x_min, Real x_max);
+ inline bool is_in_range(Real a, Real x_min, Real x_max);
- static inline Real getTolerance() { return tolerance; };
- static inline void setTolerance(Real tol) { tolerance = tol; };
+ inline Real getTolerance() { return Math::tolerance; };
+ inline void setTolerance(Real tol) { Math::tolerance = tol; };
- template <UInt p, typename T> static inline T pow(T x);
+ template <UInt p, typename T> inline T pow(T x);
+
+ template <class T1, class T2,
+ std::enable_if_t<std::is_integral<T1>::value and
+ std::is_integral<T2>::value> * = nullptr>
+ inline Real kronecker(T1 i, T2 j) {
+ return static_cast<Real>(i == j);
+ }
/// reduce all the values of an array, the summation is done in place and the
/// array is modified
- static Real reduce(Array<Real> & array);
+ Real reduce(Array<Real> & array);
class NewtonRaphson {
public:
NewtonRaphson(Real tolerance, Real max_iteration)
: tolerance(tolerance), max_iteration(max_iteration) {}
template <class Functor> Real solve(const Functor & funct, Real x_0);
private:
Real tolerance;
Real max_iteration;
};
struct NewtonRaphsonFunctor {
explicit NewtonRaphsonFunctor(std::string name) : name(std::move(name)) {}
+
virtual ~NewtonRaphsonFunctor() = default;
+
+ NewtonRaphsonFunctor(const NewtonRaphsonFunctor & other) = default;
+ NewtonRaphsonFunctor(NewtonRaphsonFunctor && other) noexcept = default;
+ NewtonRaphsonFunctor &
+ operator=(const NewtonRaphsonFunctor & other) = default;
+ NewtonRaphsonFunctor &
+ operator=(NewtonRaphsonFunctor && other) noexcept = default;
+
virtual Real f(Real x) const = 0;
virtual Real f_prime(Real x) const = 0;
std::string name;
};
-
-private:
- /// tolerance for functions that need one
- static Real tolerance;
-};
-
+} // namespace Math
} // namespace akantu
-
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "aka_math_tmpl.hh"
-#endif /* __AKANTU_AKA_MATH_H__ */
+#endif /* AKANTU_AKA_MATH_H_ */
diff --git a/src/common/aka_math_tmpl.hh b/src/common/aka_math_tmpl.hh
index 5f9aa3765..fc01665c6 100644
--- a/src/common/aka_math_tmpl.hh
+++ b/src/common/aka_math_tmpl.hh
@@ -1,782 +1,834 @@
/**
* @file aka_math_tmpl.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Mathilde Radiguet <mathilde.radiguet@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the inline functions of the math toolkit
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_blas_lapack.hh"
#include "aka_math.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
-#include <cstring>
#include <typeinfo>
/* -------------------------------------------------------------------------- */
namespace akantu {
-/* -------------------------------------------------------------------------- */
-inline void Math::matrix_vector(UInt im, UInt in, Real * A, Real * x, Real * y,
- Real alpha) {
+namespace Math {
+ /* ------------------------------------------------------------------------ */
+ inline void matrix_vector(UInt im, UInt in,
+ Real * A, // NOLINT(readability-non-const-parameter)
+ Real * x, // NOLINT(readability-non-const-parameter)
+ Real * y, Real alpha) {
#ifdef AKANTU_USE_BLAS
- /// y = alpha*op(A)*x + beta*y
- char tran_A = 'N';
- int incx = 1;
- int incy = 1;
- double beta = 0.;
- int m = im;
- int n = in;
+ /// y = alpha*op(A)*x + beta*y
+ char tran_A = 'N';
+ int incx = 1;
+ int incy = 1;
+ double beta = 0.;
+ int m = im;
+ int n = in;
- aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
+ aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
#else
- memset(y, 0, im * sizeof(Real));
- for (UInt i = 0; i < im; ++i) {
- for (UInt j = 0; j < in; ++j) {
- y[i] += A[i + j * im] * x[j];
+ std::fill_n(y, im, 0.);
+ for (UInt i = 0; i < im; ++i) {
+ for (UInt j = 0; j < in; ++j) {
+ y[i] += A[i + j * im] * x[j];
+ }
+ y[i] *= alpha;
}
- y[i] *= alpha;
- }
#endif
-}
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::matrixt_vector(UInt im, UInt in, Real * A, Real * x, Real * y,
- Real alpha) {
+ /* ------------------------------------------------------------------------ */
+ inline void
+ matrixt_vector(UInt im, UInt in,
+ Real * A, // NOLINT(readability-non-const-parameter)
+ Real * x, // NOLINT(readability-non-const-parameter)
+ Real * y, Real alpha) {
#ifdef AKANTU_USE_BLAS
- /// y = alpha*op(A)*x + beta*y
- char tran_A = 'T';
- int incx = 1;
- int incy = 1;
- double beta = 0.;
- int m = im;
- int n = in;
-
- aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
+ /// y = alpha*op(A)*x + beta*y
+ char tran_A = 'T';
+ int incx = 1;
+ int incy = 1;
+ double beta = 0.;
+ int m = im;
+ int n = in;
+
+ aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
#else
- memset(y, 0, in * sizeof(Real));
- for (UInt i = 0; i < im; ++i) {
- for (UInt j = 0; j < in; ++j) {
- y[j] += A[j * im + i] * x[i];
+ std::fill_n(y, in, 0.);
+ for (UInt i = 0; i < im; ++i) {
+ for (UInt j = 0; j < in; ++j) {
+ y[j] += A[j * im + i] * x[i];
+ }
+ y[i] *= alpha;
}
- y[i] *= alpha;
- }
#endif
-}
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::matrix_matrix(UInt im, UInt in, UInt ik, Real * A, Real * B,
- Real * C, Real alpha) {
+ /* ------------------------------------------------------------------------ */
+ inline void matrix_matrix(UInt im, UInt in, UInt ik,
+ Real * A, // NOLINT(readability-non-const-parameter)
+ Real * B, // NOLINT(readability-non-const-parameter)
+ Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
- /// C := alpha*op(A)*op(B) + beta*C
- char trans_a = 'N';
- char trans_b = 'N';
- double beta = 0.;
- int m = im, n = in, k = ik;
-
- aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &k, &beta, C, &m);
+ /// C := alpha*op(A)*op(B) + beta*C
+ char trans_a = 'N';
+ char trans_b = 'N';
+ double beta = 0.;
+ int m = im, n = in, k = ik;
+
+ aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &k, &beta, C,
+ &m);
#else
- memset(C, 0, im * in * sizeof(Real));
- for (UInt j = 0; j < in; ++j) {
- UInt _jb = j * ik;
- UInt _jc = j * im;
- for (UInt i = 0; i < im; ++i) {
- for (UInt l = 0; l < ik; ++l) {
- UInt _la = l * im;
- C[i + _jc] += A[i + _la] * B[l + _jb];
+ std::fill_n(C, im * in, 0.);
+ for (UInt j = 0; j < in; ++j) {
+ UInt _jb = j * ik;
+ UInt _jc = j * im;
+ for (UInt i = 0; i < im; ++i) {
+ for (UInt l = 0; l < ik; ++l) {
+ UInt _la = l * im;
+ C[i + _jc] += A[i + _la] * B[l + _jb];
+ }
+ C[i + _jc] *= alpha;
}
- C[i + _jc] *= alpha;
}
- }
#endif
-}
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::matrixt_matrix(UInt im, UInt in, UInt ik, Real * A, Real * B,
- Real * C, Real alpha) {
+ /* ------------------------------------------------------------------------ */
+ inline void
+ matrixt_matrix(UInt im, UInt in, UInt ik,
+ Real * A, // NOLINT(readability-non-const-parameter)
+ Real * B, // NOLINT(readability-non-const-parameter)
+ Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
- /// C := alpha*op(A)*op(B) + beta*C
- char trans_a = 'T';
- char trans_b = 'N';
- double beta = 0.;
- int m = im, n = in, k = ik;
-
- aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &k, &beta, C, &m);
+ /// C := alpha*op(A)*op(B) + beta*C
+ char trans_a = 'T';
+ char trans_b = 'N';
+ double beta = 0.;
+ int m = im, n = in, k = ik;
+
+ aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &k, &beta, C,
+ &m);
#else
- memset(C, 0, im * in * sizeof(Real));
- for (UInt j = 0; j < in; ++j) {
- UInt _jc = j * im;
- UInt _jb = j * ik;
- for (UInt i = 0; i < im; ++i) {
- UInt _ia = i * ik;
- for (UInt l = 0; l < ik; ++l) {
- C[i + _jc] += A[l + _ia] * B[l + _jb];
+ std::fill_n(C, im * in, 0.);
+ for (UInt j = 0; j < in; ++j) {
+ UInt _jc = j * im;
+ UInt _jb = j * ik;
+ for (UInt i = 0; i < im; ++i) {
+ UInt _ia = i * ik;
+ for (UInt l = 0; l < ik; ++l) {
+ C[i + _jc] += A[l + _ia] * B[l + _jb];
+ }
+ C[i + _jc] *= alpha;
}
- C[i + _jc] *= alpha;
}
- }
#endif
-}
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::matrix_matrixt(UInt im, UInt in, UInt ik, Real * A, Real * B,
- Real * C, Real alpha) {
+ /* ------------------------------------------------------------------------ */
+ inline void
+ matrix_matrixt(UInt im, UInt in, UInt ik,
+ Real * A, // NOLINT(readability-non-const-parameter)
+ Real * B, // NOLINT(readability-non-const-parameter)
+ Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
- /// C := alpha*op(A)*op(B) + beta*C
- char trans_a = 'N';
- char trans_b = 'T';
- double beta = 0.;
- int m = im, n = in, k = ik;
-
- aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &n, &beta, C, &m);
+ /// C := alpha*op(A)*op(B) + beta*C
+ char trans_a = 'N';
+ char trans_b = 'T';
+ double beta = 0.;
+ int m = im, n = in, k = ik;
+
+ aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &n, &beta, C,
+ &m);
#else
- memset(C, 0, im * in * sizeof(Real));
- for (UInt j = 0; j < in; ++j) {
- UInt _jc = j * im;
- for (UInt i = 0; i < im; ++i) {
- for (UInt l = 0; l < ik; ++l) {
- UInt _la = l * im;
- UInt _lb = l * in;
- C[i + _jc] += A[i + _la] * B[j + _lb];
+ std::fill_n(C, im * in, 0.);
+ for (UInt j = 0; j < in; ++j) {
+ UInt _jc = j * im;
+ for (UInt i = 0; i < im; ++i) {
+ for (UInt l = 0; l < ik; ++l) {
+ UInt _la = l * im;
+ UInt _lb = l * in;
+ C[i + _jc] += A[i + _la] * B[j + _lb];
+ }
+ C[i + _jc] *= alpha;
}
- C[i + _jc] *= alpha;
}
- }
#endif
-}
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::matrixt_matrixt(UInt im, UInt in, UInt ik, Real * A, Real * B,
- Real * C, Real alpha) {
+ /* ------------------------------------------------------------------------ */
+ inline void
+ matrixt_matrixt(UInt im, UInt in, UInt ik,
+ Real * A, // NOLINT(readability-non-const-parameter)
+ Real * B, // NOLINT(readability-non-const-parameter)
+ Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
- /// C := alpha*op(A)*op(B) + beta*C
- char trans_a = 'T';
- char trans_b = 'T';
- double beta = 0.;
- int m = im, n = in, k = ik;
-
- aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &n, &beta, C, &m);
+ /// C := alpha*op(A)*op(B) + beta*C
+ char trans_a = 'T';
+ char trans_b = 'T';
+ double beta = 0.;
+ int m = im, n = in, k = ik;
+
+ aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &n, &beta, C,
+ &m);
#else
- memset(C, 0, im * in * sizeof(Real));
- for (UInt j = 0; j < in; ++j) {
- UInt _jc = j * im;
- for (UInt i = 0; i < im; ++i) {
- UInt _ia = i * ik;
- for (UInt l = 0; l < ik; ++l) {
- UInt _lb = l * in;
- C[i + _jc] += A[l + _ia] * B[j + _lb];
+ std::fill_n(C, im * in, 0.);
+ for (UInt j = 0; j < in; ++j) {
+ UInt _jc = j * im;
+ for (UInt i = 0; i < im; ++i) {
+ UInt _ia = i * ik;
+ for (UInt l = 0; l < ik; ++l) {
+ UInt _lb = l * in;
+ C[i + _jc] += A[l + _ia] * B[j + _lb];
+ }
+ C[i + _jc] *= alpha;
}
- C[i + _jc] *= alpha;
}
- }
#endif
-}
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::aXplusY(UInt n, Real alpha, Real * x, Real * y) {
+ /* ------------------------------------------------------------------------ */
+ inline void aXplusY(UInt n, Real alpha,
+ Real * x, // NOLINT(readability-non-const-parameter)
+ Real * y) {
#ifdef AKANTU_USE_BLAS
- /// y := alpha x + y
- int incx = 1, incy = 1;
- aka_axpy(&n, &alpha, x, &incx, y, &incy);
+ /// y := alpha x + y
+ int incx = 1, incy = 1;
+ aka_axpy(&n, &alpha, x, &incx, y, &incy);
#else
- for (UInt i = 0; i < n; ++i)
- *(y++) += alpha * *(x++);
+ for (UInt i = 0; i < n; ++i) {
+ *(y++) += alpha * *(x++);
+ }
#endif
-}
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::vectorDot(Real * v1, Real * v2, UInt in) {
+ /* ------------------------------------------------------------------------ */
+ inline Real vectorDot(Real * v1, // NOLINT(readability-non-const-parameter)
+ Real * v2, // NOLINT(readability-non-const-parameter)
+ UInt in) {
#ifdef AKANTU_USE_BLAS
- /// d := v1 . v2
- int incx = 1, incy = 1, n = in;
- Real d = aka_dot(&n, v1, &incx, v2, &incy);
+ /// d := v1 . v2
+ int incx = 1, incy = 1, n = in;
+ Real d = aka_dot(&n, v1, &incx, v2, &incy);
#else
- Real d = 0;
- for (UInt i = 0; i < in; ++i) {
- d += v1[i] * v2[i];
- }
+ Real d = 0;
+ for (UInt i = 0; i < in; ++i) {
+ d += v1[i] * v2[i];
+ }
#endif
- return d;
-}
+ return d;
+ }
-/* -------------------------------------------------------------------------- */
-template <bool tr_A, bool tr_B>
-inline void Math::matMul(UInt m, UInt n, UInt k, Real alpha, Real * A, Real * B,
- __attribute__((unused)) Real beta, Real * C) {
- if (tr_A) {
- if (tr_B)
- matrixt_matrixt(m, n, k, A, B, C, alpha);
- else
- matrixt_matrix(m, n, k, A, B, C, alpha);
- } else {
- if (tr_B)
- matrix_matrixt(m, n, k, A, B, C, alpha);
- else
- matrix_matrix(m, n, k, A, B, C, alpha);
- }
-}
+ /* ------------------------------------------------------------------------ */
+ template <bool tr_A, bool tr_B>
+ inline void matMul(UInt m, UInt n, UInt k, Real alpha,
+ Real * A, // NOLINT(readability-non-const-parameter)
+ Real * B, // NOLINT(readability-non-const-parameter)
+ Real /*beta*/, Real * C) {
+ if (tr_A) {
+ if (tr_B) {
+ matrixt_matrixt(m, n, k, A, B, C, alpha);
+ } else {
+ matrixt_matrix(m, n, k, A, B, C, alpha);
+ }
+ } else {
+ if (tr_B) {
+ matrix_matrixt(m, n, k, A, B, C, alpha);
+ } else {
+ matrix_matrix(m, n, k, A, B, C, alpha);
+ }
+ }
+ }
-/* -------------------------------------------------------------------------- */
-template <bool tr_A>
-inline void Math::matVectMul(UInt m, UInt n, Real alpha, Real * A, Real * x,
- __attribute__((unused)) Real beta, Real * y) {
- if (tr_A) {
- matrixt_vector(m, n, A, x, y, alpha);
- } else {
- matrix_vector(m, n, A, x, y, alpha);
+ /* ------------------------------------------------------------------------ */
+ template <bool tr_A>
+ inline void matVectMul(UInt m, UInt n, Real alpha,
+ Real * A, // NOLINT(readability-non-const-parameter)
+ Real * x, // NOLINT(readability-non-const-parameter)
+ Real /*beta*/, Real * y) {
+ if (tr_A) {
+ matrixt_vector(m, n, A, x, y, alpha);
+ } else {
+ matrix_vector(m, n, A, x, y, alpha);
+ }
}
-}
-/* -------------------------------------------------------------------------- */
-template <typename T> inline void Math::matrixEig(UInt n, T * A, T * d, T * V) {
+ /* ------------------------------------------------------------------------ */
+ template <typename T>
+ inline void matrixEig(UInt n,
+ T * A, // NOLINT(readability-non-const-parameter)
+ T * d, T * V) {
+
+ // Matrix A is row major, so the lapack function in fortran will
+ // process A^t. Asking for the left eigenvectors of A^t will give the
+ // transposed right eigenvectors of A so in the C++ code the right
+ // eigenvectors.
+ char jobvr{'N'};
+ if (V != nullptr) {
+ jobvr = 'V'; // compute left eigenvectors
+ }
- // Matrix A is row major, so the lapack function in fortran will process
- // A^t. Asking for the left eigenvectors of A^t will give the transposed right
- // eigenvectors of A so in the C++ code the right eigenvectors.
- char jobvr, jobvl;
- if (V != nullptr)
- jobvr = 'V'; // compute left eigenvectors
- else
- jobvr = 'N'; // compute left eigenvectors
+ char jobvl{'N'}; // compute right eigenvectors
- jobvl = 'N'; // compute right eigenvectors
+ auto * di = new T[n]; // imaginary part of the eigenvalues
- auto * di = new T[n]; // imaginary part of the eigenvalues
+ int info;
+ int N = n;
- int info;
- int N = n;
+ T wkopt;
+ int lwork = -1;
+ // query and allocate the optimal workspace
+ aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, nullptr, &N, V, &N, &wkopt,
+ &lwork, &info);
- T wkopt;
- int lwork = -1;
- // query and allocate the optimal workspace
- aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, nullptr, &N, V, &N, &wkopt,
- &lwork, &info);
+ lwork = int(wkopt);
+ auto * work = new T[lwork];
+ // solve the eigenproblem
+ aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, nullptr, &N, V, &N, work,
+ &lwork, &info);
- lwork = int(wkopt);
- auto * work = new T[lwork];
- // solve the eigenproblem
- aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, nullptr, &N, V, &N, work,
- &lwork, &info);
+ AKANTU_DEBUG_ASSERT(
+ info == 0,
+ "Problem computing eigenvalues/vectors. DGEEV exited with the value "
+ << info);
- AKANTU_DEBUG_ASSERT(
- info == 0,
- "Problem computing eigenvalues/vectors. DGEEV exited with the value "
- << info);
+ delete[] work;
+ delete[] di; // I hope for you that there was no complex eigenvalues !!!
+ }
- delete[] work;
- delete[] di; // I hope for you that there was no complex eigenvalues !!!
-}
+ /* ------------------------------------------------------------------------ */
+ inline void
+ matrix22_eigenvalues(Real * A, // NOLINT(readability-non-const-parameter)
+ Real * Adiag) {
+ /// d = determinant of Matrix A
+ Real d = det2(A);
+ /// b = trace of Matrix A
+ Real b = A[0] + A[3];
+
+ Real c = std::sqrt(b * b - 4 * d);
+ Adiag[0] = .5 * (b + c);
+ Adiag[1] = .5 * (b - c);
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::matrix22_eigenvalues(Real * A, Real * Adiag) {
- /// d = determinant of Matrix A
- Real d = det2(A);
- /// b = trace of Matrix A
- Real b = A[0] + A[3];
+ /* ------------------------------------------------------------------------ */
+ inline void
+ matrix33_eigenvalues(Real * A, // NOLINT(readability-non-const-parameter)
+ Real * Adiag) {
+ matrixEig(3, A, Adiag);
+ }
- Real c = sqrt(b * b - 4 * d);
- Adiag[0] = .5 * (b + c);
- Adiag[1] = .5 * (b - c);
-}
+ /* ------------------------------------------------------------------------ */
+ template <UInt dim>
+ inline void eigenvalues(Real * A, // NOLINT(readability-non-const-parameter)
+ Real * d) {
+ if (dim == 1) {
+ d[0] = A[0];
+ } else if (dim == 2) {
+ matrix22_eigenvalues(A, d);
+ }
+ // else if(dim == 3) { matrix33_eigenvalues(A, d); }
+ else {
+ matrixEig(dim, A, d);
+ }
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::matrix33_eigenvalues(Real * A, Real * Adiag) {
- matrixEig(3, A, Adiag);
-}
+ /* ------------------------------------------------------------------------ */
+ inline Real det2(const Real * mat) {
+ return mat[0] * mat[3] - mat[1] * mat[2];
+ }
-/* -------------------------------------------------------------------------- */
-template <UInt dim> inline void Math::eigenvalues(Real * A, Real * d) {
- if (dim == 1) {
- d[0] = A[0];
- } else if (dim == 2) {
- matrix22_eigenvalues(A, d);
+ /* ------------------------------------------------------------------------ */
+ inline Real det3(const Real * mat) {
+ return mat[0] * (mat[4] * mat[8] - mat[7] * mat[5]) -
+ mat[3] * (mat[1] * mat[8] - mat[7] * mat[2]) +
+ mat[6] * (mat[1] * mat[5] - mat[4] * mat[2]);
}
- // else if(dim == 3) { matrix33_eigenvalues(A, d); }
- else
- matrixEig(dim, A, d);
-}
-/* -------------------------------------------------------------------------- */
-inline Real Math::det2(const Real * mat) {
- return mat[0] * mat[3] - mat[1] * mat[2];
-}
+ /* ------------------------------------------------------------------------ */
+ template <UInt n> inline Real det(const Real * mat) {
+ if (n == 1) {
+ return *mat;
+ }
+ if (n == 2) {
+ return det2(mat);
+ }
+ if (n == 3) {
+ return det3(mat);
+ }
+ return det(n, mat);
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::det3(const Real * mat) {
- return mat[0] * (mat[4] * mat[8] - mat[7] * mat[5]) -
- mat[3] * (mat[1] * mat[8] - mat[7] * mat[2]) +
- mat[6] * (mat[1] * mat[5] - mat[4] * mat[2]);
-}
+ /* ------------------------------------------------------------------------ */
+ template <typename T> inline T det(UInt n, const T * A) {
+ int N = n;
+ int info;
+ auto * ipiv = new int[N + 1];
-/* -------------------------------------------------------------------------- */
-template <UInt n> inline Real Math::det(const Real * mat) {
- if (n == 1)
- return *mat;
- else if (n == 2)
- return det2(mat);
- else if (n == 3)
- return det3(mat);
- else
- return det(n, mat);
-}
+ auto * LU = new T[N * N];
+ std::copy(A, A + N * N, LU);
-/* -------------------------------------------------------------------------- */
-template <typename T> inline T Math::det(UInt n, const T * A) {
- int N = n;
- int info;
- auto * ipiv = new int[N + 1];
+ // LU factorization of A
+ aka_getrf(&N, &N, LU, &N, ipiv, &info);
+ if (info > 0) {
+ AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
+ << " )");
+ }
- auto * LU = new T[N * N];
- std::copy(A, A + N * N, LU);
+ // det(A) = det(L) * det(U) = 1 * det(U) = product_i U_{ii}
+ T det = 1.;
+ for (int i = 0; i < N; ++i) {
+ det *= (2 * (ipiv[i] == i) - 1) * LU[i * n + i];
+ }
- // LU factorization of A
- aka_getrf(&N, &N, LU, &N, ipiv, &info);
- if (info > 0) {
- AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
- << " )");
+ delete[] ipiv;
+ delete[] LU;
+ return det;
}
- // det(A) = det(L) * det(U) = 1 * det(U) = product_i U_{ii}
- T det = 1.;
- for (int i = 0; i < N; ++i)
- det *= (2 * (ipiv[i] == i) - 1) * LU[i * n + i];
+ /* ------------------------------------------------------------------------ */
+ inline void normal2(const Real * vec, Real * normal) {
+ normal[0] = vec[1];
+ normal[1] = -vec[0];
+ normalize2(normal);
+ }
- delete[] ipiv;
- delete[] LU;
- return det;
-}
+ /* ------------------------------------------------------------------------ */
+ inline void normal3(const Real * vec1, const Real * vec2, Real * normal) {
+ vectorProduct3(vec1, vec2, normal);
+ normalize3(normal);
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::normal2(const Real * vec, Real * normal) {
- normal[0] = vec[1];
- normal[1] = -vec[0];
- Math::normalize2(normal);
-}
+ /* ------------------------------------------------------------------------ */
+ inline void normalize2(Real * vec) {
+ Real norm = norm2(vec);
+ vec[0] /= norm;
+ vec[1] /= norm;
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::normal3(const Real * vec1, const Real * vec2, Real * normal) {
- Math::vectorProduct3(vec1, vec2, normal);
- Math::normalize3(normal);
-}
+ /* ------------------------------------------------------------------------ */
+ inline void normalize3(Real * vec) {
+ Real norm = norm3(vec);
+ vec[0] /= norm;
+ vec[1] /= norm;
+ vec[2] /= norm;
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::normalize2(Real * vec) {
- Real norm = Math::norm2(vec);
- vec[0] /= norm;
- vec[1] /= norm;
-}
+ /* ------------------------------------------------------------------------ */
+ inline Real norm2(const Real * vec) {
+ return sqrt(vec[0] * vec[0] + vec[1] * vec[1]);
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::normalize3(Real * vec) {
- Real norm = Math::norm3(vec);
- vec[0] /= norm;
- vec[1] /= norm;
- vec[2] /= norm;
-}
+ /* ------------------------------------------------------------------------ */
+ inline Real norm3(const Real * vec) {
+ return sqrt(vec[0] * vec[0] + vec[1] * vec[1] + vec[2] * vec[2]);
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::norm2(const Real * vec) {
- return sqrt(vec[0] * vec[0] + vec[1] * vec[1]);
-}
+ /* ------------------------------------------------------------------------ */
+ inline Real norm(UInt n, const Real * vec) {
+ Real norm = 0.;
+ for (UInt i = 0; i < n; ++i) {
+ norm += vec[i] * vec[i];
+ }
+ return sqrt(norm);
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::norm3(const Real * vec) {
- return sqrt(vec[0] * vec[0] + vec[1] * vec[1] + vec[2] * vec[2]);
-}
+ /* ------------------------------------------------------------------------ */
+ inline void inv2(const Real * mat, Real * inv) {
+ Real det_mat = det2(mat);
-/* -------------------------------------------------------------------------- */
-inline Real Math::norm(UInt n, const Real * vec) {
- Real norm = 0.;
- for (UInt i = 0; i < n; ++i) {
- norm += vec[i] * vec[i];
+ inv[0] = mat[3] / det_mat;
+ inv[1] = -mat[1] / det_mat;
+ inv[2] = -mat[2] / det_mat;
+ inv[3] = mat[0] / det_mat;
}
- return sqrt(norm);
-}
-/* -------------------------------------------------------------------------- */
-inline void Math::inv2(const Real * mat, Real * inv) {
- Real det_mat = det2(mat);
-
- inv[0] = mat[3] / det_mat;
- inv[1] = -mat[1] / det_mat;
- inv[2] = -mat[2] / det_mat;
- inv[3] = mat[0] / det_mat;
-}
+ /* ------------------------------------------------------------------------ */
+ inline void inv3(const Real * mat, Real * inv) {
+ Real det_mat = det3(mat);
+
+ inv[0] = (mat[4] * mat[8] - mat[7] * mat[5]) / det_mat;
+ inv[1] = (mat[2] * mat[7] - mat[8] * mat[1]) / det_mat;
+ inv[2] = (mat[1] * mat[5] - mat[4] * mat[2]) / det_mat;
+ inv[3] = (mat[5] * mat[6] - mat[8] * mat[3]) / det_mat;
+ inv[4] = (mat[0] * mat[8] - mat[6] * mat[2]) / det_mat;
+ inv[5] = (mat[2] * mat[3] - mat[5] * mat[0]) / det_mat;
+ inv[6] = (mat[3] * mat[7] - mat[6] * mat[4]) / det_mat;
+ inv[7] = (mat[1] * mat[6] - mat[7] * mat[0]) / det_mat;
+ inv[8] = (mat[0] * mat[4] - mat[3] * mat[1]) / det_mat;
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::inv3(const Real * mat, Real * inv) {
- Real det_mat = det3(mat);
-
- inv[0] = (mat[4] * mat[8] - mat[7] * mat[5]) / det_mat;
- inv[1] = (mat[2] * mat[7] - mat[8] * mat[1]) / det_mat;
- inv[2] = (mat[1] * mat[5] - mat[4] * mat[2]) / det_mat;
- inv[3] = (mat[5] * mat[6] - mat[8] * mat[3]) / det_mat;
- inv[4] = (mat[0] * mat[8] - mat[6] * mat[2]) / det_mat;
- inv[5] = (mat[2] * mat[3] - mat[5] * mat[0]) / det_mat;
- inv[6] = (mat[3] * mat[7] - mat[6] * mat[4]) / det_mat;
- inv[7] = (mat[1] * mat[6] - mat[7] * mat[0]) / det_mat;
- inv[8] = (mat[0] * mat[4] - mat[3] * mat[1]) / det_mat;
-}
+ /* ------------------------------------------------------------------------ */
+ template <UInt n> inline void inv(const Real * A, Real * Ainv) {
+ if (n == 1) {
+ *Ainv = 1. / *A;
+ } else if (n == 2) {
+ inv2(A, Ainv);
+ } else if (n == 3) {
+ inv3(A, Ainv);
+ } else {
+ inv(n, A, Ainv);
+ }
+ }
-/* -------------------------------------------------------------------------- */
-template <UInt n> inline void Math::inv(const Real * A, Real * Ainv) {
- if (n == 1)
- *Ainv = 1. / *A;
- else if (n == 2)
- inv2(A, Ainv);
- else if (n == 3)
- inv3(A, Ainv);
- else
- inv(n, A, Ainv);
-}
+ /* ------------------------------------------------------------------------ */
+ template <typename T> inline void inv(UInt n, const T * A, T * invA) {
+ int N = n;
+ int info;
+ auto * ipiv = new int[N + 1];
+ int lwork = N * N;
+ auto * work = new T[lwork];
-/* -------------------------------------------------------------------------- */
-template <typename T> inline void Math::inv(UInt n, const T * A, T * invA) {
- int N = n;
- int info;
- auto * ipiv = new int[N + 1];
- int lwork = N * N;
- auto * work = new T[lwork];
+ std::copy(A, A + n * n, invA);
- std::copy(A, A + n * n, invA);
+ aka_getrf(&N, &N, invA, &N, ipiv, &info);
+ if (info > 0) {
+ AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
+ << " )");
+ }
- aka_getrf(&N, &N, invA, &N, ipiv, &info);
- if (info > 0) {
- AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
- << " )");
- }
+ aka_getri(&N, invA, &N, ipiv, work, &lwork, &info);
+ if (info != 0) {
+ AKANTU_ERROR("Cannot invert the matrix (info: " << info << " )");
+ }
- aka_getri(&N, invA, &N, ipiv, work, &lwork, &info);
- if (info != 0) {
- AKANTU_ERROR("Cannot invert the matrix (info: " << info << " )");
+ delete[] ipiv;
+ delete[] work;
}
- delete[] ipiv;
- delete[] work;
-}
+ /* ------------------------------------------------------------------------ */
+ template <typename T>
+ inline void solve(UInt n, const T * A, T * x, const T * b) {
+ int N = n;
+ int info;
+ auto * ipiv = new int[N];
+ auto * lu_A = new T[N * N];
-/* -------------------------------------------------------------------------- */
-template <typename T>
-inline void Math::solve(UInt n, const T * A, T * x, const T * b) {
- int N = n;
- int info;
- auto * ipiv = new int[N];
- auto * lu_A = new T[N * N];
+ std::copy(A, A + N * N, lu_A);
- std::copy(A, A + N * N, lu_A);
+ aka_getrf(&N, &N, lu_A, &N, ipiv, &info);
+ if (info > 0) {
+ AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
+ << " )");
+ }
- aka_getrf(&N, &N, lu_A, &N, ipiv, &info);
- if (info > 0) {
- AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
- << " )");
- }
+ char trans = 'N';
+ int nrhs = 1;
- char trans = 'N';
- int nrhs = 1;
+ std::copy(b, b + N, x);
- std::copy(b, b + N, x);
+ aka_getrs(&trans, &N, &nrhs, lu_A, &N, ipiv, x, &N, &info);
+ if (info != 0) {
+ AKANTU_ERROR("Cannot solve the system (info: " << info << " )");
+ }
- aka_getrs(&trans, &N, &nrhs, lu_A, &N, ipiv, x, &N, &info);
- if (info != 0) {
- AKANTU_ERROR("Cannot solve the system (info: " << info << " )");
+ delete[] ipiv;
+ delete[] lu_A;
}
- delete[] ipiv;
- delete[] lu_A;
-}
-
-/* -------------------------------------------------------------------------- */
-/* -------------------------------------------------------------------------- */
-inline Real Math::matrixDoubleDot22(Real * A, Real * B) {
- Real d;
- d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3];
- return d;
-}
+ /* ------------------------------------------------------------------------ */
+ /* ------------------------------------------------------------------------ */
+ inline Real
+ matrixDoubleDot22(Real * A, // NOLINT(readability-non-const-parameter)
+ Real * B // NOLINT(readability-non-const-parameter)
+ ) {
+ Real d;
+ d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3];
+ return d;
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::matrixDoubleDot33(Real * A, Real * B) {
- Real d;
- d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3] + A[4] * B[4] +
- A[5] * B[5] + A[6] * B[6] + A[7] * B[7] + A[8] * B[8];
- return d;
-}
+ /* ------------------------------------------------------------------------ */
+ inline Real
+ matrixDoubleDot33(Real * A, // NOLINT(readability-non-const-parameter)
+ Real * B // NOLINT(readability-non-const-parameter)
+ ) {
+ Real d;
+ d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3] + A[4] * B[4] +
+ A[5] * B[5] + A[6] * B[6] + A[7] * B[7] + A[8] * B[8];
+ return d;
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::matrixDoubleDot(UInt n, Real * A, Real * B) {
- Real d = 0.;
- for (UInt i = 0; i < n; ++i) {
- for (UInt j = 0; j < n; ++j) {
- d += A[i * n + j] * B[i * n + j];
+ /* ------------------------------------------------------------------------ */
+ inline Real
+ matrixDoubleDot(UInt n,
+ Real * A, // NOLINT(readability-non-const-parameter)
+ Real * B // NOLINT(readability-non-const-parameter)
+ ) {
+ Real d = 0.;
+ for (UInt i = 0; i < n; ++i) {
+ for (UInt j = 0; j < n; ++j) {
+ d += A[i * n + j] * B[i * n + j];
+ }
}
+ return d;
}
- return d;
-}
-/* -------------------------------------------------------------------------- */
-inline void Math::vectorProduct3(const Real * v1, const Real * v2, Real * res) {
- res[0] = v1[1] * v2[2] - v1[2] * v2[1];
- res[1] = v1[2] * v2[0] - v1[0] * v2[2];
- res[2] = v1[0] * v2[1] - v1[1] * v2[0];
-}
+ /* ------------------------------------------------------------------------ */
+ inline void vectorProduct3(const Real * v1, const Real * v2, Real * res) {
+ res[0] = v1[1] * v2[2] - v1[2] * v2[1];
+ res[1] = v1[2] * v2[0] - v1[0] * v2[2];
+ res[2] = v1[0] * v2[1] - v1[1] * v2[0];
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::vectorDot2(const Real * v1, const Real * v2) {
- return (v1[0] * v2[0] + v1[1] * v2[1]);
-}
+ /* ------------------------------------------------------------------------ */
+ inline Real vectorDot2(const Real * v1, const Real * v2) {
+ return (v1[0] * v2[0] + v1[1] * v2[1]);
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::vectorDot3(const Real * v1, const Real * v2) {
- return (v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2]);
-}
+ /* ------------------------------------------------------------------------ */
+ inline Real vectorDot3(const Real * v1, const Real * v2) {
+ return (v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2]);
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::distance_2d(const Real * x, const Real * y) {
- return sqrt((y[0] - x[0]) * (y[0] - x[0]) + (y[1] - x[1]) * (y[1] - x[1]));
-}
+ /* ------------------------------------------------------------------------ */
+ inline Real distance_2d(const Real * x, const Real * y) {
+ return std::sqrt((y[0] - x[0]) * (y[0] - x[0]) +
+ (y[1] - x[1]) * (y[1] - x[1]));
+ }
-/* -------------------------------------------------------------------------- */
-inline Real Math::triangle_inradius(const Real * coord1, const Real * coord2,
- const Real * coord3) {
- /**
- * @f{eqnarray*}{
- * r &=& A / s \\
- * A &=& 1/4 * \sqrt{(a + b + c) * (a - b + c) * (a + b - c) (-a + b + c)} \\
- * s &=& \frac{a + b + c}{2}
- * @f}
- */
-
- Real a, b, c;
- a = distance_2d(coord1, coord2);
- b = distance_2d(coord2, coord3);
- c = distance_2d(coord1, coord3);
-
- Real s;
- s = (a + b + c) * 0.5;
-
- return sqrt((s - a) * (s - b) * (s - c) / s);
-}
+ /* ------------------------------------------------------------------------ */
+ inline Real triangle_inradius(const Real * coord1, const Real * coord2,
+ const Real * coord3) {
+ /**
+ * @f{eqnarray*}{
+ * r &=& A / s \\
+ * A &=& 1/4 * \sqrt{(a + b + c) * (a - b + c) * (a + b - c) (-a + b + c)}
+ * \\ s &=& \frac{a + b + c}{2}
+ * @f}
+ */
-/* -------------------------------------------------------------------------- */
-inline Real Math::distance_3d(const Real * x, const Real * y) {
- return sqrt((y[0] - x[0]) * (y[0] - x[0]) + (y[1] - x[1]) * (y[1] - x[1]) +
- (y[2] - x[2]) * (y[2] - x[2]));
-}
+ auto a = distance_2d(coord1, coord2);
+ auto b = distance_2d(coord2, coord3);
+ auto c = distance_2d(coord1, coord3);
-/* -------------------------------------------------------------------------- */
-inline Real Math::tetrahedron_volume(const Real * coord1, const Real * coord2,
- const Real * coord3, const Real * coord4) {
- Real xx[9], vol;
-
- xx[0] = coord2[0];
- xx[1] = coord2[1];
- xx[2] = coord2[2];
- xx[3] = coord3[0];
- xx[4] = coord3[1];
- xx[5] = coord3[2];
- xx[6] = coord4[0];
- xx[7] = coord4[1];
- xx[8] = coord4[2];
- vol = det3(xx);
-
- xx[0] = coord1[0];
- xx[1] = coord1[1];
- xx[2] = coord1[2];
- xx[3] = coord3[0];
- xx[4] = coord3[1];
- xx[5] = coord3[2];
- xx[6] = coord4[0];
- xx[7] = coord4[1];
- xx[8] = coord4[2];
- vol -= det3(xx);
-
- xx[0] = coord1[0];
- xx[1] = coord1[1];
- xx[2] = coord1[2];
- xx[3] = coord2[0];
- xx[4] = coord2[1];
- xx[5] = coord2[2];
- xx[6] = coord4[0];
- xx[7] = coord4[1];
- xx[8] = coord4[2];
- vol += det3(xx);
-
- xx[0] = coord1[0];
- xx[1] = coord1[1];
- xx[2] = coord1[2];
- xx[3] = coord2[0];
- xx[4] = coord2[1];
- xx[5] = coord2[2];
- xx[6] = coord3[0];
- xx[7] = coord3[1];
- xx[8] = coord3[2];
- vol -= det3(xx);
-
- vol /= 6;
-
- return vol;
-}
+ auto s = (a + b + c) * 0.5;
-/* -------------------------------------------------------------------------- */
-inline Real Math::tetrahedron_inradius(const Real * coord1, const Real * coord2,
- const Real * coord3,
- const Real * coord4) {
+ return std::sqrt((s - a) * (s - b) * (s - c) / s);
+ }
- Real l12, l13, l14, l23, l24, l34;
- l12 = distance_3d(coord1, coord2);
- l13 = distance_3d(coord1, coord3);
- l14 = distance_3d(coord1, coord4);
- l23 = distance_3d(coord2, coord3);
- l24 = distance_3d(coord2, coord4);
- l34 = distance_3d(coord3, coord4);
+ /* ------------------------------------------------------------------------ */
+ inline Real distance_3d(const Real * x, const Real * y) {
+ return std::sqrt((y[0] - x[0]) * (y[0] - x[0]) +
+ (y[1] - x[1]) * (y[1] - x[1]) +
+ (y[2] - x[2]) * (y[2] - x[2]));
+ }
- Real s1, s2, s3, s4;
+ /* ------------------------------------------------------------------------ */
+ inline Real tetrahedron_volume(const Real * coord1, const Real * coord2,
+ const Real * coord3, const Real * coord4) {
+ Real xx[9];
+
+ xx[0] = coord2[0];
+ xx[1] = coord2[1];
+ xx[2] = coord2[2];
+ xx[3] = coord3[0];
+ xx[4] = coord3[1];
+ xx[5] = coord3[2];
+ xx[6] = coord4[0];
+ xx[7] = coord4[1];
+ xx[8] = coord4[2];
+ auto vol = det3(xx);
+
+ xx[0] = coord1[0];
+ xx[1] = coord1[1];
+ xx[2] = coord1[2];
+ xx[3] = coord3[0];
+ xx[4] = coord3[1];
+ xx[5] = coord3[2];
+ xx[6] = coord4[0];
+ xx[7] = coord4[1];
+ xx[8] = coord4[2];
+ vol -= det3(xx);
+
+ xx[0] = coord1[0];
+ xx[1] = coord1[1];
+ xx[2] = coord1[2];
+ xx[3] = coord2[0];
+ xx[4] = coord2[1];
+ xx[5] = coord2[2];
+ xx[6] = coord4[0];
+ xx[7] = coord4[1];
+ xx[8] = coord4[2];
+ vol += det3(xx);
+
+ xx[0] = coord1[0];
+ xx[1] = coord1[1];
+ xx[2] = coord1[2];
+ xx[3] = coord2[0];
+ xx[4] = coord2[1];
+ xx[5] = coord2[2];
+ xx[6] = coord3[0];
+ xx[7] = coord3[1];
+ xx[8] = coord3[2];
+ vol -= det3(xx);
+
+ vol /= 6;
+
+ return vol;
+ }
- s1 = (l12 + l23 + l13) * 0.5;
- s1 = sqrt(s1 * (s1 - l12) * (s1 - l23) * (s1 - l13));
+ /* ------------------------------------------------------------------------ */
+ inline Real tetrahedron_inradius(const Real * coord1, const Real * coord2,
+ const Real * coord3, const Real * coord4) {
+ auto l12 = distance_3d(coord1, coord2);
+ auto l13 = distance_3d(coord1, coord3);
+ auto l14 = distance_3d(coord1, coord4);
+ auto l23 = distance_3d(coord2, coord3);
+ auto l24 = distance_3d(coord2, coord4);
+ auto l34 = distance_3d(coord3, coord4);
- s2 = (l12 + l24 + l14) * 0.5;
- s2 = sqrt(s2 * (s2 - l12) * (s2 - l24) * (s2 - l14));
+ auto s1 = (l12 + l23 + l13) * 0.5;
+ s1 = std::sqrt(s1 * (s1 - l12) * (s1 - l23) * (s1 - l13));
- s3 = (l23 + l34 + l24) * 0.5;
- s3 = sqrt(s3 * (s3 - l23) * (s3 - l34) * (s3 - l24));
+ auto s2 = (l12 + l24 + l14) * 0.5;
+ s2 = std::sqrt(s2 * (s2 - l12) * (s2 - l24) * (s2 - l14));
- s4 = (l13 + l34 + l14) * 0.5;
- s4 = sqrt(s4 * (s4 - l13) * (s4 - l34) * (s4 - l14));
+ auto s3 = (l23 + l34 + l24) * 0.5;
+ s3 = std::sqrt(s3 * (s3 - l23) * (s3 - l34) * (s3 - l24));
- Real volume = Math::tetrahedron_volume(coord1, coord2, coord3, coord4);
+ auto s4 = (l13 + l34 + l14) * 0.5;
+ s4 = std::sqrt(s4 * (s4 - l13) * (s4 - l34) * (s4 - l14));
- return 3 * volume / (s1 + s2 + s3 + s4);
-}
+ auto volume = tetrahedron_volume(coord1, coord2, coord3, coord4);
-/* -------------------------------------------------------------------------- */
-inline void Math::barycenter(const Real * coord, UInt nb_points,
- UInt spatial_dimension, Real * barycenter) {
- memset(barycenter, 0, spatial_dimension * sizeof(Real));
- for (UInt n = 0; n < nb_points; ++n) {
- UInt offset = n * spatial_dimension;
- for (UInt i = 0; i < spatial_dimension; ++i) {
- barycenter[i] += coord[offset + i] / (Real)nb_points;
+ return 3 * volume / (s1 + s2 + s3 + s4);
+ }
+
+ /* ------------------------------------------------------------------------ */
+ inline void barycenter(const Real * coord, UInt nb_points,
+ UInt spatial_dimension, Real * barycenter) {
+ std::fill_n(barycenter, spatial_dimension, 0.);
+ for (UInt n = 0; n < nb_points; ++n) {
+ UInt offset = n * spatial_dimension;
+ for (UInt i = 0; i < spatial_dimension; ++i) {
+ barycenter[i] += coord[offset + i] / (Real)nb_points;
+ }
}
}
-}
-/* -------------------------------------------------------------------------- */
-inline void Math::vector_2d(const Real * x, const Real * y, Real * res) {
- res[0] = y[0] - x[0];
- res[1] = y[1] - x[1];
-}
+ /* ------------------------------------------------------------------------ */
+ inline void vector_2d(const Real * x, const Real * y, Real * res) {
+ res[0] = y[0] - x[0];
+ res[1] = y[1] - x[1];
+ }
-/* -------------------------------------------------------------------------- */
-inline void Math::vector_3d(const Real * x, const Real * y, Real * res) {
- res[0] = y[0] - x[0];
- res[1] = y[1] - x[1];
- res[2] = y[2] - x[2];
-}
+ /* ------------------------------------------------------------------------ */
+ inline void vector_3d(const Real * x, const Real * y, Real * res) {
+ res[0] = y[0] - x[0];
+ res[1] = y[1] - x[1];
+ res[2] = y[2] - x[2];
+ }
-/* -------------------------------------------------------------------------- */
-/// Combined absolute and relative tolerance test proposed in
-/// Real-time collision detection by C. Ericson (2004)
-inline bool Math::are_float_equal(const Real x, const Real y) {
- Real abs_max = std::max(std::abs(x), std::abs(y));
- abs_max = std::max(abs_max, Real(1.));
- return std::abs(x - y) <= (tolerance * abs_max);
-}
+ /* ------------------------------------------------------------------------ */
+ /// Combined absolute and relative tolerance test proposed in
+ /// Real-time collision detection by C. Ericson (2004)
+ inline bool are_float_equal(const Real x, const Real y) {
+ Real abs_max = std::max(std::abs(x), std::abs(y));
+ abs_max = std::max(abs_max, Real(1.));
+ return std::abs(x - y) <= (tolerance * abs_max);
+ }
-/* -------------------------------------------------------------------------- */
-inline bool Math::isnan(Real x) {
+ /* ------------------------------------------------------------------------ */
+ inline bool isnan(Real x) {
#if defined(__INTEL_COMPILER)
#pragma warning(push)
#pragma warning(disable : 1572)
#endif // defined(__INTEL_COMPILER)
- // x = x return false means x = quiet_NaN
- return !(x == x);
+ // x = x return false means x = quiet_NaN
+ return !(x == x);
#if defined(__INTEL_COMPILER)
#pragma warning(pop)
#endif // defined(__INTEL_COMPILER)
-}
+ }
-/* -------------------------------------------------------------------------- */
-inline bool Math::are_vector_equal(UInt n, Real * x, Real * y) {
- bool test = true;
- for (UInt i = 0; i < n; ++i) {
- test &= are_float_equal(x[i], y[i]);
+ /* ------------------------------------------------------------------------ */
+ inline bool are_vector_equal(UInt n, Real * x, Real * y) {
+ bool test = true;
+ for (UInt i = 0; i < n; ++i) {
+ test &= are_float_equal(x[i], y[i]);
+ }
+
+ return test;
}
- return test;
-}
+ /* ------------------------------------------------------------------------ */
+ inline bool intersects(Real x_min, Real x_max, Real y_min, Real y_max) {
+ return not((x_max < y_min) or (x_min > y_max));
+ }
-/* -------------------------------------------------------------------------- */
-inline bool Math::intersects(Real x_min, Real x_max, Real y_min, Real y_max) {
- return not((x_max < y_min) or (x_min > y_max));
-}
+ /* ------------------------------------------------------------------------ */
+ inline bool is_in_range(Real a, Real x_min, Real x_max) {
+ return ((a >= x_min) and (a <= x_max));
+ }
-/* -------------------------------------------------------------------------- */
-inline bool Math::is_in_range(Real a, Real x_min, Real x_max) {
- return ((a >= x_min) and (a <= x_max));
-}
+ /* ------------------------------------------------------------------------ */
+ template <UInt p, typename T> inline T pow(T x) {
+ return (pow<p - 1, T>(x) * x);
+ }
+ template <> inline UInt pow<0, UInt>(__attribute__((unused)) UInt x) {
+ return (1);
+ }
+ template <> inline Real pow<0, Real>(__attribute__((unused)) Real x) {
+ return (1.);
+ }
-/* -------------------------------------------------------------------------- */
-template <UInt p, typename T> inline T Math::pow(T x) {
- return (pow<p - 1, T>(x) * x);
-}
-template <> inline UInt Math::pow<0, UInt>(__attribute__((unused)) UInt x) {
- return (1);
-}
-template <> inline Real Math::pow<0, Real>(__attribute__((unused)) Real x) {
- return (1.);
-}
+ /* ------------------------------------------------------------------------ */
+
+ template <class Functor>
+ Real NewtonRaphson::solve(const Functor & funct, Real x_0) {
+ Real x = x_0;
+ Real f_x = funct.f(x);
+ UInt iter = 0;
+ while (std::abs(f_x) > this->tolerance && iter < this->max_iteration) {
+ x -= f_x / funct.f_prime(x);
+ f_x = funct.f(x);
+ iter++;
+ }
-/* -------------------------------------------------------------------------- */
+ AKANTU_DEBUG_ASSERT(iter < this->max_iteration,
+ "Newton Raphson ("
+ << funct.name << ") solve did not converge in "
+ << this->max_iteration << " iterations (tolerance: "
+ << this->tolerance << ")");
+
+ return x;
+ }
-template <class Functor>
-Real Math::NewtonRaphson::solve(const Functor & funct, Real x_0) {
- Real x = x_0;
- Real f_x = funct.f(x);
- UInt iter = 0;
- while (std::abs(f_x) > this->tolerance && iter < this->max_iteration) {
- x -= f_x / funct.f_prime(x);
- f_x = funct.f(x);
- iter++;
- }
-
- AKANTU_DEBUG_ASSERT(iter < this->max_iteration,
- "Newton Raphson ("
- << funct.name << ") solve did not converge in "
- << this->max_iteration << " iterations (tolerance: "
- << this->tolerance << ")");
-
- return x;
-}
+} // namespace Math
} // namespace akantu
diff --git a/src/common/aka_memory.cc b/src/common/aka_memory.cc
index dba456d81..8bb7b3474 100644
--- a/src/common/aka_memory.cc
+++ b/src/common/aka_memory.cc
@@ -1,62 +1,62 @@
/**
* @file aka_memory.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief static memory wrapper
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <utility>
#include "aka_memory.hh"
#include "aka_static_memory.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Memory::Memory(ID id, MemoryID memory_id)
: static_memory(StaticMemory::getStaticMemory()), id(std::move(id)),
memory_id(memory_id) {}
/* -------------------------------------------------------------------------- */
Memory::~Memory() {
if (StaticMemory::isInstantiated()) {
std::list<ID>::iterator it;
for (it = handeld_vectors_id.begin(); it != handeld_vectors_id.end();
++it) {
AKANTU_DEBUG(dblAccessory, "Deleting the vector " << *it);
static_memory.sfree(memory_id, *it);
}
- static_memory.destroy();
+ StaticMemory::destroy();
}
handeld_vectors_id.clear();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/common/aka_memory.hh b/src/common/aka_memory.hh
index 827abd2a8..ae4f599a5 100644
--- a/src/common/aka_memory.hh
+++ b/src/common/aka_memory.hh
@@ -1,106 +1,106 @@
/**
* @file aka_memory.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief wrapper for the static_memory, all object which wants
* to access the static_memory as to inherit from the class memory
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_static_memory.hh"
/* -------------------------------------------------------------------------- */
#include <list>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MEMORY_HH__
-#define __AKANTU_MEMORY_HH__
+#ifndef AKANTU_MEMORY_HH_
+#define AKANTU_MEMORY_HH_
namespace akantu {
class Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
protected:
Memory(ID id, MemoryID memory_id = 0);
virtual ~Memory();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// malloc
template <class T>
inline Array<T> & alloc(const ID & name, UInt size, UInt nb_component);
/// malloc
template <class T>
inline Array<T> & alloc(const ID & name, UInt size, UInt nb_component,
const T & init_value);
/* ------------------------------------------------------------------------ */
/// free an array
inline void dealloc(const ID & name);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
template <typename T> inline Array<T> & getArray(const ID & name);
template <typename T> inline const Array<T> & getArray(const ID & name) const;
public:
AKANTU_GET_MACRO(MemoryID, memory_id, const MemoryID &);
AKANTU_GET_MACRO(ID, id, const ID &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the static memory instance
StaticMemory & static_memory;
/// list of allocated vectors id
std::list<ID> handeld_vectors_id;
protected:
ID id;
/// the id registred in the static memory
MemoryID memory_id;
};
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "aka_memory_inline_impl.hh"
-#endif /* __AKANTU_MEMORY_HH__ */
+#endif /* AKANTU_MEMORY_HH_ */
diff --git a/src/common/aka_named_argument.hh b/src/common/aka_named_argument.hh
index 3824c6247..a00ebdde0 100644
--- a/src/common/aka_named_argument.hh
+++ b/src/common/aka_named_argument.hh
@@ -1,165 +1,166 @@
/**
* @file aka_named_argument.hh
*
* @author Marco Arena
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 16 2017
* @date last modification: Wed Dec 06 2017
*
* @brief tool to use named arguments in functions
*
*
* Public Domain ? https://gist.github.com/ilpropheta/7576dce4c3249df89f85
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_compatibilty_with_cpp_standard.hh"
/* -------------------------------------------------------------------------- */
#include <tuple>
#include <type_traits>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_NAMED_ARGUMENT_HH__
-#define __AKANTU_AKA_NAMED_ARGUMENT_HH__
+#ifndef AKANTU_AKA_NAMED_ARGUMENT_HH_
+#define AKANTU_AKA_NAMED_ARGUMENT_HH_
namespace akantu {
namespace named_argument {
struct param_t_trait {};
/* -- Pack utils (proxy version) ------------------------------------------ */
/// Proxy containing [tag, value]
template <typename tag, typename type> struct param_t : param_t_trait {
using _tag = tag;
using _type = type;
template <typename T>
- explicit param_t(T && value) : _value(std::forward<T>(value)) {}
+ explicit param_t(T && value) // NOLINT
+ : _value(std::forward<T>(value)) {}
type _value;
};
/*
* Tagged proxy that allows syntax _name = value
* operator=(T&&) returns a param_t instance
**/
template <typename tag> struct param_proxy {
using _tag = tag;
template <typename T> decltype(auto) operator=(T && value) {
return param_t<tag, decltype(value)>{std::forward<T>(value)};
}
};
/* Same as type_at but it's supposed to be used by passing
a pack of param_t (_tag is looked for instead of a
plain type). This and type_at should be refactored.
*/
template <typename T, typename head, typename... tail> struct type_at_p {
enum {
_tmp = (std::is_same<T, typename std::decay_t<head>::_tag>::value)
? 0
: type_at_p<T, tail...>::_pos
};
enum { _pos = _tmp == -1 ? -1 : 1 + _tmp };
};
template <typename T, typename head> struct type_at_p<T, head> {
enum {
_pos =
(std::is_same<T, typename std::decay<head>::type::_tag>::value ? 1
: -1)
};
};
template <typename... Ts> struct type_at {
enum { _pos = -1 };
};
template <typename T, typename head, typename... tail>
struct type_at<T, head, tail...> {
enum { _tmp = type_at_p<T, head, tail...>::_pos };
enum { _pos = _tmp == 1 ? 0 : (_tmp == -1 ? -1 : _tmp - 1) };
};
/* Same as get_at but it's supposed to be used by passing
a pack of param_t (_type is retrieved instead)
This and get_at should be refactored.
*/
template <int pos, int curr> struct get_at {
static_assert(pos >= 0, "Required parameter");
template <typename head, typename... tail>
- static decltype(auto) get(head &&, tail &&... t) {
+ static decltype(auto) get(head && /*unused*/, tail &&... t) {
return get_at<pos, curr + 1>::get(std::forward<tail>(t)...);
}
};
template <int pos> struct get_at<pos, pos> {
static_assert(pos >= 0, "Required parameter");
template <typename head, typename... tail>
- static decltype(auto) get(head && h, tail &&...) {
+ static decltype(auto) get(head && h, tail &&... /*unused*/) {
return std::forward<decltype(h._value)>(h._value);
}
};
// Optional version
template <int pos, int curr> struct get_optional {
template <typename T, typename... pack>
- static decltype(auto) get(T &&, pack &&... _pack) {
+ static decltype(auto) get(T && /*unused*/, pack &&... _pack) {
return get_at<pos, curr>::get(std::forward<pack>(_pack)...);
}
};
template <int curr> struct get_optional<-1, curr> {
template <typename T, typename... pack>
- static decltype(auto) get(T && _default, pack &&...) {
+ static decltype(auto) get(T && _default, pack &&... /*unused*/) {
return std::forward<T>(_default);
}
};
} // namespace named_argument
// CONVENIENCE MACROS FOR CLASS DESIGNERS ==========
#define TAG_OF_ARGUMENT(_name) p_##_name
#define TAG_OF_ARGUMENT_WNS(_name) TAG_OF_ARGUMENT(_name)
#define REQUIRED_NAMED_ARG(_name) \
named_argument::get_at< \
named_argument::type_at<TAG_OF_ARGUMENT_WNS(_name), pack...>::_pos, \
0>::get(std::forward<pack>(_pack)...)
#define REQUIRED_NAMED_ARG(_name) \
named_argument::get_at< \
named_argument::type_at<TAG_OF_ARGUMENT_WNS(_name), pack...>::_pos, \
0>::get(std::forward<pack>(_pack)...)
#define OPTIONAL_NAMED_ARG(_name, _defaultVal) \
named_argument::get_optional< \
named_argument::type_at<TAG_OF_ARGUMENT_WNS(_name), pack...>::_pos, \
0>::get(_defaultVal, std::forward<pack>(_pack)...)
#define DECLARE_NAMED_ARGUMENT(name) \
struct TAG_OF_ARGUMENT(name) {}; \
named_argument::param_proxy<TAG_OF_ARGUMENT_WNS(name)> _##name \
__attribute__((unused))
namespace {
struct use_named_args_t {};
use_named_args_t use_named_args __attribute__((unused));
} // namespace
template <typename T> struct is_named_argument : public std::false_type {};
template <typename... type>
struct is_named_argument<named_argument::param_t<type...>>
: public std::true_type {};
template <typename... pack>
using are_named_argument =
aka::conjunction<is_named_argument<std::decay_t<pack>>...>;
} // namespace akantu
-#endif /* __AKANTU_AKA_NAMED_ARGUMENT_HH__ */
+#endif /* AKANTU_AKA_NAMED_ARGUMENT_HH_ */
diff --git a/src/common/aka_random_generator.hh b/src/common/aka_random_generator.hh
index 60f48f111..f531373c0 100644
--- a/src/common/aka_random_generator.hh
+++ b/src/common/aka_random_generator.hh
@@ -1,271 +1,283 @@
/**
* @file aka_random_generator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Nov 08 2017
*
* @brief generic random generator
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <random>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_RANDOM_GENERATOR_HH__
-#define __AKANTU_AKA_RANDOM_GENERATOR_HH__
+#ifndef AKANTU_AKA_RANDOM_GENERATOR_HH_
+#define AKANTU_AKA_RANDOM_GENERATOR_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* List of available distributions */
/* -------------------------------------------------------------------------- */
// clang-format off
#define AKANTU_RANDOM_DISTRIBUTION_TYPES \
((uniform , std::uniform_real_distribution )) \
((exponential , std::exponential_distribution )) \
((gamma , std::gamma_distribution )) \
((weibull , std::weibull_distribution )) \
((extreme_value, std::extreme_value_distribution)) \
((normal , std::normal_distribution )) \
((lognormal , std::lognormal_distribution )) \
((chi_squared , std::chi_squared_distribution )) \
((cauchy , std::cauchy_distribution )) \
((fisher_f , std::fisher_f_distribution )) \
((student_t , std::student_t_distribution ))
// clang-format on
#define AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(elem) BOOST_PP_CAT(_rdt_, elem)
#define AKANTU_RANDOM_DISTRIBUTION_PREFIX(s, data, elem) \
AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(BOOST_PP_TUPLE_ELEM(2, 0, elem))
enum RandomDistributionType {
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_RANDOM_DISTRIBUTION_PREFIX, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)),
_rdt_not_defined
};
/* -------------------------------------------------------------------------- */
/* Generator */
/* -------------------------------------------------------------------------- */
template <typename T> class RandomGenerator {
/* ------------------------------------------------------------------------ */
private:
- static long int _seed;
- static std::default_random_engine generator;
+ static long int _seed; // NOLINT
+ static std::default_random_engine generator; // NOLINT
/* ------------------------------------------------------------------------ */
public:
inline T operator()() { return generator(); }
/// function to print the contain of the class
- void printself(std::ostream & stream, int) const {
+ void printself(std::ostream & stream, int /* indent */) const {
stream << "RandGenerator [seed=" << _seed << "]";
}
/* ------------------------------------------------------------------------ */
public:
static void seed(long int s) {
_seed = s;
generator.seed(_seed);
}
static long int seed() { return _seed; }
- static constexpr T min() { return generator.min(); }
- static constexpr T max() { return generator.max(); }
+ static constexpr T min() { return std::default_random_engine::min(); }
+ static constexpr T max() { return std::default_random_engine::max(); }
};
#if defined(__clang__)
-template <typename T> long int RandomGenerator<T>::_seed;
+template <typename T> long int RandomGenerator<T>::_seed; // NOLINT
template <typename T> std::default_random_engine RandomGenerator<T>::generator;
#endif
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#undef AKANTU_RANDOM_DISTRIBUTION_PREFIX
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE(r, data, elem) \
case AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem)): { \
stream << BOOST_PP_STRINGIZE(AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem))); \
break; \
}
inline std::ostream & operator<<(std::ostream & stream,
RandomDistributionType type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
default:
stream << UInt(type) << " not a RandomDistributionType";
break;
}
return stream;
}
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE
/* -------------------------------------------------------------------------- */
/* Some Helper */
/* -------------------------------------------------------------------------- */
template <typename T, class Distribution> class RandomDistributionTypeHelper {
enum { value = _rdt_not_defined };
};
/* -------------------------------------------------------------------------- */
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE(r, data, elem) \
template <typename T> \
struct RandomDistributionTypeHelper<T, BOOST_PP_TUPLE_ELEM(2, 1, elem) < \
- T>> { \
+ T> > { \
enum { \
value = AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem)) \
}; \
\
static void printself(std::ostream & stream) { \
stream << BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 0, elem)); \
} \
};
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE
/* -------------------------------------------------------------------------- */
template <class T> class RandomDistribution {
public:
virtual ~RandomDistribution() = default;
+
+ RandomDistribution() = default;
+ RandomDistribution(const RandomDistribution & other) = default;
+ RandomDistribution(RandomDistribution && other) noexcept = default;
+ RandomDistribution & operator=(const RandomDistribution & other) = default;
+ RandomDistribution &
+ operator=(RandomDistribution && other) noexcept = default;
+
virtual T operator()(RandomGenerator<UInt> & gen) = 0;
virtual std::unique_ptr<RandomDistribution<T>> make_unique() const = 0;
virtual void printself(std::ostream & stream, int = 0) const = 0;
};
template <class T, class Distribution>
class RandomDistributionProxy : public RandomDistribution<T> {
public:
explicit RandomDistributionProxy(Distribution dist)
: distribution(std::move(dist)) {}
T operator()(RandomGenerator<UInt> & gen) override {
return distribution(gen);
}
std::unique_ptr<RandomDistribution<T>> make_unique() const override {
return std::make_unique<RandomDistributionProxy<T, Distribution>>(
distribution);
}
- void printself(std::ostream & stream, int = 0) const override {
+ void printself(std::ostream & stream, int /* indent */ = 0) const override {
RandomDistributionTypeHelper<T, Distribution>::printself(stream);
stream << " [ " << distribution << " ]";
}
private:
Distribution distribution;
};
/* -------------------------------------------------------------------------- */
/* RandomParameter */
/* -------------------------------------------------------------------------- */
template <typename T> class RandomParameter {
public:
template <class Distribution>
explicit RandomParameter(T base_value, Distribution dist)
: base_value(base_value),
type(RandomDistributionType(
RandomDistributionTypeHelper<T, Distribution>::value)),
distribution_proxy(
std::make_unique<RandomDistributionProxy<T, Distribution>>(
std::move(dist))) {}
explicit RandomParameter(T base_value)
: base_value(base_value),
type(RandomDistributionType(
RandomDistributionTypeHelper<
T, std::uniform_real_distribution<T>>::value)),
distribution_proxy(
std::make_unique<
RandomDistributionProxy<T, std::uniform_real_distribution<T>>>(
std::uniform_real_distribution<T>(0., 0.))) {}
RandomParameter(const RandomParameter & other)
: base_value(other.base_value), type(other.type),
distribution_proxy(other.distribution_proxy->make_unique()) {}
RandomParameter & operator=(const RandomParameter & other) {
distribution_proxy = other.distribution_proxy->make_unique();
base_value = other.base_value;
type = other.type;
return *this;
}
+ RandomParameter(RandomParameter && other) noexcept = default;
+ RandomParameter & operator=(RandomParameter && other) noexcept = default;
+
virtual ~RandomParameter() = default;
inline void setBaseValue(const T & value) { this->base_value = value; }
inline T getBaseValue() const { return this->base_value; }
template <template <typename> class Generator, class iterator>
void setValues(iterator it, iterator end) {
RandomGenerator<UInt> gen;
- for (; it != end; ++it)
+ for (; it != end; ++it) {
*it = this->base_value + (*distribution_proxy)(gen);
+ }
}
virtual void printself(std::ostream & stream,
__attribute__((unused)) int indent = 0) const {
stream << base_value;
stream << " + " << *distribution_proxy;
}
private:
/// Value with no random variations
T base_value;
/// Random distribution type
RandomDistributionType type;
/// Proxy to store a std random distribution
std::unique_ptr<RandomDistribution<T>> distribution_proxy;
};
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
RandomDistribution<T> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
RandomParameter<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AKANTU_AKA_RANDOM_GENERATOR_HH__ */
+#endif /* AKANTU_AKA_RANDOM_GENERATOR_HH_ */
diff --git a/src/common/aka_safe_enum.hh b/src/common/aka_safe_enum.hh
index 630f14dc7..1705846c8 100644
--- a/src/common/aka_safe_enum.hh
+++ b/src/common/aka_safe_enum.hh
@@ -1,94 +1,94 @@
/**
* @file aka_safe_enum.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Tue Nov 07 2017
*
* @brief Safe enums type (see More C++ Idioms/Type Safe Enum on Wikibooks
* http://en.wikibooks.org/wiki/More_C%2B%2B_Idioms/Type_Safe_Enum)
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_SAFE_ENUM_HH__
-#define __AKANTU_AKA_SAFE_ENUM_HH__
+#ifndef AKANTU_AKA_SAFE_ENUM_HH_
+#define AKANTU_AKA_SAFE_ENUM_HH_
namespace akantu {
/// Safe enumerated type
template <typename def, typename inner = typename def::type>
class safe_enum : public def {
using type = typename def::type;
public:
constexpr explicit safe_enum(type v = def::_end_) : val(v) {}
constexpr inner underlying() const { return val; }
constexpr bool operator==(const safe_enum & s) const {
return this->val == s.val;
}
constexpr bool operator!=(const safe_enum & s) const {
return this->val != s.val;
}
constexpr bool operator<(const safe_enum & s) const {
return this->val < s.val;
}
constexpr bool operator<=(const safe_enum & s) const {
return this->val <= s.val;
}
constexpr bool operator>(const safe_enum & s) const {
return this->val > s.val;
}
constexpr bool operator>=(const safe_enum & s) const {
return this->val >= s.val;
}
constexpr operator inner() { return val; };
public:
// Works only if enumerations are contiguous.
class const_iterator {
public:
constexpr explicit const_iterator(type v) : it(v) {}
constexpr const_iterator & operator++() {
++it;
return *this;
}
constexpr safe_enum operator*() { return safe_enum(static_cast<type>(it)); }
constexpr bool operator!=(const_iterator const & it) { return it.it != this->it; }
private:
int it;
};
constexpr auto begin() const { return const_iterator(def::_begin_); }
constexpr auto end() const { return const_iterator(def::_end_); }
private:
inner val;
};
} // namespace akantu
-#endif /* __AKANTU_AKA_SAFE_ENUM_HH__ */
+#endif /* AKANTU_AKA_SAFE_ENUM_HH_ */
diff --git a/src/common/aka_static_memory.cc b/src/common/aka_static_memory.cc
index 4254d2d1a..eec8a3cbb 100644
--- a/src/common/aka_static_memory.cc
+++ b/src/common/aka_static_memory.cc
@@ -1,159 +1,157 @@
/**
* @file aka_static_memory.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Memory management
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include <stdexcept>
/* -------------------------------------------------------------------------- */
#include "aka_static_memory.hh"
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
bool StaticMemory::is_instantiated = false;
StaticMemory * StaticMemory::single_static_memory = nullptr;
UInt StaticMemory::nb_reference = 0;
/* -------------------------------------------------------------------------- */
StaticMemory & StaticMemory::getStaticMemory() {
- if (!single_static_memory) {
+ if (single_static_memory == nullptr) {
single_static_memory = new StaticMemory();
is_instantiated = true;
}
nb_reference++;
return *single_static_memory;
}
/* -------------------------------------------------------------------------- */
void StaticMemory::destroy() {
nb_reference--;
if (nb_reference == 0) {
delete single_static_memory;
}
}
/* -------------------------------------------------------------------------- */
StaticMemory::~StaticMemory() {
AKANTU_DEBUG_IN();
MemoryMap::iterator memory_it;
for (memory_it = memories.begin(); memory_it != memories.end(); ++memory_it) {
ArrayMap::iterator vector_it;
for (vector_it = (memory_it->second).begin();
vector_it != (memory_it->second).end(); ++vector_it) {
delete vector_it->second;
}
(memory_it->second).clear();
}
memories.clear();
is_instantiated = false;
StaticMemory::single_static_memory = nullptr;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StaticMemory::sfree(const MemoryID & memory_id, const ID & name) {
AKANTU_DEBUG_IN();
try {
auto & vectors = const_cast<ArrayMap &>(getMemory(memory_id));
ArrayMap::iterator vector_it;
vector_it = vectors.find(name);
if (vector_it != vectors.end()) {
AKANTU_DEBUG_INFO("Array " << name
<< " removed from the static memory number "
<< memory_id);
delete vector_it->second;
vectors.erase(vector_it);
AKANTU_DEBUG_OUT();
return;
}
} catch (debug::Exception & e) {
AKANTU_EXCEPTION("The memory "
<< memory_id << " does not exist (perhaps already freed) ["
<< e.what() << "]");
AKANTU_DEBUG_OUT();
return;
}
AKANTU_DEBUG_INFO("The vector " << name
<< " does not exist (perhaps already freed)");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StaticMemory::printself(std::ostream & stream, int indent) const {
- std::string space = "";
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
- ;
+ std::string space(indent, AKANTU_INDENT);
std::streamsize prec = stream.precision();
stream.precision(2);
stream << space << "StaticMemory [" << std::endl;
UInt nb_memories = memories.size();
stream << space << " + nb memories : " << nb_memories << std::endl;
Real tot_size = 0;
MemoryMap::const_iterator memory_it;
for (memory_it = memories.begin(); memory_it != memories.end(); ++memory_it) {
Real mem_size = 0;
stream << space << AKANTU_INDENT << "Memory [" << std::endl;
UInt mem_id = memory_it->first;
stream << space << AKANTU_INDENT << " + memory id : " << mem_id
<< std::endl;
UInt nb_vectors = (memory_it->second).size();
stream << space << AKANTU_INDENT << " + nb vectors : " << nb_vectors
<< std::endl;
stream.precision(prec);
ArrayMap::const_iterator vector_it;
for (vector_it = (memory_it->second).begin();
vector_it != (memory_it->second).end(); ++vector_it) {
(vector_it->second)->printself(stream, indent + 2);
mem_size += (vector_it->second)->getMemorySize();
}
stream << space << AKANTU_INDENT
<< " + total size : " << printMemorySize<char>(mem_size)
<< std::endl;
stream << space << AKANTU_INDENT << "]" << std::endl;
tot_size += mem_size;
}
stream << space << " + total size : " << printMemorySize<char>(tot_size)
<< std::endl;
stream << space << "]" << std::endl;
stream.precision(prec);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/common/aka_static_memory.hh b/src/common/aka_static_memory.hh
index 69afd6652..24ba0c5a9 100644
--- a/src/common/aka_static_memory.hh
+++ b/src/common/aka_static_memory.hh
@@ -1,156 +1,156 @@
/**
* @file aka_static_memory.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Memory management
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* The class handling the memory, allocation/reallocation/desallocation
* The objects can register their array and ask for allocation or realocation
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_STATIC_MEMORY_HH__
-#define __AKANTU_STATIC_MEMORY_HH__
+#ifndef AKANTU_STATIC_MEMORY_HH_
+#define AKANTU_STATIC_MEMORY_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <map>
namespace akantu {
class ArrayBase;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
using ArrayMap = std::map<ID, ArrayBase *>;
using MemoryMap = std::map<MemoryID, ArrayMap>;
/**
* @class StaticMemory
* @brief Class for memory management common to all objects (this class as to
* be accessed by an interface class memory)
*/
class StaticMemory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
/// Default constructor
StaticMemory() = default;
public:
virtual ~StaticMemory();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the global instance of the StaticMemory
static StaticMemory & getStaticMemory();
static bool isInstantiated() { return is_instantiated; };
/// remove a reference on the static memory
- void destroy();
+ static void destroy();
/// access to an Array
inline const ArrayBase & getArray(const MemoryID & memory_id,
const ID & name) const;
/// get all vectors of a memory
inline const ArrayMap & getMemory(const MemoryID & memory_id) const;
/* ------------------------------------------------------------------------ */
/* Class Methods */
/* ------------------------------------------------------------------------ */
public:
/**
* Allocation of an array of type
*
* @param memory_id the id of the memory accessing to the static memory
* @param name name of the array (for example connectivity)
* @param size number of size (for example number of nodes)
* @param nb_component number of component (for example spatial dimension)
*
* @return pointer an array of memory actual size: size * nb_component *
* sizeof(T)
*/
template <typename T>
Array<T> & smalloc(const MemoryID & memory_id, const ID & name, UInt size,
UInt nb_component);
template <typename T>
Array<T> & smalloc(const MemoryID & memory_id, const ID & name, UInt size,
UInt nb_component, const T & init_value);
/**
* free the memory associated to the array name
*
* @param memory_id the id of the memory accessing to the static memory
* @param name the name of an existing array
*/
void sfree(const MemoryID & memory_id, const ID & name);
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// is the static memory instantiated
static bool is_instantiated;
/// unique instance of the StaticMemory
static StaticMemory * single_static_memory;
/// map of all allocated arrays, indexed by their names
MemoryMap memories;
/// number of references on the static memory
static UInt nb_reference;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const StaticMemory & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "aka_static_memory_inline_impl.hh"
#include "aka_static_memory_tmpl.hh"
-#endif /* __AKANTU_STATIC_MEMORY_HH__ */
+#endif /* AKANTU_STATIC_MEMORY_HH_ */
diff --git a/src/common/aka_static_memory_inline_impl.hh b/src/common/aka_static_memory_inline_impl.hh
index affcf88a7..9942790fb 100644
--- a/src/common/aka_static_memory_inline_impl.hh
+++ b/src/common/aka_static_memory_inline_impl.hh
@@ -1,67 +1,65 @@
/**
* @file aka_static_memory_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
* @date last modification: Wed Feb 03 2016
*
* @brief Implementation of inline functions of the class StaticMemory
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_static_memory.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
inline const ArrayMap &
StaticMemory::getMemory(const MemoryID & memory_id) const {
AKANTU_DEBUG_IN();
- MemoryMap::const_iterator memory_it;
- memory_it = memories.find(memory_id);
+ auto memory_it = memories.find(memory_id);
if (memory_it == memories.end()) {
AKANTU_SILENT_EXCEPTION("StaticMemory as no memory with ID " << memory_id);
}
AKANTU_DEBUG_OUT();
return memory_it->second;
}
/* -------------------------------------------------------------------------- */
inline const ArrayBase & StaticMemory::getArray(const MemoryID & memory_id,
const ID & name) const {
AKANTU_DEBUG_IN();
- const ArrayMap & vectors = getMemory(memory_id);
+ const ArrayMap & vectors = this->getMemory(memory_id);
- ArrayMap::const_iterator vectors_it;
- vectors_it = vectors.find(name);
+ auto vectors_it = vectors.find(name);
if (vectors_it == vectors.end()) {
AKANTU_SILENT_EXCEPTION("StaticMemory as no array named "
<< name << " for the Memory " << memory_id);
}
AKANTU_DEBUG_OUT();
return *(vectors_it->second);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/common/aka_typelist.hh b/src/common/aka_typelist.hh
index 97056bf4b..15c211272 100644
--- a/src/common/aka_typelist.hh
+++ b/src/common/aka_typelist.hh
@@ -1,154 +1,154 @@
/**
* @file aka_typelist.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Mon Jun 19 2017
*
* @brief Objects that support the visitor design pattern
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TYPELIST_HH__
-#define __AKANTU_TYPELIST_HH__
+#ifndef AKANTU_TYPELIST_HH_
+#define AKANTU_TYPELIST_HH_
#include "aka_common.hh"
namespace akantu {
struct Empty_type {};
class Null_type {};
template <class T, class U> struct Typelist {
typedef T Head;
typedef U Tail;
};
template <typename T1 = Null_type, typename T2 = Null_type,
typename T3 = Null_type, typename T4 = Null_type,
typename T5 = Null_type, typename T6 = Null_type,
typename T7 = Null_type, typename T8 = Null_type,
typename T9 = Null_type, typename T10 = Null_type,
typename T11 = Null_type, typename T12 = Null_type,
typename T13 = Null_type, typename T14 = Null_type,
typename T15 = Null_type, typename T16 = Null_type,
typename T17 = Null_type, typename T18 = Null_type,
typename T19 = Null_type, typename T20 = Null_type>
struct MakeTypelist {
private:
typedef typename MakeTypelist<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
T13, T14, T15, T16, T17, T18, T19, T20>::Result
TailResult;
public:
typedef Typelist<T1, TailResult> Result;
};
template <> struct MakeTypelist<> { typedef Null_type Result; };
////////////////////////////////////////////////////////////////////////////////
// class template Length
// Computes the length of a typelist
// Invocation (TList is a typelist):
// Length<TList>::value
// returns a compile-time constant containing the length of TList, not counting
// the end terminator (which by convention is Null_type)
////////////////////////////////////////////////////////////////////////////////
template <class TList> struct Length;
template <> struct Length<Null_type> {
enum { value = 0 };
};
template <class T, class U> struct Length<Typelist<T, U>> {
enum { value = 1 + Length<U>::value };
};
////////////////////////////////////////////////////////////////////////////////
// class template TypeAt
// Finds the type at a given index in a typelist
// Invocation (TList is a typelist and index is a compile-time integral
// constant):
// TypeAt<TList, index>::Result
// returns the type in position 'index' in TList
// If you pass an out-of-bounds index, the result is a compile-time error
////////////////////////////////////////////////////////////////////////////////
template <class TList, unsigned int index> struct TypeAt;
template <class Head, class Tail> struct TypeAt<Typelist<Head, Tail>, 0> {
typedef Head Result;
};
template <class Head, class Tail, unsigned int i>
struct TypeAt<Typelist<Head, Tail>, i> {
typedef typename TypeAt<Tail, i - 1>::Result Result;
};
////////////////////////////////////////////////////////////////////////////////
// class template Erase
// Erases the first occurence, if any, of a type in a typelist
// Invocation (TList is a typelist and T is a type):
// Erase<TList, T>::Result
// returns a typelist that is TList without the first occurence of T
////////////////////////////////////////////////////////////////////////////////
template <class TList, class T> struct Erase;
template <class T> // Specialization 1
struct Erase<Null_type, T> {
typedef Null_type Result;
};
template <class T, class Tail> // Specialization 2
struct Erase<Typelist<T, Tail>, T> {
typedef Tail Result;
};
template <class Head, class Tail, class T> // Specialization 3
struct Erase<Typelist<Head, Tail>, T> {
typedef Typelist<Head, typename Erase<Tail, T>::Result> Result;
};
template <class TList, class T> struct IndexOf;
template <class T> struct IndexOf<Null_type, T> {
enum { value = -1 };
};
template <class T, class Tail> struct IndexOf<Typelist<T, Tail>, T> {
enum { value = 0 };
};
template <class Head, class Tail, class T>
struct IndexOf<Typelist<Head, Tail>, T> {
private:
enum { temp = IndexOf<Tail, T>::value };
public:
enum { value = (temp == -1 ? -1 : 1 + temp) };
};
} // namespace akantu
-#endif /* __AKANTU_TYPELIST_HH__ */
+#endif /* AKANTU_TYPELIST_HH_ */
diff --git a/src/common/aka_types.hh b/src/common/aka_types.hh
index 790ef8591..11e464ebe 100644
--- a/src/common/aka_types.hh
+++ b/src/common/aka_types.hh
@@ -1,1500 +1,1548 @@
/**
* @file aka_types.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 17 2011
* @date last modification: Tue Feb 20 2018
*
* @brief description of the "simple" types
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_math.hh"
/* -------------------------------------------------------------------------- */
#include <initializer_list>
#include <iomanip>
#include <type_traits>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_TYPES_HH__
-#define __AKANTU_AKA_TYPES_HH__
+#ifndef AKANTU_AKA_TYPES_HH_
+#define AKANTU_AKA_TYPES_HH_
namespace akantu {
enum NormType { L_1 = 1, L_2 = 2, L_inf = UInt(-1) };
/**
* DimHelper is a class to generalize the setup of a dim array from 3
* values. This gives a common interface in the TensorStorage class
* independently of its derived inheritance (Vector, Matrix, Tensor3)
* @tparam dim
*/
template <UInt dim> struct DimHelper {
- static inline void setDims(UInt m, UInt n, UInt p, UInt dims[dim]);
+ static inline void setDims(UInt m, UInt n, UInt p,
+ std::array<UInt, dim> dims);
};
/* -------------------------------------------------------------------------- */
template <> struct DimHelper<1> {
- static inline void setDims(UInt m, __attribute__((unused)) UInt n,
- __attribute__((unused)) UInt p, UInt dims[1]) {
+ static inline void setDims(UInt m, UInt /*n*/, UInt /*p*/,
+ std::array<UInt, 1> dims) {
dims[0] = m;
}
};
/* -------------------------------------------------------------------------- */
template <> struct DimHelper<2> {
- static inline void setDims(UInt m, UInt n, __attribute__((unused)) UInt p,
- UInt dims[2]) {
+ static inline void setDims(UInt m, UInt n, UInt /*p*/,
+ std::array<UInt, 2> dims) {
dims[0] = m;
dims[1] = n;
}
};
/* -------------------------------------------------------------------------- */
template <> struct DimHelper<3> {
- static inline void setDims(UInt m, UInt n, UInt p, UInt dims[3]) {
+ static inline void setDims(UInt m, UInt n, UInt p, std::array<UInt, 3> dims) {
dims[0] = m;
dims[1] = n;
dims[2] = p;
}
};
/* -------------------------------------------------------------------------- */
template <typename T, UInt ndim, class RetType> class TensorStorage;
/* -------------------------------------------------------------------------- */
/* Proxy classes */
/* -------------------------------------------------------------------------- */
namespace tensors {
template <class A, class B> struct is_copyable {
enum : bool { value = false };
};
template <class A> struct is_copyable<A, A> {
enum : bool { value = true };
};
template <class A> struct is_copyable<A, typename A::RetType> {
enum : bool { value = true };
};
template <class A> struct is_copyable<A, typename A::RetType::proxy> {
enum : bool { value = true };
};
} // namespace tensors
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace types {
namespace details {
template <typename reference_> class vector_iterator {
public:
using difference_type = std::ptrdiff_t;
using value_type = std::decay_t<reference_>;
using pointer = value_type *;
using reference = reference_;
using iterator_category = std::input_iterator_tag;
vector_iterator(pointer ptr) : ptr(ptr) {}
// input iterator ++it
vector_iterator & operator++() {
++ptr;
return *this;
}
// input iterator it++
vector_iterator operator++(int) {
auto cpy = *this;
++ptr;
return cpy;
}
vector_iterator & operator+=(int n) {
ptr += n;
return *this;
}
vector_iterator operator+(int n) {
vector_iterator cpy(*this);
cpy += n;
return cpy;
}
// input iterator it != other_it
bool operator!=(const vector_iterator & other) const {
return ptr != other.ptr;
}
bool operator==(const vector_iterator & other) const {
return ptr == other.ptr;
}
difference_type operator-(const vector_iterator & other) const {
return this->ptr - other.ptr;
}
// input iterator dereference *it
reference operator*() { return *ptr; }
pointer operator->() { return ptr; }
private:
pointer ptr;
};
} // namespace details
} // namespace types
/**
* @class TensorProxy aka_types.hh
* The TensorProxy class is a proxy class to the
* TensorStorage it handles the wrapped case. That is to say if an accessor
* should give access to a Tensor wrapped on some data, like the
* Array<T>::iterator they can return a TensorProxy that will be automatically
* transformed as a TensorStorage wrapped on the same data
* @tparam T stored type
* @tparam ndim order of the tensor
* @tparam _RetType real derived type
*/
-template <typename T, UInt ndim, class _RetType>
+template <typename T, UInt ndim, class RetType_>
class TensorProxy : public TensorProxyTrait {
protected:
- using RetTypeProxy = typename _RetType::proxy;
+ using RetTypeProxy = typename RetType_::proxy;
constexpr TensorProxy(T * data, UInt m, UInt n, UInt p) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->values = data;
}
template <class Other, typename = std::enable_if_t<
tensors::is_copyable<TensorProxy, Other>::value>>
explicit TensorProxy(const Other & other) {
this->values = other.storage();
- for (UInt i = 0; i < ndim; ++i)
+ for (UInt i = 0; i < ndim; ++i) {
this->n[i] = other.size(i);
+ }
}
public:
- using RetType = _RetType;
+ using RetType = RetType_;
UInt size(UInt i) const {
AKANTU_DEBUG_ASSERT(i < ndim, "This tensor has only " << ndim
<< " dimensions, not "
<< (i + 1));
return n[i];
}
inline UInt size() const {
UInt _size = 1;
- for (UInt d = 0; d < ndim; ++d)
+ for (UInt d = 0; d < ndim; ++d) {
_size *= this->n[d];
+ }
return _size;
}
T * storage() const { return values; }
template <class Other, typename = std::enable_if_t<
tensors::is_copyable<TensorProxy, Other>::value>>
inline TensorProxy & operator=(const Other & other) {
AKANTU_DEBUG_ASSERT(
other.size() == this->size(),
"You are trying to copy two tensors with different sizes");
- memcpy(this->values, other.storage(), this->size() * sizeof(T));
+ std::copy_n(other.storage(), this->size(), this->values);
return *this;
}
// template <class Other, typename = std::enable_if_t<
// tensors::is_copyable<TensorProxy, Other>::value>>
// inline TensorProxy & operator=(const Other && other) {
// AKANTU_DEBUG_ASSERT(
// other.size() == this->size(),
// "You are trying to copy two tensors with different sizes");
// memcpy(this->values, other.storage(), this->size() * sizeof(T));
// return *this;
// }
template <typename O> inline RetTypeProxy & operator*=(const O & o) {
RetType(*this) *= o;
return static_cast<RetTypeProxy &>(*this);
}
template <typename O> inline RetTypeProxy & operator/=(const O & o) {
RetType(*this) /= o;
return static_cast<RetTypeProxy &>(*this);
}
protected:
T * values;
- UInt n[ndim];
+ std::array<UInt, ndim> n;
};
/* -------------------------------------------------------------------------- */
template <typename T> class VectorProxy : public TensorProxy<T, 1, Vector<T>> {
using parent = TensorProxy<T, 1, Vector<T>>;
using type = Vector<T>;
public:
constexpr VectorProxy(T * data, UInt n) : parent(data, n, 0, 0) {}
template <class Other> explicit VectorProxy(Other & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline VectorProxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
// inline VectorProxy<T> & operator=(const VectorProxy && other) {
// parent::operator=(other);
// return *this;
// }
using iterator = types::details::vector_iterator<T &>;
using const_iterator = types::details::vector_iterator<const T &>;
iterator begin() { return iterator(this->storage()); }
iterator end() { return iterator(this->storage() + this->size()); }
const_iterator begin() const { return const_iterator(this->storage()); }
const_iterator end() const {
return const_iterator(this->storage() + this->size());
}
/* ------------------------------------------------------------------------ */
T & operator()(UInt index) { return this->values[index]; };
const T & operator()(UInt index) const { return this->values[index]; };
};
template <typename T> class MatrixProxy : public TensorProxy<T, 2, Matrix<T>> {
using parent = TensorProxy<T, 2, Matrix<T>>;
using type = Matrix<T>;
public:
MatrixProxy(T * data, UInt m, UInt n) : parent(data, m, n, 0) {}
template <class Other> explicit MatrixProxy(Other & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline MatrixProxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
};
template <typename T>
class Tensor3Proxy : public TensorProxy<T, 3, Tensor3<T>> {
using parent = TensorProxy<T, 3, Tensor3<T>>;
using type = Tensor3<T>;
public:
Tensor3Proxy(const T * data, UInt m, UInt n, UInt k)
: parent(data, m, n, k) {}
Tensor3Proxy(const Tensor3Proxy & src) : parent(src) {}
Tensor3Proxy(const Tensor3<T> & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline Tensor3Proxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
};
/* -------------------------------------------------------------------------- */
/* Tensor base class */
/* -------------------------------------------------------------------------- */
template <typename T, UInt ndim, class RetType>
class TensorStorage : public TensorTrait {
public:
using value_type = T;
friend class Array<T>;
protected:
template <class TensorType> void copySize(const TensorType & src) {
- for (UInt d = 0; d < ndim; ++d)
- this->n[d] = src.size(d);
+ for (UInt d = 0; d < ndim; ++d) {
+ this->n[d] = src.size(d); // NOLINT
+ }
this->_size = src.size();
}
- TensorStorage() : values(nullptr) {
- for (UInt d = 0; d < ndim; ++d)
- this->n[d] = 0;
- _size = 0;
- }
-
+ TensorStorage() = default;
TensorStorage(const TensorProxy<T, ndim, RetType> & proxy) {
this->copySize(proxy);
this->values = proxy.storage();
this->wrapped = true;
}
public:
TensorStorage(const TensorStorage & src) = delete;
TensorStorage(const TensorStorage & src, bool deep_copy) : values(nullptr) {
- if (deep_copy)
+ if (deep_copy) {
this->deepCopy(src);
- else
+ } else {
this->shallowCopy(src);
+ }
}
protected:
TensorStorage(UInt m, UInt n, UInt p, const T & def) {
static_assert(std::is_trivially_constructible<T>{},
"Cannot create a tensor on non trivial types");
DimHelper<ndim>::setDims(m, n, p, this->n);
this->computeSize();
- this->values = new T[this->_size];
+ this->values = new T[this->_size]; // NOLINT
this->set(def);
this->wrapped = false;
}
TensorStorage(T * data, UInt m, UInt n, UInt p) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->computeSize();
this->values = data;
this->wrapped = true;
}
public:
/* ------------------------------------------------------------------------ */
template <class TensorType> inline void shallowCopy(const TensorType & src) {
this->copySize(src);
- if (!this->wrapped)
+ if (!this->wrapped) {
delete[] this->values;
+ }
this->values = src.storage();
this->wrapped = true;
}
/* ------------------------------------------------------------------------ */
template <class TensorType> inline void deepCopy(const TensorType & src) {
this->copySize(src);
- if (!this->wrapped)
+ if (!this->wrapped) {
delete[] this->values;
+ }
static_assert(std::is_trivially_constructible<T>{},
"Cannot create a tensor on non trivial types");
- this->values = new T[this->_size];
+ this->values = new T[this->_size]; // NOLINT
static_assert(std::is_trivially_copyable<T>{},
"Cannot copy a tensor on non trivial types");
- memcpy((void *)this->values, (void *)src.storage(),
- this->_size * sizeof(T));
+ std::copy_n(src.storage(), this->_size, this->values);
this->wrapped = false;
}
virtual ~TensorStorage() {
- if (!this->wrapped)
+ if (!this->wrapped) {
delete[] this->values;
+ }
}
/* ------------------------------------------------------------------------ */
- inline TensorStorage & operator=(const TensorStorage & src) {
- return this->operator=(aka::as_type<RetType>(src));
+ inline TensorStorage & operator=(const TensorStorage & other) {
+ if(this == &other) {
+ return *this;
+ }
+ this->operator=(aka::as_type<RetType>(other));
+ return *this;
}
+ inline TensorStorage & operator=(TensorStorage && other) noexcept = default;
+
/* ------------------------------------------------------------------------ */
inline TensorStorage & operator=(const RetType & src) {
if (this != &src) {
if (this->wrapped) {
static_assert(std::is_trivially_copyable<T>{},
"Cannot copy a tensor on non trivial types");
// this test is not sufficient for Tensor of order higher than 1
AKANTU_DEBUG_ASSERT(this->_size == src.size(),
"Tensors of different size ("
<< this->_size << " != " << src.size() << ")");
- memcpy((void *)this->values, (void *)src.storage(),
- this->_size * sizeof(T));
+ std::copy_n(src.storage(), this->_size, this->values);
} else {
deepCopy(src);
}
}
return *this;
}
/* ------------------------------------------------------------------------ */
template <class R>
inline RetType & operator+=(const TensorStorage<T, ndim, R> & other) {
T * a = this->storage();
T * b = other.storage();
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
- for (UInt i = 0; i < _size; ++i)
+ for (UInt i = 0; i < _size; ++i) {
*(a++) += *(b++);
+ }
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
template <class R>
inline RetType & operator-=(const TensorStorage<T, ndim, R> & other) {
T * a = this->storage();
T * b = other.storage();
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
- for (UInt i = 0; i < _size; ++i)
+ for (UInt i = 0; i < _size; ++i) {
*(a++) -= *(b++);
+ }
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
inline RetType & operator+=(const T & x) {
T * a = this->values;
- for (UInt i = 0; i < _size; ++i)
+ for (UInt i = 0; i < _size; ++i) {
*(a++) += x;
+ }
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
inline RetType & operator-=(const T & x) {
T * a = this->values;
- for (UInt i = 0; i < _size; ++i)
+ for (UInt i = 0; i < _size; ++i) {
*(a++) -= x;
+ }
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
inline RetType & operator*=(const T & x) {
T * a = this->storage();
- for (UInt i = 0; i < _size; ++i)
+ for (UInt i = 0; i < _size; ++i) {
*(a++) *= x;
+ }
return *(static_cast<RetType *>(this));
}
/* ---------------------------------------------------------------------- */
inline RetType & operator/=(const T & x) {
T * a = this->values;
- for (UInt i = 0; i < _size; ++i)
+ for (UInt i = 0; i < _size; ++i) {
*(a++) /= x;
+ }
return *(static_cast<RetType *>(this));
}
/// \f[Y = \alpha X + Y\f]
inline RetType & aXplusY(const TensorStorage & other, const T & alpha = 1.) {
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
Math::aXplusY(this->_size, alpha, other.storage(), this->storage());
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
T * storage() const { return values; }
UInt size() const { return _size; }
UInt size(UInt i) const {
AKANTU_DEBUG_ASSERT(i < ndim, "This tensor has only " << ndim
<< " dimensions, not "
<< (i + 1));
return n[i];
};
/* ------------------------------------------------------------------------ */
- inline void clear() { memset(values, 0, _size * sizeof(T)); };
inline void set(const T & t) { std::fill_n(values, _size, t); };
-
+ inline void zero() { this->set(0.); };
+
template <class TensorType> inline void copy(const TensorType & other) {
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be copied");
- memcpy(values, other.storage(), _size * sizeof(T));
+ std::copy_n(other.storage(), _size, values);
}
bool isWrapped() const { return this->wrapped; }
protected:
inline void computeSize() {
_size = 1;
- for (UInt d = 0; d < ndim; ++d)
+ for (UInt d = 0; d < ndim; ++d) {
_size *= this->n[d];
+ }
}
protected:
template <typename R, NormType norm_type> struct NormHelper {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
- for (; it < end; ++it)
+ for (; it < end; ++it) {
_norm += std::pow(std::abs(*it), norm_type);
+ }
return std::pow(_norm, 1. / norm_type);
}
};
template <typename R> struct NormHelper<R, L_1> {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
- for (; it < end; ++it)
+ for (; it < end; ++it) {
_norm += std::abs(*it);
+ }
return _norm;
}
};
template <typename R> struct NormHelper<R, L_2> {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
- for (; it < end; ++it)
+ for (; it < end; ++it) {
_norm += *it * *it;
+ }
return sqrt(_norm);
}
};
template <typename R> struct NormHelper<R, L_inf> {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
- for (; it < end; ++it)
+ for (; it < end; ++it) {
_norm = std::max(std::abs(*it), _norm);
+ }
return _norm;
}
};
public:
/*----------------------------------------------------------------------- */
/// "Entrywise" norm norm<L_p> @f[ \|\boldsymbol{T}\|_p = \left(
/// \sum_i^{n[0]}\sum_j^{n[1]}\sum_k^{n[2]} |T_{ijk}|^p \right)^{\frac{1}{p}}
/// @f]
template <NormType norm_type> inline T norm() const {
return NormHelper<T, norm_type>::norm(*this);
}
protected:
- UInt n[ndim];
- UInt _size;
- T * values;
+ std::array<UInt, ndim> n{};
+ UInt _size{0};
+ T * values{nullptr};
bool wrapped{false};
};
/* -------------------------------------------------------------------------- */
/* Vector */
/* -------------------------------------------------------------------------- */
template <typename T> class Vector : public TensorStorage<T, 1, Vector<T>> {
using parent = TensorStorage<T, 1, Vector<T>>;
public:
using value_type = typename parent::value_type;
using proxy = VectorProxy<T>;
public:
Vector() : parent() {}
explicit Vector(UInt n, const T & def = T()) : parent(n, 0, 0, def) {}
Vector(T * data, UInt n) : parent(data, n, 0, 0) {}
Vector(const Vector & src, bool deep_copy = true) : parent(src, deep_copy) {}
Vector(const TensorProxy<T, 1, Vector> & src) : parent(src) {}
Vector(std::initializer_list<T> list) : parent(list.size(), 0, 0, T()) {
UInt i = 0;
for (auto val : list) {
operator()(i++) = val;
}
}
public:
using iterator = types::details::vector_iterator<T &>;
using const_iterator = types::details::vector_iterator<const T &>;
iterator begin() { return iterator(this->storage()); }
iterator end() { return iterator(this->storage() + this->size()); }
const_iterator begin() const { return const_iterator(this->storage()); }
const_iterator end() const {
return const_iterator(this->storage() + this->size());
}
public:
~Vector() override = default;
/* ------------------------------------------------------------------------ */
inline Vector & operator=(const Vector & src) {
parent::operator=(src);
return *this;
}
+ inline Vector & operator=(Vector && src) noexcept = default;
+
/* ------------------------------------------------------------------------ */
inline T & operator()(UInt i) {
AKANTU_DEBUG_ASSERT((i < this->n[0]),
"Access out of the vector! "
<< "Index (" << i
<< ") is out of the vector of size (" << this->n[0]
<< ")");
return *(this->values + i);
}
inline const T & operator()(UInt i) const {
AKANTU_DEBUG_ASSERT((i < this->n[0]),
"Access out of the vector! "
<< "Index (" << i
<< ") is out of the vector of size (" << this->n[0]
<< ")");
return *(this->values + i);
}
inline T & operator[](UInt i) { return this->operator()(i); }
inline const T & operator[](UInt i) const { return this->operator()(i); }
/* ------------------------------------------------------------------------ */
inline Vector<T> & operator*=(Real x) { return parent::operator*=(x); }
inline Vector<T> & operator/=(Real x) { return parent::operator/=(x); }
/* ------------------------------------------------------------------------ */
inline Vector<T> & operator*=(const Vector<T> & vect) {
AKANTU_DEBUG_ASSERT(this->_size == vect._size,
"The vectors have non matching sizes");
T * a = this->storage();
T * b = vect.storage();
- for (UInt i = 0; i < this->_size; ++i)
+ for (UInt i = 0; i < this->_size; ++i) {
*(a++) *= *(b++);
+ }
return *this;
}
/* ------------------------------------------------------------------------ */
inline Real dot(const Vector<T> & vect) const {
return Math::vectorDot(this->values, vect.storage(), this->_size);
}
/* ------------------------------------------------------------------------ */
inline Real mean() const {
Real mean = 0;
T * a = this->storage();
- for (UInt i = 0; i < this->_size; ++i)
+ for (UInt i = 0; i < this->_size; ++i) {
mean += *(a++);
+ }
return mean / this->_size;
}
/* ------------------------------------------------------------------------ */
inline Vector & crossProduct(const Vector<T> & v1, const Vector<T> & v2) {
AKANTU_DEBUG_ASSERT(this->size() == 3,
"crossProduct is only defined in 3D (n=" << this->size()
<< ")");
AKANTU_DEBUG_ASSERT(
this->size() == v1.size() && this->size() == v2.size(),
"crossProduct is not a valid operation non matching size vectors");
Math::vectorProduct3(v1.storage(), v2.storage(), this->values);
return *this;
}
inline Vector crossProduct(const Vector<T> & v) {
Vector<T> tmp(this->size());
tmp.crossProduct(*this, v);
return tmp;
}
/* ------------------------------------------------------------------------ */
inline void solve(const Matrix<T> & A, const Vector<T> & b) {
AKANTU_DEBUG_ASSERT(
this->size() == A.rows() && this->_size == A.cols(),
"The size of the solution vector mismatches the size of the matrix");
AKANTU_DEBUG_ASSERT(
this->_size == b._size,
"The rhs vector has a mismatch in size with the matrix");
Math::solve(this->_size, A.storage(), this->values, b.storage());
}
/* ------------------------------------------------------------------------ */
template <bool tr_A>
inline void mul(const Matrix<T> & A, const Vector<T> & x, T alpha = T(1));
/* ------------------------------------------------------------------------ */
inline Real norm() const { return parent::template norm<L_2>(); }
template <NormType nt> inline Real norm() const {
return parent::template norm<nt>();
}
/* ------------------------------------------------------------------------ */
inline Vector<Real> & normalize() {
Real n = norm();
operator/=(n);
return *this;
}
/* ------------------------------------------------------------------------ */
/// norm of (*this - x)
inline Real distance(const Vector<T> & y) const {
Real * vx = this->values;
Real * vy = y.storage();
Real sum_2 = 0;
- for (UInt i = 0; i < this->_size; ++i, ++vx, ++vy)
+ for (UInt i = 0; i < this->_size; ++i, ++vx, ++vy) { // NOLINT
sum_2 += (*vx - *vy) * (*vx - *vy);
+ }
return sqrt(sum_2);
}
/* ------------------------------------------------------------------------ */
inline bool equal(const Vector<T> & v,
Real tolerance = Math::getTolerance()) const {
T * a = this->storage();
T * b = v.storage();
UInt i = 0;
- while (i < this->_size && (std::abs(*(a++) - *(b++)) < tolerance))
+ while (i < this->_size && (std::abs(*(a++) - *(b++)) < tolerance)) {
++i;
+ }
return i == this->_size;
}
/* ------------------------------------------------------------------------ */
inline short compare(const Vector<T> & v,
Real tolerance = Math::getTolerance()) const {
T * a = this->storage();
T * b = v.storage();
for (UInt i(0); i < this->_size; ++i, ++a, ++b) {
- if (std::abs(*a - *b) > tolerance)
+ if (std::abs(*a - *b) > tolerance) {
return (((*a - *b) > tolerance) ? 1 : -1);
+ }
}
return 0;
}
/* ------------------------------------------------------------------------ */
inline bool operator==(const Vector<T> & v) const { return equal(v); }
inline bool operator!=(const Vector<T> & v) const { return !operator==(v); }
inline bool operator<(const Vector<T> & v) const { return compare(v) == -1; }
inline bool operator>(const Vector<T> & v) const { return compare(v) == 1; }
template <typename Func, typename Acc>
decltype(auto) accumulate(const Vector<T> & v, Acc && accumulator,
Func && func) const {
T * a = this->storage();
T * b = v.storage();
for (UInt i(0); i < this->_size; ++i, ++a, ++b) {
accumulator = func(*a, *b, std::forward<Acc>(accumulator));
}
return accumulator;
}
inline bool operator<=(const Vector<T> & v) const {
bool res = true;
return accumulate(v, res, [](auto && a, auto && b, auto && accumulator) {
return accumulator & (a <= b);
});
}
inline bool operator>=(const Vector<T> & v) const {
bool res = true;
return accumulate(v, res, [](auto && a, auto && b, auto && accumulator) {
return accumulator & (a >= b);
});
}
/* ------------------------------------------------------------------------ */
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
+ for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
+ }
stream << "[";
for (UInt i = 0; i < this->_size; ++i) {
- if (i != 0)
+ if (i != 0) {
stream << ", ";
+ }
stream << this->values[i];
}
stream << "]";
}
/* ---------------------------------------------------------------------- */
static inline Vector<T> zeros(UInt n) {
Vector<T> tmp(n);
tmp.set(T());
return tmp;
}
};
using RVector = Vector<Real>;
/* ------------------------------------------------------------------------ */
template <>
inline bool Vector<UInt>::equal(const Vector<UInt> & v,
__attribute__((unused)) Real tolerance) const {
UInt * a = this->storage();
UInt * b = v.storage();
UInt i = 0;
- while (i < this->_size && (*(a++) == *(b++)))
+ while (i < this->_size && (*(a++) == *(b++))) {
++i;
+ }
return i == this->_size;
}
/* -------------------------------------------------------------------------- */
namespace types {
namespace details {
template <typename Mat> class column_iterator {
public:
using difference_type = std::ptrdiff_t;
using value_type = decltype(std::declval<Mat>().operator()(0));
using pointer = value_type *;
using reference = value_type &;
using iterator_category = std::input_iterator_tag;
column_iterator(Mat & mat, UInt col) : mat(mat), col(col) {}
decltype(auto) operator*() { return mat(col); }
decltype(auto) operator++() {
++col;
AKANTU_DEBUG_ASSERT(col <= mat.cols(), "The iterator is out of bound");
return *this;
}
decltype(auto) operator++(int) {
auto tmp = *this;
++col;
AKANTU_DEBUG_ASSERT(col <= mat.cols(), "The iterator is out of bound");
return tmp;
}
bool operator!=(const column_iterator & other) const {
return col != other.col;
}
bool operator==(const column_iterator & other) const {
return not operator!=(other);
}
private:
Mat & mat;
UInt col;
};
} // namespace details
} // namespace types
/* ------------------------------------------------------------------------ */
/* Matrix */
/* ------------------------------------------------------------------------ */
template <typename T> class Matrix : public TensorStorage<T, 2, Matrix<T>> {
using parent = TensorStorage<T, 2, Matrix<T>>;
public:
using value_type = typename parent::value_type;
using proxy = MatrixProxy<T>;
public:
Matrix() : parent() {}
Matrix(UInt m, UInt n, const T & def = T()) : parent(m, n, 0, def) {}
Matrix(T * data, UInt m, UInt n) : parent(data, m, n, 0) {}
Matrix(const Matrix & src, bool deep_copy = true) : parent(src, deep_copy) {}
Matrix(const MatrixProxy<T> & src) : parent(src) {}
Matrix(std::initializer_list<std::initializer_list<T>> list) {
static_assert(std::is_trivially_copyable<T>{},
"Cannot create a tensor on non trivial types");
std::size_t n = 0;
std::size_t m = list.size();
for (auto row : list) {
n = std::max(n, row.size());
}
DimHelper<2>::setDims(m, n, 0, this->n);
this->computeSize();
this->values = new T[this->_size];
this->set(0);
- UInt i = 0, j = 0;
+ UInt i{0};
+ UInt j{0};
for (auto & row : list) {
for (auto & val : row) {
at(i, j++) = val;
}
++i;
j = 0;
}
}
~Matrix() override = default;
/* ------------------------------------------------------------------------ */
inline Matrix & operator=(const Matrix & src) {
parent::operator=(src);
return *this;
}
+ inline Matrix & operator=(Matrix && src) noexcept = default;
public:
/* ---------------------------------------------------------------------- */
UInt rows() const { return this->n[0]; }
UInt cols() const { return this->n[1]; }
/* ---------------------------------------------------------------------- */
inline T & at(UInt i, UInt j) {
AKANTU_DEBUG_ASSERT(((i < this->n[0]) && (j < this->n[1])),
"Access out of the matrix! "
<< "Index (" << i << ", " << j
<< ") is out of the matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return *(this->values + i + j * this->n[0]);
}
inline const T & at(UInt i, UInt j) const {
AKANTU_DEBUG_ASSERT(((i < this->n[0]) && (j < this->n[1])),
"Access out of the matrix! "
<< "Index (" << i << ", " << j
<< ") is out of the matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return *(this->values + i + j * this->n[0]);
}
/* ------------------------------------------------------------------------ */
inline T & operator()(UInt i, UInt j) { return this->at(i, j); }
inline const T & operator()(UInt i, UInt j) const { return this->at(i, j); }
/// give a line vector wrapped on the column i
inline VectorProxy<T> operator()(UInt j) {
AKANTU_DEBUG_ASSERT(j < this->n[1],
"Access out of the matrix! "
<< "You are trying to access the column vector "
<< j << " in a matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return VectorProxy<T>(this->values + j * this->n[0], this->n[0]);
}
- inline const VectorProxy<T> operator()(UInt j) const {
+ inline VectorProxy<T> operator()(UInt j) const {
AKANTU_DEBUG_ASSERT(j < this->n[1],
"Access out of the matrix! "
<< "You are trying to access the column vector "
<< j << " in a matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return VectorProxy<T>(this->values + j * this->n[0], this->n[0]);
}
public:
decltype(auto) begin() {
return types::details::column_iterator<Matrix<T>>(*this, 0);
}
decltype(auto) begin() const {
return types::details::column_iterator<const Matrix<T>>(*this, 0);
}
decltype(auto) end() {
return types::details::column_iterator<Matrix<T>>(*this, this->cols());
}
decltype(auto) end() const {
return types::details::column_iterator<const Matrix<T>>(*this,
this->cols());
}
/* ------------------------------------------------------------------------ */
inline void block(const Matrix & block, UInt pos_i, UInt pos_j) {
AKANTU_DEBUG_ASSERT(pos_i + block.rows() <= rows(),
"The block size or position are not correct");
AKANTU_DEBUG_ASSERT(pos_i + block.cols() <= cols(),
"The block size or position are not correct");
- for (UInt i = 0; i < block.rows(); ++i)
- for (UInt j = 0; j < block.cols(); ++j)
+ for (UInt i = 0; i < block.rows(); ++i) {
+ for (UInt j = 0; j < block.cols(); ++j) {
this->at(i + pos_i, j + pos_j) = block(i, j);
+ }
+ }
}
inline Matrix block(UInt pos_i, UInt pos_j, UInt block_rows,
UInt block_cols) const {
AKANTU_DEBUG_ASSERT(pos_i + block_rows <= rows(),
"The block size or position are not correct");
AKANTU_DEBUG_ASSERT(pos_i + block_cols <= cols(),
"The block size or position are not correct");
Matrix block(block_rows, block_cols);
- for (UInt i = 0; i < block_rows; ++i)
- for (UInt j = 0; j < block_cols; ++j)
+ for (UInt i = 0; i < block_rows; ++i) {
+ for (UInt j = 0; j < block_cols; ++j) {
block(i, j) = this->at(i + pos_i, j + pos_j);
+ }
+ }
return block;
}
inline T & operator[](UInt idx) { return *(this->values + idx); };
inline const T & operator[](UInt idx) const { return *(this->values + idx); };
/* ---------------------------------------------------------------------- */
inline Matrix operator*(const Matrix & B) const {
Matrix C(this->rows(), B.cols());
C.mul<false, false>(*this, B);
return C;
}
/* ----------------------------------------------------------------------- */
inline Matrix & operator*=(const T & x) { return parent::operator*=(x); }
inline Matrix & operator*=(const Matrix & B) {
Matrix C(*this);
this->mul<false, false>(C, B);
return *this;
}
/* ---------------------------------------------------------------------- */
template <bool tr_A, bool tr_B>
inline void mul(const Matrix & A, const Matrix & B, T alpha = 1.0) {
UInt k = A.cols();
- if (tr_A)
+ if (tr_A) {
k = A.rows();
+ }
#ifndef AKANTU_NDEBUG
if (tr_B) {
AKANTU_DEBUG_ASSERT(k == B.cols(),
"matrices to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->cols() == B.rows(),
"matrices to multiply have no fit dimensions");
} else {
AKANTU_DEBUG_ASSERT(k == B.rows(),
"matrices to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->cols() == B.cols(),
"matrices to multiply have no fit dimensions");
}
if (tr_A) {
AKANTU_DEBUG_ASSERT(this->rows() == A.cols(),
"matrices to multiply have no fit dimensions");
} else {
AKANTU_DEBUG_ASSERT(this->rows() == A.rows(),
"matrices to multiply have no fit dimensions");
}
#endif // AKANTU_NDEBUG
Math::matMul<tr_A, tr_B>(this->rows(), this->cols(), k, alpha, A.storage(),
B.storage(), 0., this->storage());
}
/* ---------------------------------------------------------------------- */
inline void outerProduct(const Vector<T> & A, const Vector<T> & B) {
AKANTU_DEBUG_ASSERT(
A.size() == this->rows() && B.size() == this->cols(),
"A and B are not compatible with the size of the matrix");
for (UInt i = 0; i < this->rows(); ++i) {
for (UInt j = 0; j < this->cols(); ++j) {
this->values[i + j * this->rows()] += A[i] * B[j];
}
}
}
private:
class EigenSorter {
public:
EigenSorter(const Vector<T> & eigs) : eigs(eigs) {}
bool operator()(const UInt & a, const UInt & b) const {
return (eigs(a) > eigs(b));
}
private:
const Vector<T> & eigs;
};
public:
/* ---------------------------------------------------------------------- */
inline void eig(Vector<T> & eigenvalues, Matrix<T> & eigenvectors,
bool sort = true) const {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"eig is not a valid operation on a rectangular matrix");
AKANTU_DEBUG_ASSERT(eigenvalues.size() == this->cols(),
"eigenvalues should be of size " << this->cols()
<< ".");
#ifndef AKANTU_NDEBUG
- if (eigenvectors.storage() != nullptr)
+ if (eigenvectors.storage() != nullptr) {
AKANTU_DEBUG_ASSERT((eigenvectors.rows() == eigenvectors.cols()) &&
(eigenvectors.rows() == this->cols()),
"Eigenvectors needs to be a square matrix of size "
<< this->cols() << " x " << this->cols() << ".");
+ }
#endif
Matrix<T> tmp = *this;
Vector<T> tmp_eigs(eigenvalues.size());
Matrix<T> tmp_eig_vects(eigenvectors.rows(), eigenvectors.cols());
- if (tmp_eig_vects.rows() == 0 || tmp_eig_vects.cols() == 0)
+ if (tmp_eig_vects.rows() == 0 || tmp_eig_vects.cols() == 0) {
Math::matrixEig(tmp.cols(), tmp.storage(), tmp_eigs.storage());
- else
+ } else {
Math::matrixEig(tmp.cols(), tmp.storage(), tmp_eigs.storage(),
tmp_eig_vects.storage());
+ }
if (not sort) {
eigenvalues = tmp_eigs;
eigenvectors = tmp_eig_vects;
return;
}
Vector<UInt> perm(eigenvalues.size());
- for (UInt i = 0; i < perm.size(); ++i)
+ for (UInt i = 0; i < perm.size(); ++i) {
perm(i) = i;
+ }
std::sort(perm.storage(), perm.storage() + perm.size(),
EigenSorter(tmp_eigs));
- for (UInt i = 0; i < perm.size(); ++i)
+ for (UInt i = 0; i < perm.size(); ++i) {
eigenvalues(i) = tmp_eigs(perm(i));
+ }
- if (tmp_eig_vects.rows() != 0 && tmp_eig_vects.cols() != 0)
+ if (tmp_eig_vects.rows() != 0 && tmp_eig_vects.cols() != 0) {
for (UInt i = 0; i < perm.size(); ++i) {
for (UInt j = 0; j < eigenvectors.rows(); ++j) {
eigenvectors(j, i) = tmp_eig_vects(j, perm(i));
}
}
+ }
}
/* ---------------------------------------------------------------------- */
inline void eig(Vector<T> & eigenvalues) const {
Matrix<T> empty;
eig(eigenvalues, empty);
}
/* ---------------------------------------------------------------------- */
inline void eye(T alpha = 1.) {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"eye is not a valid operation on a rectangular matrix");
- this->clear();
+ this->zero();
for (UInt i = 0; i < this->cols(); ++i) {
this->values[i + i * this->rows()] = alpha;
}
}
/* ---------------------------------------------------------------------- */
static inline Matrix<T> eye(UInt m, T alpha = 1.) {
Matrix<T> tmp(m, m);
tmp.eye(alpha);
return tmp;
}
/* ---------------------------------------------------------------------- */
inline T trace() const {
AKANTU_DEBUG_ASSERT(
this->cols() == this->rows(),
"trace is not a valid operation on a rectangular matrix");
T trace = 0.;
for (UInt i = 0; i < this->rows(); ++i) {
trace += this->values[i + i * this->rows()];
}
return trace;
}
/* ---------------------------------------------------------------------- */
inline Matrix transpose() const {
Matrix tmp(this->cols(), this->rows());
for (UInt i = 0; i < this->rows(); ++i) {
for (UInt j = 0; j < this->cols(); ++j) {
tmp(j, i) = operator()(i, j);
}
}
return tmp;
}
/* ---------------------------------------------------------------------- */
inline void inverse(const Matrix & A) {
AKANTU_DEBUG_ASSERT(A.cols() == A.rows(),
"inv is not a valid operation on a rectangular matrix");
AKANTU_DEBUG_ASSERT(this->cols() == A.cols(),
"the matrix should have the same size as its inverse");
- if (this->cols() == 1)
+ if (this->cols() == 1) {
*this->values = 1. / *A.storage();
- else if (this->cols() == 2)
+ } else if (this->cols() == 2) {
Math::inv2(A.storage(), this->values);
- else if (this->cols() == 3)
+ } else if (this->cols() == 3) {
Math::inv3(A.storage(), this->values);
- else
+ } else {
Math::inv(this->cols(), A.storage(), this->values);
+ }
}
inline Matrix inverse() {
Matrix inv(this->rows(), this->cols());
inv.inverse(*this);
return inv;
}
/* --------------------------------------------------------------------- */
inline T det() const {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"inv is not a valid operation on a rectangular matrix");
- if (this->cols() == 1)
+ if (this->cols() == 1) {
return *(this->values);
- else if (this->cols() == 2)
+ }
+ if (this->cols() == 2) {
return Math::det2(this->values);
- else if (this->cols() == 3)
+ }
+ if (this->cols() == 3) {
return Math::det3(this->values);
- else
- return Math::det(this->cols(), this->values);
+ }
+ return Math::det(this->cols(), this->values);
}
/* --------------------------------------------------------------------- */
inline T doubleDot(const Matrix<T> & other) const {
AKANTU_DEBUG_ASSERT(
this->cols() == this->rows(),
"doubleDot is not a valid operation on a rectangular matrix");
- if (this->cols() == 1)
+ if (this->cols() == 1) {
return *(this->values) * *(other.storage());
- else if (this->cols() == 2)
+ }
+ if (this->cols() == 2) {
return Math::matrixDoubleDot22(this->values, other.storage());
- else if (this->cols() == 3)
+ }
+ if (this->cols() == 3) {
return Math::matrixDoubleDot33(this->values, other.storage());
- else
- AKANTU_ERROR("doubleDot is not defined for other spatial dimensions"
- << " than 1, 2 or 3.");
- return T();
+ }
+
+ AKANTU_ERROR("doubleDot is not defined for other spatial dimensions"
+ << " than 1, 2 or 3.");
}
/* ---------------------------------------------------------------------- */
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
+ for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
+ }
stream << "[";
for (UInt i = 0; i < this->n[0]; ++i) {
- if (i != 0)
+ if (i != 0) {
stream << ", ";
+ }
stream << "[";
for (UInt j = 0; j < this->n[1]; ++j) {
- if (j != 0)
+ if (j != 0) {
stream << ", ";
+ }
stream << operator()(i, j);
}
stream << "]";
}
stream << "]";
};
};
/* ------------------------------------------------------------------------ */
template <typename T>
template <bool tr_A>
inline void Vector<T>::mul(const Matrix<T> & A, const Vector<T> & x, T alpha) {
#ifndef AKANTU_NDEBUG
UInt n = x.size();
if (tr_A) {
AKANTU_DEBUG_ASSERT(n == A.rows(),
"matrix and vector to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->size() == A.cols(),
"matrix and vector to multiply have no fit dimensions");
} else {
AKANTU_DEBUG_ASSERT(n == A.cols(),
"matrix and vector to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->size() == A.rows(),
"matrix and vector to multiply have no fit dimensions");
}
#endif
Math::matVectMul<tr_A>(A.rows(), A.cols(), alpha, A.storage(), x.storage(),
0., this->storage());
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const Matrix<T> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const Vector<T> & _this) {
_this.printself(stream);
return stream;
}
/* ------------------------------------------------------------------------ */
/* Tensor3 */
/* ------------------------------------------------------------------------ */
template <typename T> class Tensor3 : public TensorStorage<T, 3, Tensor3<T>> {
using parent = TensorStorage<T, 3, Tensor3<T>>;
public:
using value_type = typename parent::value_type;
using proxy = Tensor3Proxy<T>;
public:
Tensor3() : parent(){};
Tensor3(UInt m, UInt n, UInt p, const T & def = T()) : parent(m, n, p, def) {}
Tensor3(T * data, UInt m, UInt n, UInt p) : parent(data, m, n, p) {}
Tensor3(const Tensor3 & src, bool deep_copy = true)
: parent(src, deep_copy) {}
Tensor3(const proxy & src) : parent(src) {}
public:
/* ------------------------------------------------------------------------ */
inline Tensor3 & operator=(const Tensor3 & src) {
parent::operator=(src);
return *this;
}
/* ---------------------------------------------------------------------- */
inline T & operator()(UInt i, UInt j, UInt k) {
AKANTU_DEBUG_ASSERT(
(i < this->n[0]) && (j < this->n[1]) && (k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the element "
<< "(" << i << ", " << j << ", " << k << ") in a tensor of size ("
<< this->n[0] << ", " << this->n[1] << ", " << this->n[2] << ")");
return *(this->values + (k * this->n[0] + i) * this->n[1] + j);
}
inline const T & operator()(UInt i, UInt j, UInt k) const {
AKANTU_DEBUG_ASSERT(
(i < this->n[0]) && (j < this->n[1]) && (k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the element "
<< "(" << i << ", " << j << ", " << k << ") in a tensor of size ("
<< this->n[0] << ", " << this->n[1] << ", " << this->n[2] << ")");
return *(this->values + (k * this->n[0] + i) * this->n[1] + j);
}
inline MatrixProxy<T> operator()(UInt k) {
AKANTU_DEBUG_ASSERT((k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the slice " << k
<< " in a tensor3 of size (" << this->n[0] << ", "
<< this->n[1] << ", " << this->n[2] << ")");
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
- inline const MatrixProxy<T> operator()(UInt k) const {
+ inline MatrixProxy<T> operator()(UInt k) const {
AKANTU_DEBUG_ASSERT((k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the slice " << k
<< " in a tensor3 of size (" << this->n[0] << ", "
<< this->n[1] << ", " << this->n[2] << ")");
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline MatrixProxy<T> operator[](UInt k) {
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
- inline const MatrixProxy<T> operator[](UInt k) const {
+ inline MatrixProxy<T> operator[](UInt k) const {
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
};
/* -------------------------------------------------------------------------- */
// support operations for the creation of other vectors
/* -------------------------------------------------------------------------- */
template <typename T>
Vector<T> operator*(const T & scalar, const Vector<T> & a) {
Vector<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Vector<T> operator*(const Vector<T> & a, const T & scalar) {
Vector<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Vector<T> operator/(const Vector<T> & a, const T & scalar) {
Vector<T> r(a);
r /= scalar;
return r;
}
template <typename T>
Vector<T> operator*(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r *= b;
return r;
}
template <typename T>
Vector<T> operator+(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r += b;
return r;
}
template <typename T>
Vector<T> operator-(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r -= b;
return r;
}
template <typename T>
Vector<T> operator*(const Matrix<T> & A, const Vector<T> & b) {
Vector<T> r(b.size());
r.template mul<false>(A, b);
return r;
}
/* -------------------------------------------------------------------------- */
template <typename T>
Matrix<T> operator*(const T & scalar, const Matrix<T> & a) {
Matrix<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Matrix<T> operator*(const Matrix<T> & a, const T & scalar) {
Matrix<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Matrix<T> operator/(const Matrix<T> & a, const T & scalar) {
Matrix<T> r(a);
r /= scalar;
return r;
}
template <typename T>
Matrix<T> operator+(const Matrix<T> & a, const Matrix<T> & b) {
Matrix<T> r(a);
r += b;
return r;
}
template <typename T>
Matrix<T> operator-(const Matrix<T> & a, const Matrix<T> & b) {
Matrix<T> r(a);
r -= b;
return r;
}
} // namespace akantu
#include <iterator>
namespace std {
template <typename R>
struct iterator_traits<::akantu::types::details::vector_iterator<R>> {
protected:
using iterator = ::akantu::types::details::vector_iterator<R>;
public:
using iterator_category = typename iterator::iterator_category;
using value_type = typename iterator::value_type;
using difference_type = typename iterator::difference_type;
using pointer = typename iterator::pointer;
using reference = typename iterator::reference;
};
template <typename Mat>
struct iterator_traits<::akantu::types::details::column_iterator<Mat>> {
protected:
using iterator = ::akantu::types::details::column_iterator<Mat>;
public:
using iterator_category = typename iterator::iterator_category;
using value_type = typename iterator::value_type;
using difference_type = typename iterator::difference_type;
using pointer = typename iterator::pointer;
using reference = typename iterator::reference;
};
} // namespace std
-#endif /* __AKANTU_AKA_TYPES_HH__ */
+#endif /* AKANTU_AKA_TYPES_HH_ */
diff --git a/src/common/aka_visitor.hh b/src/common/aka_visitor.hh
index 1c91477e4..f5392d8af 100644
--- a/src/common/aka_visitor.hh
+++ b/src/common/aka_visitor.hh
@@ -1,163 +1,163 @@
/**
* @file aka_visitor.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Mon Jun 19 2017
*
* @brief Objects that support the visitor design pattern
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_VISITOR_HH__
-#define __AKANTU_VISITOR_HH__
+#ifndef AKANTU_VISITOR_HH_
+#define AKANTU_VISITOR_HH_
#include "aka_typelist.hh"
namespace akantu {
///////////////////////////////////////////////////////////////////////////
// visitor class template, adapted from the Andrei Alexandrescu's
// "Modern C++ Design"
enum Visit_type { Mutable, Immutable };
template <class T, typename R = void, Visit_type = Mutable> class StrictVisitor;
template <class T, typename R> class StrictVisitor<T, R, Mutable> {
public:
typedef R ReturnType;
typedef T ParamType;
virtual ~StrictVisitor() {}
virtual ReturnType Visit(ParamType &) = 0;
};
template <class T, typename R> class StrictVisitor<T, R, Immutable> {
public:
typedef R ReturnType;
typedef const T ParamType;
virtual ~StrictVisitor() {}
virtual ReturnType Visit(ParamType &) = 0;
};
/// class template StrictVisitor (specialization)
template <class Head, class Tail, typename R>
class StrictVisitor<Typelist<Head, Tail>, R, Mutable>
: public StrictVisitor<Head, R, Mutable>,
public StrictVisitor<Tail, R, Mutable> {
public:
typedef R ReturnType;
typedef Head ParamType;
// using StrictVisitor<Head, R>::Visit;
// using StrictVisitor<Tail, R>::Visit;
};
template <class Head, typename R>
class StrictVisitor<Typelist<Head, Null_type>, R, Mutable>
: public StrictVisitor<Head, R, Mutable> {
public:
typedef R ReturnType;
typedef Head ParamType;
using StrictVisitor<Head, R, Mutable>::Visit;
};
template <class Head, class Tail, typename R>
class StrictVisitor<Typelist<Head, Tail>, R, Immutable>
: public StrictVisitor<Head, R, Immutable>,
public StrictVisitor<Tail, R, Immutable> {
public:
typedef R ReturnType;
typedef Head ParamType;
// using StrictVisitor<Head, R>::Visit;
// using StrictVisitor<Tail, R>::Visit;
};
template <class Head, typename R>
class StrictVisitor<Typelist<Head, Null_type>, R, Immutable>
: public StrictVisitor<Head, R, Immutable> {
public:
typedef R ReturnType;
typedef Head ParamType;
using StrictVisitor<Head, R, Immutable>::Visit;
};
////////////////////////////////////////////////////////////////////////////////
// class template NonStrictVisitor
// Implements non-strict visitation (you can implement only part of the Visit
// functions)
//
template <class R> struct DefaultFunctor {
template <class T> R operator()(T &) { return R(); }
};
template <class T, typename R = void, Visit_type V = Mutable,
class F = DefaultFunctor<R>>
class BaseVisitorImpl;
template <class Head, class Tail, typename R, Visit_type V, class F>
class BaseVisitorImpl<Typelist<Head, Tail>, R, V, F>
: public StrictVisitor<Head, R, V>, public BaseVisitorImpl<Tail, R, V, F> {
public:
typedef typename StrictVisitor<Head, R, V>::ParamType ParamType;
virtual R Visit(ParamType & h) { return F()(h); }
};
template <class Head, typename R, Visit_type V, class F>
class BaseVisitorImpl<Typelist<Head, Null_type>, R, V, F>
: public StrictVisitor<Head, R, V> {
public:
typedef typename StrictVisitor<Head, R, V>::ParamType ParamType;
virtual R Visit(ParamType & h) { return F()(h); }
};
/// Visitor
template <class R> struct Strict {};
template <typename R, class TList, Visit_type V = Mutable,
template <class> class FunctorPolicy = DefaultFunctor>
class Visitor : public BaseVisitorImpl<TList, R, V, FunctorPolicy<R>> {
public:
typedef R ReturnType;
template <class Visited> ReturnType GenericVisit(Visited & host) {
StrictVisitor<Visited, ReturnType, V> & subObj = *this;
return subObj.Visit(host);
}
};
template <typename R, class TList, Visit_type V>
class Visitor<R, TList, V, Strict> : public StrictVisitor<TList, R, V> {
public:
typedef R ReturnType;
template <class Visited> ReturnType GenericVisit(Visited & host) {
StrictVisitor<Visited, ReturnType, V> & subObj = *this;
return subObj.Visit(host);
}
};
} // namespace akantu
-#endif /* __AKANTU_VISITOR_HH__ */
+#endif /* AKANTU_VISITOR_HH_ */
diff --git a/src/common/aka_voigthelper.hh b/src/common/aka_voigthelper.hh
index 89ce3ab51..59f19dde2 100644
--- a/src/common/aka_voigthelper.hh
+++ b/src/common/aka_voigthelper.hh
@@ -1,100 +1,100 @@
/**
* @file aka_voigthelper.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 20 2013
* @date last modification: Mon Jan 29 2018
*
* @brief Helper file for Voigt notation
* Wikipedia convention: @f[2*\epsilon_{ij} (i!=j) = voigt_\epsilon_{I}@f]
* http://en.wikipedia.org/wiki/Voigt_notation
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKA_VOIGTHELPER_HH__
-#define __AKA_VOIGTHELPER_HH__
+#ifndef AKA_VOIGTHELPER_HH_
+#define AKA_VOIGTHELPER_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim> class VoigtHelper {
static_assert(dim > 0U, "Cannot be < 1D");
static_assert(dim < 4U, "Cannot be > 3D");
public:
/* ------------------------------------------------------------------------ */
template <class M, class V>
static inline void matrixToVoigt(M && matrix, V && vector);
template <class M> static inline decltype(auto) matrixToVoigt(M && matrix);
template <class M, class V>
static inline void matrixToVoigtWithFactors(M && matrix, V && vector);
template <class M>
static inline decltype(auto) matrixToVoigtWithFactors(M && matrix);
template <class M, class V>
static inline void voigtToMatrix(V && vector, M && matrix);
template <class V> static inline decltype(auto) voigtToMatrix(V && vector);
/* ------------------------------------------------------------------------ */
/// transfer the B matrix to a Voigt notation B matrix
inline static void transferBMatrixToSymVoigtBMatrix(
const Matrix<Real> & B, Matrix<Real> & Bvoigt, UInt nb_nodes_per_element);
/// transfer the BNL matrix to a Voigt notation B matrix (See Bathe et al.
/// IJNME vol 9, 1975)
inline static void transferBMatrixToBNL(const Matrix<Real> & B,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element);
/// transfer the BL2 matrix to a Voigt notation B matrix (See Bathe et al.
/// IJNME vol 9, 1975)
inline static void transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element);
public:
static constexpr UInt size{(dim * (dim - 1)) / 2 + dim};
// matrix of vector index I as function of tensor indices i,j
static const UInt mat[dim][dim];
// array of matrix indices ij as function of vector index I
static const UInt vec[dim * dim][2];
// factors to multiply the strain by for voigt notation
static const Real factors[size];
};
} // namespace akantu
#include "aka_voigthelper_tmpl.hh"
#endif
diff --git a/src/common/aka_voigthelper_tmpl.hh b/src/common/aka_voigthelper_tmpl.hh
index 96fbd5e1c..9ac5094e1 100644
--- a/src/common/aka_voigthelper_tmpl.hh
+++ b/src/common/aka_voigthelper_tmpl.hh
@@ -1,232 +1,241 @@
/**
* @file aka_voigthelper_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 20 2013
* @date last modification: Wed Dec 06 2017
*
* @brief implementation of the voight helper
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_voigthelper.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AKA_VOIGTHELPER_TMPL_HH__
-#define __AKANTU_AKA_VOIGTHELPER_TMPL_HH__
+#ifndef AKANTU_AKA_VOIGTHELPER_TMPL_HH_
+#define AKANTU_AKA_VOIGTHELPER_TMPL_HH_
namespace akantu {
template <UInt dim> constexpr UInt VoigtHelper<dim>::size;
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M, class V>
inline void VoigtHelper<dim>::matrixToVoigt(M && matrix, V && vector) {
for (UInt I = 0; I < size; ++I) {
auto i = vec[I][0];
auto j = vec[I][1];
vector(I) = matrix(i, j);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M>
inline decltype(auto) VoigtHelper<dim>::matrixToVoigt(M && matrix) {
Vector<Real> vector(size);
matrixToVoigt(std::forward<M>(matrix), vector);
return vector;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M, class V>
inline void VoigtHelper<dim>::matrixToVoigtWithFactors(M && matrix,
V && vector) {
for (UInt I = 0; I < size; ++I) {
auto i = vec[I][0];
auto j = vec[I][1];
vector(I) = factors[I] * matrix(i, j);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M>
inline decltype(auto) VoigtHelper<dim>::matrixToVoigtWithFactors(M && matrix) {
Vector<Real> vector(size);
matrixToVoigtWithFactors(std::forward<M>(matrix), vector);
return vector;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M, class V>
inline void VoigtHelper<dim>::voigtToMatrix(V && vector, M && matrix) {
for (UInt I = 0; I < size; ++I) {
auto i = vec[I][0];
auto j = vec[I][1];
matrix(i, j) = matrix(j, i) = vector(I);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class V>
inline decltype(auto) VoigtHelper<dim>::voigtToMatrix(V && vector) {
Matrix<Real> matrix(dim, dim);
voigtToMatrix(std::forward<V>(vector), matrix);
return matrix;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
const Matrix<Real> & B, Matrix<Real> & Bvoigt, UInt nb_nodes_per_element) {
- Bvoigt.clear();
+ Bvoigt.zero();
- for (UInt i = 0; i < dim; ++i)
- for (UInt n = 0; n < nb_nodes_per_element; ++n)
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Bvoigt(i, i + n * dim) = B(i, n);
+ }
+ }
if (dim == 2) {
/// in 2D, fill the @f$ [\frac{\partial N_i}{\partial x}, \frac{\partial
/// N_i}{\partial y}]@f$ row
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Bvoigt(2, 1 + n * 2) = B(0, n);
Bvoigt(2, 0 + n * 2) = B(1, n);
}
}
if (dim == 3) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Real dndx = B(0, n);
Real dndy = B(1, n);
Real dndz = B(2, n);
/// in 3D, fill the @f$ [0, \frac{\partial N_i}{\partial y},
/// \frac{N_i}{\partial z}]@f$ row
Bvoigt(3, 1 + n * 3) = dndz;
Bvoigt(3, 2 + n * 3) = dndy;
/// in 3D, fill the @f$ [\frac{\partial N_i}{\partial x}, 0,
/// \frac{N_i}{\partial z}]@f$ row
Bvoigt(4, 0 + n * 3) = dndz;
Bvoigt(4, 2 + n * 3) = dndx;
/// in 3D, fill the @f$ [\frac{\partial N_i}{\partial x},
/// \frac{N_i}{\partial y}, 0]@f$ row
Bvoigt(5, 0 + n * 3) = dndy;
Bvoigt(5, 1 + n * 3) = dndx;
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void VoigtHelper<dim>::transferBMatrixToBNL(const Matrix<Real> & B,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
- Bvoigt.clear();
+ Bvoigt.zero();
// see Finite element formulations for large deformation dynamic analysis,
// Bathe et al. IJNME vol 9, 1975, page 364 B_{NL}
for (UInt i = 0; i < dim; ++i) {
for (UInt m = 0; m < nb_nodes_per_element; ++m) {
for (UInt n = 0; n < dim; ++n) {
// std::cout << B(n, m) << std::endl;
Bvoigt(i * dim + n, m * dim + i) = B(n, m);
}
}
}
// TODO: Verify the 2D and 1D case
}
/* -------------------------------------------------------------------------- */
template <>
inline void VoigtHelper<1>::transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
- Bvoigt.clear();
- for (UInt j = 0; j < nb_nodes_per_element; ++j)
+ Bvoigt.zero();
+ for (UInt j = 0; j < nb_nodes_per_element; ++j) {
Bvoigt(0, j) = grad_u(0, 0) * B(0, j);
+ }
}
/* -------------------------------------------------------------------------- */
template <>
inline void VoigtHelper<3>::transferBMatrixToBL2(const Matrix<Real> & dNdX,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
- Bvoigt.clear();
+ Bvoigt.zero();
- for (UInt I = 0; I < 3; ++I)
- for (UInt a = 0; a < nb_nodes_per_element; ++a)
- for (UInt i = 0; i < 3; ++i)
+ for (UInt I = 0; I < 3; ++I) {
+ for (UInt a = 0; a < nb_nodes_per_element; ++a) {
+ for (UInt i = 0; i < 3; ++i) {
Bvoigt(I, a * 3 + i) = grad_u(i, I) * dNdX(I, a);
+ }
+ }
+ }
for (UInt Iv = 3; Iv < 6; ++Iv) {
for (UInt a = 0; a < nb_nodes_per_element; ++a) {
for (UInt k = 0; k < 3; ++k) {
UInt aux = Iv - 3;
for (UInt m = 0; m < 3; ++m) {
if (m != aux) {
UInt index1 = m;
UInt index2 = 3 - m - aux;
Bvoigt(Iv, a * 3 + k) += grad_u(k, index1) * dNdX(index2, a);
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void VoigtHelper<2>::transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
- Bvoigt.clear();
+ Bvoigt.zero();
- for (UInt i = 0; i < 2; ++i)
- for (UInt j = 0; j < nb_nodes_per_element; ++j)
- for (UInt k = 0; k < 2; ++k)
+ for (UInt i = 0; i < 2; ++i) {
+ for (UInt j = 0; j < nb_nodes_per_element; ++j) {
+ for (UInt k = 0; k < 2; ++k) {
Bvoigt(i, j * 2 + k) = grad_u(k, i) * B(i, j);
+ }
+ }
+ }
for (UInt j = 0; j < nb_nodes_per_element; ++j) {
for (UInt k = 0; k < 2; ++k) {
for (UInt m = 0; m < 2; ++m) {
UInt index1 = m;
UInt index2 = (2 - 1) - m;
Bvoigt(2, j * 2 + k) += grad_u(k, index1) * B(index2, j);
}
}
}
}
} // namespace akantu
-#endif /* __AKANTU_AKA_VOIGTHELPER_TMPL_HH__ */
+#endif /* AKANTU_AKA_VOIGTHELPER_TMPL_HH_ */
diff --git a/src/fe_engine/cohesive_element.hh b/src/fe_engine/cohesive_element.hh
index 30cb04006..2e7367366 100644
--- a/src/fe_engine/cohesive_element.hh
+++ b/src/fe_engine/cohesive_element.hh
@@ -1,89 +1,89 @@
/**
* @file cohesive_element.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Oct 11 2017
*
* @brief Generates the cohesive element structres (defined in
* element_class.hh)
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COHESIVE_ELEMENT_HH__
-#define __AKANTU_COHESIVE_ELEMENT_HH__
+#ifndef AKANTU_COHESIVE_ELEMENT_HH_
+#define AKANTU_COHESIVE_ELEMENT_HH_
namespace akantu {
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_2d_4, _gt_cohesive_2d_4,
_itp_lagrange_segment_2, _ek_cohesive, 2,
_git_segment, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_2d_6, _gt_cohesive_2d_6,
_itp_lagrange_segment_3, _ek_cohesive, 2,
_git_segment, 3);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_1d_2, _gt_cohesive_1d_2,
_itp_lagrange_point_1, _ek_cohesive, 1,
_git_point, 1);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_6, _gt_cohesive_3d_6,
_itp_lagrange_triangle_3, _ek_cohesive, 3,
_git_triangle, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_12, _gt_cohesive_3d_12,
_itp_lagrange_triangle_6, _ek_cohesive, 3,
_git_triangle, 3);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_8, _gt_cohesive_3d_8,
_itp_lagrange_quadrangle_4, _ek_cohesive,
3, _git_segment, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_16, _gt_cohesive_3d_16,
_itp_serendip_quadrangle_8, _ek_cohesive,
3, _git_segment, 3);
template <ElementType> struct CohesiveFacetProperty {
static const ElementType cohesive_type = _not_defined;
};
#define AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(ftype, ctype) \
template <> struct CohesiveFacetProperty<ftype> { \
static const ElementType cohesive_type = ctype; \
}
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_point_1, _cohesive_1d_2);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_segment_2, _cohesive_2d_4);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_segment_3, _cohesive_2d_6);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_triangle_3, _cohesive_3d_6);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_triangle_6, _cohesive_3d_12);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_quadrangle_4, _cohesive_3d_8);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_quadrangle_8, _cohesive_3d_16);
} // namespace akantu
-#endif /* __AKANTU_COHESIVE_ELEMENT_HH__ */
+#endif /* AKANTU_COHESIVE_ELEMENT_HH_ */
diff --git a/src/fe_engine/element.hh b/src/fe_engine/element.hh
index cd3aab32a..64891a668 100644
--- a/src/fe_engine/element.hh
+++ b/src/fe_engine/element.hh
@@ -1,127 +1,127 @@
/**
* @file element.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Tue Jan 23 2018
*
* @brief Element helper class
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_HH__
-#define __AKANTU_ELEMENT_HH__
+#ifndef AKANTU_ELEMENT_HH_
+#define AKANTU_ELEMENT_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Element */
/* -------------------------------------------------------------------------- */
class Element {
public:
ElementType type;
UInt element;
GhostType ghost_type;
// ElementKind kind;
// ElementType type{_not_defined};
// UInt element{0};
// GhostType ghost_type{_not_ghost};
// ElementKind kind{_ek_regular};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline ElementKind kind() const;
inline bool operator==(const Element & elem) const {
return std::tie(type, element, ghost_type) ==
std::tie(elem.type, elem.element, elem.ghost_type);
}
inline bool operator!=(const Element & elem) const {
return std::tie(type, element, ghost_type) !=
std::tie(elem.type, elem.element, elem.ghost_type);
}
// inline bool operator==(const Element & elem) const {
// return ((element == elem.element) && (type == elem.type) &&
// (ghost_type == elem.ghost_type) && (kind == elem.kind));
// }
// inline bool operator!=(const Element & elem) const {
// return ((element != elem.element) || (type != elem.type) ||
// (ghost_type != elem.ghost_type) || (kind != elem.kind));
// }
inline bool operator<(const Element & rhs) const;
};
namespace {
const Element ElementNull{_not_defined, UInt(-1), _casper};
// Element{_not_defined, 0, _casper, _ek_not_defined};
} // namespace
/* -------------------------------------------------------------------------- */
inline bool Element::operator<(const Element & rhs) const {
// bool res =
// (rhs == ElementNull) ||
// ((this->kind < rhs.kind) ||
// ((this->kind == rhs.kind) &&
// ((this->ghost_type < rhs.ghost_type) ||
// ((this->ghost_type == rhs.ghost_type) &&
// ((this->type < rhs.type) ||
// ((this->type == rhs.type) && (this->element < rhs.element)))))));
return ((rhs == ElementNull) ||
std::tie(ghost_type, type, element) <
std::tie(rhs.ghost_type, rhs.type, rhs.element));
}
} // namespace akantu
namespace std {
inline string to_string(const akantu::Element & _this) {
if (_this == akantu::ElementNull) {
return "ElementNull";
}
string str = "Element [" + to_string(_this.type) + ", " +
to_string(_this.element) + ", " + to_string(_this.ghost_type) +
"]";
return str;
}
} // namespace std
namespace akantu {
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Element & _this) {
stream << std::to_string(_this);
return stream;
}
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_HH__ */
+#endif /* AKANTU_ELEMENT_HH_ */
diff --git a/src/fe_engine/element_class.hh b/src/fe_engine/element_class.hh
index 6d91f8f69..4d3c747bf 100644
--- a/src/fe_engine/element_class.hh
+++ b/src/fe_engine/element_class.hh
@@ -1,407 +1,410 @@
/**
* @file element_class.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Declaration of the ElementClass main class and the
* Integration and Interpolation elements
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_CLASS_HH__
-#define __AKANTU_ELEMENT_CLASS_HH__
+#ifndef AKANTU_ELEMENT_CLASS_HH_
+#define AKANTU_ELEMENT_CLASS_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/// default element class structure
template <ElementType element_type> struct ElementClassProperty {
static const GeometricalType geometrical_type{_gt_not_defined};
static const InterpolationType interpolation_type{_itp_not_defined};
static const ElementKind element_kind{_ek_regular};
static const UInt spatial_dimension{0};
static const GaussIntegrationType gauss_integration_type{_git_not_defined};
static const UInt polynomial_degree{0};
};
#if !defined(DOXYGEN)
/// Macro to generate the element class structures for different element types
#define AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(elem_type, geom_type, \
interp_type, elem_kind, sp, \
gauss_int_type, min_int_order) \
template <> struct ElementClassProperty<elem_type> { \
static const GeometricalType geometrical_type{geom_type}; \
static const InterpolationType interpolation_type{interp_type}; \
static const ElementKind element_kind{elem_kind}; \
static const UInt spatial_dimension{sp}; \
static const GaussIntegrationType gauss_integration_type{gauss_int_type}; \
static const UInt polynomial_degree{min_int_order}; \
}
#else
#define AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(elem_type, geom_type, \
interp_type, elem_kind, sp, \
gauss_int_type, min_int_order)
#endif
/* -------------------------------------------------------------------------- */
/* Geometry */
/* -------------------------------------------------------------------------- */
/// Default GeometricalShape structure
template <GeometricalType geometrical_type> struct GeometricalShape {
static const GeometricalShapeType shape{_gst_point};
};
/// Templated GeometricalShape with function contains
template <GeometricalShapeType shape> struct GeometricalShapeContains {
/// Check if the point (vector in 2 and 3D) at natural coordinate coor
template <class vector_type>
static inline bool contains(const vector_type & coord);
};
#if !defined(DOXYGEN)
/// Macro to generate the GeometricalShape structures for different geometrical
/// types
#define AKANTU_DEFINE_SHAPE(geom_type, geom_shape) \
template <> struct GeometricalShape<geom_type> { \
static const GeometricalShapeType shape{geom_shape}; \
}
AKANTU_DEFINE_SHAPE(_gt_hexahedron_20, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_hexahedron_8, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_pentahedron_15, _gst_prism);
AKANTU_DEFINE_SHAPE(_gt_pentahedron_6, _gst_prism);
AKANTU_DEFINE_SHAPE(_gt_point, _gst_point);
AKANTU_DEFINE_SHAPE(_gt_quadrangle_4, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_quadrangle_8, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_segment_2, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_segment_3, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_tetrahedron_10, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_tetrahedron_4, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_triangle_3, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_triangle_6, _gst_triangle);
#endif
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type>
struct GeometricalElementProperty {};
template <ElementType element_type>
struct ElementClassExtraGeometryProperties {};
/* -------------------------------------------------------------------------- */
/// Templated GeometricalElement with function getInradius
template <GeometricalType geometrical_type,
GeometricalShapeType shape =
GeometricalShape<geometrical_type>::shape>
class GeometricalElement {
using geometrical_property = GeometricalElementProperty<geometrical_type>;
public:
/// compute the in-radius: \todo should be renamed for characteristic length
static inline Real getInradius(const Matrix<Real> & /*coord*/) {
AKANTU_TO_IMPLEMENT();
}
/// true if the natural coordinates are in the element
template <class vector_type>
static inline bool contains(const vector_type & coord);
public:
static AKANTU_GET_MACRO_NOT_CONST(SpatialDimension,
geometrical_property::spatial_dimension,
UInt);
static AKANTU_GET_MACRO_NOT_CONST(NbNodesPerElement,
geometrical_property::nb_nodes_per_element,
UInt);
static inline constexpr auto getNbFacetTypes() {
return geometrical_property::nb_facet_types;
};
static inline UInt getNbFacetsPerElement(UInt t);
static inline UInt getNbFacetsPerElement();
static inline constexpr auto getFacetLocalConnectivityPerElement(UInt t = 0);
};
/* -------------------------------------------------------------------------- */
/* Interpolation */
/* -------------------------------------------------------------------------- */
/// default InterpolationProperty structure
template <InterpolationType interpolation_type> struct InterpolationProperty {};
#if !defined(DOXYGEN)
/// Macro to generate the InterpolationProperty structures for different
/// interpolation types
#define AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(itp_type, itp_kind, \
nb_nodes, ndim) \
template <> struct InterpolationProperty<itp_type> { \
static constexpr InterpolationKind kind{itp_kind}; \
static constexpr UInt nb_nodes_per_element{nb_nodes}; \
static constexpr UInt natural_space_dimension{ndim}; \
}
#else
#define AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(itp_type, itp_kind, \
nb_nodes, ndim)
#endif
/* -------------------------------------------------------------------------- */
/// Generic (templated by the enum InterpolationType which specifies the order
/// and the dimension of the interpolation) class handling the elemental
/// interpolation
template <InterpolationType interpolation_type,
InterpolationKind kind =
InterpolationProperty<interpolation_type>::kind>
class InterpolationElement {
public:
using interpolation_property = InterpolationProperty<interpolation_type>;
/// compute the shape values for a given set of points in natural coordinates
static inline void computeShapes(const Matrix<Real> & natural_coord,
Matrix<Real> & N);
/// compute the shape values for a given point in natural coordinates
template <class vector_type>
- static inline void computeShapes(const vector_type &, vector_type &) {
+ static inline void computeShapes(const vector_type & /*unused*/,
+ vector_type & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with variation of natural coordinates on a given set
* of points in natural coordinates
*/
static inline void computeDNDS(const Matrix<Real> & natural_coord,
Tensor3<Real> & dnds);
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with
* variation of natural coordinates on a given point in natural
* coordinates
*/
template <class vector_type, class matrix_type>
- static inline void computeDNDS(const vector_type &, matrix_type &) {
+ static inline void computeDNDS(const vector_type & /*unused*/,
+ matrix_type & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
/// compute jacobian (or integration variable change factor) for a given point
/// in the case of spatial_dimension != natural_space_dimension
- static inline void computeSpecialJacobian(const Matrix<Real> &, Real &) {
+ static inline void computeSpecialJacobian(const Matrix<Real> & /*unused*/,
+ Real & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
/// interpolate a field given (arbitrary) natural coordinates
static inline void
interpolateOnNaturalCoordinates(const Vector<Real> & natural_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated);
/// interpolate a field given the shape functions on the interpolation point
static inline void interpolate(const Matrix<Real> & nodal_values,
const Vector<Real> & shapes,
Vector<Real> & interpolated);
/// interpolate a field given the shape functions on the interpolations points
static inline void interpolate(const Matrix<Real> & nodal_values,
const Matrix<Real> & shapes,
Matrix<Real> & interpolated);
/// compute the gradient of a given field on the given natural coordinates
static inline void
gradientOnNaturalCoordinates(const Vector<Real> & natural_coords,
const Matrix<Real> & f, Matrix<Real> & gradient);
public:
static AKANTU_GET_MACRO_NOT_CONST(
ShapeSize,
InterpolationProperty<interpolation_type>::nb_nodes_per_element, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
ShapeDerivativesSize,
(InterpolationProperty<interpolation_type>::nb_nodes_per_element *
InterpolationProperty<interpolation_type>::natural_space_dimension),
UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NaturalSpaceDimension,
InterpolationProperty<interpolation_type>::natural_space_dimension, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NbNodesPerInterpolationElement,
InterpolationProperty<interpolation_type>::nb_nodes_per_element, UInt);
};
/* -------------------------------------------------------------------------- */
/* Integration */
/* -------------------------------------------------------------------------- */
template <GaussIntegrationType git_class, UInt nb_points>
struct GaussIntegrationTypeData {
/// quadrature points in natural coordinates
static Real quad_positions[];
/// weights for the Gauss integration
static Real quad_weights[];
};
template <ElementType type,
UInt n = ElementClassProperty<type>::polynomial_degree>
class GaussIntegrationElement {
public:
static UInt getNbQuadraturePoints();
- static const Matrix<Real> getQuadraturePoints();
- static const Vector<Real> getWeights();
+ static Matrix<Real> getQuadraturePoints();
+ static Vector<Real> getWeights();
};
/* -------------------------------------------------------------------------- */
/* ElementClass */
/* -------------------------------------------------------------------------- */
template <ElementType element_type,
ElementKind element_kind =
ElementClassProperty<element_type>::element_kind>
class ElementClass
: public GeometricalElement<
ElementClassProperty<element_type>::geometrical_type>,
public InterpolationElement<
ElementClassProperty<element_type>::interpolation_type> {
protected:
using geometrical_element =
GeometricalElement<ElementClassProperty<element_type>::geometrical_type>;
using interpolation_element = InterpolationElement<
ElementClassProperty<element_type>::interpolation_type>;
using element_property = ElementClassProperty<element_type>;
using interpolation_property =
typename interpolation_element::interpolation_property;
public:
/**
* compute @f$ J = \frac{\partial x_j}{\partial s_i} @f$ the variation of real
* coordinates along with variation of natural coordinates on a given point in
* natural coordinates
*/
static inline void computeJMat(const Matrix<Real> & dnds,
const Matrix<Real> & node_coords,
Matrix<Real> & J);
/**
* compute the Jacobian matrix by computing the variation of real coordinates
* along with variation of natural coordinates on a given set of points in
* natural coordinates
*/
static inline void computeJMat(const Tensor3<Real> & dnds,
const Matrix<Real> & node_coords,
Tensor3<Real> & J);
/// compute the jacobians of a serie of natural coordinates
static inline void computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians);
/// compute jacobian (or integration variable change factor) for a set of
/// points
static inline void computeJacobian(const Tensor3<Real> & J,
Vector<Real> & jacobians);
/// compute jacobian (or integration variable change factor) for a given point
static inline void computeJacobian(const Matrix<Real> & J, Real & jacobians);
/// compute shape derivatives (input is dxds) for a set of points
static inline void computeShapeDerivatives(const Tensor3<Real> & J,
const Tensor3<Real> & dnds,
Tensor3<Real> & shape_deriv);
/// compute shape derivatives (input is dxds) for a given point
static inline void computeShapeDerivatives(const Matrix<Real> & J,
const Matrix<Real> & dnds,
Matrix<Real> & shape_deriv);
/// compute the normal of a surface defined by the function f
static inline void
computeNormalsOnNaturalCoordinates(const Matrix<Real> & coord,
Matrix<Real> & f, Matrix<Real> & normals);
/// get natural coordinates from real coordinates
static inline void inverseMap(const Vector<Real> & real_coords,
const Matrix<Real> & node_coords,
Vector<Real> & natural_coords,
Real tolerance = 1e-10);
/// get natural coordinates from real coordinates
static inline void inverseMap(const Matrix<Real> & real_coords,
const Matrix<Real> & node_coords,
Matrix<Real> & natural_coords,
Real tolerance = 1e-10);
public:
static AKANTU_GET_MACRO_NOT_CONST(Kind, element_kind, ElementKind);
static constexpr AKANTU_GET_MACRO_NOT_CONST(
SpatialDimension, ElementClassProperty<element_type>::spatial_dimension,
UInt);
using element_class_extra_geom_property =
ElementClassExtraGeometryProperties<element_type>;
static constexpr auto getP1ElementType() {
return element_class_extra_geom_property::p1_type;
}
static constexpr auto getFacetType(UInt t = 0) {
return element_class_extra_geom_property::facet_type[t];
}
static constexpr auto getFacetTypes();
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "geometrical_element_property.hh"
#include "interpolation_element_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "element_class_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "element_class_hexahedron_8_inline_impl.hh"
#include "element_class_pentahedron_6_inline_impl.hh"
/* keep order */
#include "element_class_hexahedron_20_inline_impl.hh"
#include "element_class_pentahedron_15_inline_impl.hh"
#include "element_class_point_1_inline_impl.hh"
#include "element_class_quadrangle_4_inline_impl.hh"
#include "element_class_quadrangle_8_inline_impl.hh"
#include "element_class_segment_2_inline_impl.hh"
#include "element_class_segment_3_inline_impl.hh"
#include "element_class_tetrahedron_10_inline_impl.hh"
#include "element_class_tetrahedron_4_inline_impl.hh"
#include "element_class_triangle_3_inline_impl.hh"
#include "element_class_triangle_6_inline_impl.hh"
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "element_class_structural.hh"
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "cohesive_element.hh"
#endif
#if defined(AKANTU_IGFEM)
#include "element_class_igfem.hh"
#endif
-#endif /* __AKANTU_ELEMENT_CLASS_HH__ */
+#endif /* AKANTU_ELEMENT_CLASS_HH_ */
diff --git a/src/fe_engine/element_class_structural.hh b/src/fe_engine/element_class_structural.hh
index a86cdcee1..2d9ae92a9 100644
--- a/src/fe_engine/element_class_structural.hh
+++ b/src/fe_engine/element_class_structural.hh
@@ -1,253 +1,253 @@
/**
* @file element_class_structural.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Tue Feb 20 2018
*
* @brief Specialization of the element classes for structural elements
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_CLASS_STRUCTURAL_HH__
-#define __AKANTU_ELEMENT_CLASS_STRUCTURAL_HH__
+#ifndef AKANTU_ELEMENT_CLASS_STRUCTURAL_HH_
+#define AKANTU_ELEMENT_CLASS_STRUCTURAL_HH_
namespace akantu {
/// Macro to generate the InterpolationProperty structures for different
/// interpolation types
#define AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY( \
itp_type, itp_geom_type, ndof, nb_stress, nb_dnds_cols) \
template <> struct InterpolationProperty<itp_type> { \
static const InterpolationKind kind{_itk_structural}; \
static const UInt nb_nodes_per_element{ \
InterpolationProperty<itp_geom_type>::nb_nodes_per_element}; \
static const InterpolationType itp_geometry_type{itp_geom_type}; \
static const UInt natural_space_dimension{ \
InterpolationProperty<itp_geom_type>::natural_space_dimension}; \
static const UInt nb_degree_of_freedom{ndof}; \
static const UInt nb_stress_components{nb_stress}; \
static const UInt dnds_columns{nb_dnds_cols}; \
}
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type>
class InterpolationElement<interpolation_type, _itk_structural> {
public:
using interpolation_property = InterpolationProperty<interpolation_type>;
/// compute the shape values for a given set of points in natural coordinates
static inline void computeShapes(const Matrix<Real> & natural_coord,
const Matrix<Real> & real_coord,
Tensor3<Real> & N) {
for (UInt i = 0; i < natural_coord.cols(); ++i) {
Matrix<Real> n_t = N(i);
computeShapes(natural_coord(i), real_coord, n_t);
}
}
/// compute the shape values for a given point in natural coordinates
static inline void computeShapes(const Vector<Real> & natural_coord,
const Matrix<Real> & real_coord,
Matrix<Real> & N);
/// compute shape derivatives (input is dxds) for a set of points
static inline void computeShapeDerivatives(const Tensor3<Real> & Js,
const Tensor3<Real> & DNDSs,
const Matrix<Real> & R,
Tensor3<Real> & Bs) {
for (UInt i = 0; i < Js.size(2); ++i) {
Matrix<Real> J = Js(i);
Matrix<Real> DNDS = DNDSs(i);
Matrix<Real> DNDX(DNDS.rows(), DNDS.cols());
auto inv_J = J.inverse();
DNDX.mul<false, false>(inv_J, DNDS);
Matrix<Real> B_R = Bs(i);
Matrix<Real> B(B_R.rows(), B_R.cols());
arrangeInVoigt(DNDX, B);
B_R.mul<false, false>(B, R);
}
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with variation of natural coordinates on a given set
* of points in natural coordinates
*/
static inline void computeDNDS(const Matrix<Real> & natural_coord,
const Matrix<Real> & real_coord,
Tensor3<Real> & dnds) {
for (UInt i = 0; i < natural_coord.cols(); ++i) {
Matrix<Real> dnds_t = dnds(i);
computeDNDS(natural_coord(i), real_coord, dnds_t);
}
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with
* variation of natural coordinates on a given point in natural
* coordinates
*/
static inline void computeDNDS(const Vector<Real> & natural_coord,
const Matrix<Real> & real_coord,
Matrix<Real> & dnds);
/**
* arrange B in Voigt notation from DNDS
*/
static inline void arrangeInVoigt(const Matrix<Real> & dnds,
Matrix<Real> & B) {
// Default implementation assumes dnds is already in Voigt notation
B.deepCopy(dnds);
}
public:
static inline constexpr auto getNbNodesPerInterpolationElement() {
return interpolation_property::nb_nodes_per_element;
}
static inline constexpr auto getShapeSize() {
return interpolation_property::nb_nodes_per_element *
interpolation_property::nb_degree_of_freedom *
interpolation_property::nb_degree_of_freedom;
}
static inline constexpr auto getShapeDerivativesSize() {
return interpolation_property::nb_nodes_per_element *
interpolation_property::nb_degree_of_freedom *
interpolation_property::nb_stress_components;
}
static inline constexpr auto getNaturalSpaceDimension() {
return interpolation_property::natural_space_dimension;
}
static inline constexpr auto getNbDegreeOfFreedom() {
return interpolation_property::nb_degree_of_freedom;
}
static inline constexpr auto getNbStressComponents() {
return interpolation_property::nb_stress_components;
}
};
/// Macro to generate the element class structures for different structural
/// element types
/* -------------------------------------------------------------------------- */
#define AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY( \
elem_type, geom_type, interp_type, parent_el_type, elem_kind, sp, \
gauss_int_type, min_int_order) \
template <> struct ElementClassProperty<elem_type> { \
static const GeometricalType geometrical_type{geom_type}; \
static const InterpolationType interpolation_type{interp_type}; \
static const ElementType parent_element_type{parent_el_type}; \
static const ElementKind element_kind{elem_kind}; \
static const UInt spatial_dimension{sp}; \
static const GaussIntegrationType gauss_integration_type{gauss_int_type}; \
static const UInt polynomial_degree{min_int_order}; \
}
/* -------------------------------------------------------------------------- */
/* ElementClass for structural elements */
/* -------------------------------------------------------------------------- */
template <ElementType element_type>
class ElementClass<element_type, _ek_structural>
: public GeometricalElement<
ElementClassProperty<element_type>::geometrical_type>,
public InterpolationElement<
ElementClassProperty<element_type>::interpolation_type> {
protected:
using geometrical_element =
GeometricalElement<ElementClassProperty<element_type>::geometrical_type>;
using interpolation_element = InterpolationElement<
ElementClassProperty<element_type>::interpolation_type>;
using parent_element =
ElementClass<ElementClassProperty<element_type>::parent_element_type>;
public:
static inline void
computeRotationMatrix(Matrix<Real> & /*R*/, const Matrix<Real> & /*X*/,
const Vector<Real> & /*extra_normal*/) {
AKANTU_TO_IMPLEMENT();
}
/// compute jacobian (or integration variable change factor) for a given point
static inline void computeJMat(const Vector<Real> & natural_coords,
const Matrix<Real> & Xs, Matrix<Real> & J) {
Matrix<Real> dnds(Xs.rows(), Xs.cols());
parent_element::computeDNDS(natural_coords, dnds);
J.mul<false, true>(dnds, Xs);
}
static inline void computeJMat(const Matrix<Real> & natural_coords,
const Matrix<Real> & Xs, Tensor3<Real> & Js) {
for (UInt i = 0; i < natural_coords.cols(); ++i) {
// because non-const l-value reference does not bind to r-value
Matrix<Real> J = Js(i);
computeJMat(Vector<Real>(natural_coords(i)), Xs, J);
}
}
static inline void computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians) {
using itp = typename interpolation_element::interpolation_property;
Tensor3<Real> Js(itp::natural_space_dimension, itp::natural_space_dimension,
natural_coords.cols());
computeJMat(natural_coords, node_coords, Js);
for (UInt i = 0; i < natural_coords.cols(); ++i) {
Matrix<Real> J = Js(i);
jacobians(i) = J.det();
}
}
static inline void computeRotation(const Matrix<Real> & node_coords,
Matrix<Real> & rotation);
public:
static AKANTU_GET_MACRO_NOT_CONST(Kind, _ek_structural, ElementKind);
static AKANTU_GET_MACRO_NOT_CONST(P1ElementType, _not_defined, ElementType);
static AKANTU_GET_MACRO_NOT_CONST(FacetType, _not_defined, ElementType);
static constexpr auto getFacetType(__attribute__((unused)) UInt t = 0) {
return _not_defined;
}
static constexpr AKANTU_GET_MACRO_NOT_CONST(
SpatialDimension, ElementClassProperty<element_type>::spatial_dimension,
UInt);
static constexpr auto getFacetTypes() {
return ElementClass<_not_defined>::getFacetTypes();
}
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "element_class_hermite_inline_impl.hh"
/* keep order */
#include "element_class_bernoulli_beam_inline_impl.hh"
#include "element_class_kirchhoff_shell_inline_impl.hh"
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_ELEMENT_CLASS_STRUCTURAL_HH__ */
+#endif /* AKANTU_ELEMENT_CLASS_STRUCTURAL_HH_ */
diff --git a/src/fe_engine/element_class_tmpl.hh b/src/fe_engine/element_class_tmpl.hh
index 077888111..29ccf67a9 100644
--- a/src/fe_engine/element_class_tmpl.hh
+++ b/src/fe_engine/element_class_tmpl.hh
@@ -1,530 +1,532 @@
/**
* @file element_class_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Nov 29 2017
*
* @brief Implementation of the inline templated function of the element class
* descriptions
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "gauss_integration_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_CLASS_TMPL_HH__
-#define __AKANTU_ELEMENT_CLASS_TMPL_HH__
+#ifndef AKANTU_ELEMENT_CLASS_TMPL_HH_
+#define AKANTU_ELEMENT_CLASS_TMPL_HH_
namespace akantu {
template <ElementType element_type, ElementKind element_kind>
inline constexpr auto
ElementClass<element_type, element_kind>::getFacetTypes() {
return VectorProxy<const ElementType>(
element_class_extra_geom_property::facet_type.data(),
geometrical_element::getNbFacetTypes());
}
/* -------------------------------------------------------------------------- */
/* GeometricalElement */
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline constexpr auto
GeometricalElement<geometrical_type,
shape>::getFacetLocalConnectivityPerElement(UInt t) {
int pos = 0;
for (UInt i = 0; i < t; ++i) {
pos += geometrical_property::nb_facets[i] *
geometrical_property::nb_nodes_per_facet[i];
}
return MatrixProxy<const UInt>(
geometrical_property::facet_connectivity_vect.data() + pos,
geometrical_property::nb_facets[t],
geometrical_property::nb_nodes_per_facet[t]);
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement() {
UInt total_nb_facets = 0;
for (UInt n = 0; n < geometrical_property::nb_facet_types; ++n) {
total_nb_facets += geometrical_property::nb_facets[n];
}
return total_nb_facets;
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement(UInt t) {
return geometrical_property::nb_facets[t];
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
template <class vector_type>
inline bool GeometricalElement<geometrical_type, shape>::contains(
const vector_type & coords) {
return GeometricalShapeContains<shape>::contains(coords);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_point>::contains(const vector_type & coords) {
return (coords(0) < std::numeric_limits<Real>::epsilon());
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_square>::contains(const vector_type & coords) {
bool in = true;
- for (UInt i = 0; i < coords.size() && in; ++i)
+ for (UInt i = 0; i < coords.size() && in; ++i) {
in &= ((coords(i) >= -(1. + std::numeric_limits<Real>::epsilon())) &&
(coords(i) <= (1. + std::numeric_limits<Real>::epsilon())));
+ }
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_triangle>::contains(const vector_type & coords) {
bool in = true;
Real sum = 0;
for (UInt i = 0; (i < coords.size()) && in; ++i) {
in &= ((coords(i) >= -(Math::getTolerance())) &&
(coords(i) <= (1. + Math::getTolerance())));
sum += coords(i);
}
- if (in)
+ if (in) {
return (in && (sum <= (1. + Math::getTolerance())));
+ }
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_prism>::contains(const vector_type & coords) {
bool in = ((coords(0) >= -1.) && (coords(0) <= 1.)); // x in segment [-1, 1]
// y and z in triangle
in &= ((coords(1) >= 0) && (coords(1) <= 1.));
in &= ((coords(2) >= 0) && (coords(2) <= 1.));
Real sum = coords(1) + coords(2);
return (in && (sum <= 1));
}
/* -------------------------------------------------------------------------- */
/* InterpolationElement */
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeShapes(
const Matrix<Real> & natural_coord, Matrix<Real> & N) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(N(p));
Vector<Real> ncoord_p(natural_coord(p));
computeShapes(ncoord_p, Np);
}
}
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeDNDS(
const Matrix<Real> & natural_coord, Tensor3<Real> & dnds) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> dnds_p(dnds(p));
Vector<Real> ncoord_p(natural_coord(p));
computeDNDS(ncoord_p, dnds_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on a point a field for which values are given on the
* node of the element using the shape functions at this interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Vector<Real> & shapes,
Vector<Real> & interpolated) {
Matrix<Real> interpm(interpolated.storage(), nodal_values.rows(), 1);
Matrix<Real> shapesm(
shapes.storage(),
InterpolationProperty<interpolation_type>::nb_nodes_per_element, 1);
interpm.mul<false, false>(nodal_values, shapesm);
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on several points a field for which values are given on the
* node of the element using the shape functions at the interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated values of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Matrix<Real> & shapes,
Matrix<Real> & interpolated) {
UInt nb_points = shapes.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(shapes(p));
Vector<Real> interpolated_p(interpolated(p));
interpolate(nodal_values, Np, interpolated_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate the field on a point given in natural coordinates the field which
* values are given on the node of the element
*
* @param natural_coords natural coordinates of point where to interpolate \xi
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::interpolateOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & nodal_values,
Vector<Real> & interpolated) {
Vector<Real> shapes(
InterpolationProperty<interpolation_type>::nb_nodes_per_element);
computeShapes(natural_coords, shapes);
interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
/// @f$ gradient_{ij} = \frac{\partial f_j}{\partial s_i} = \sum_k
/// \frac{\partial N_k}{\partial s_i}f_{j n_k} @f$
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::gradientOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & f,
Matrix<Real> & gradient) {
Matrix<Real> dnds(
InterpolationProperty<interpolation_type>::natural_space_dimension,
InterpolationProperty<interpolation_type>::nb_nodes_per_element);
computeDNDS(natural_coords, dnds);
gradient.mul<false, true>(f, dnds);
}
/* -------------------------------------------------------------------------- */
/* ElementClass */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Tensor3<Real> & dnds,
const Matrix<Real> & node_coords,
Tensor3<Real> & J) {
UInt nb_points = dnds.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> J_p(J(p));
Matrix<Real> dnds_p(dnds(p));
computeJMat(dnds_p, node_coords, J_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Matrix<Real> & dnds,
const Matrix<Real> & node_coords,
Matrix<Real> & J) {
/// @f$ J = dxds = dnds * x @f$
J.mul<false, true>(dnds, node_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians) {
UInt nb_points = natural_coords.cols();
Matrix<Real> dnds(interpolation_property::natural_space_dimension,
interpolation_property::nb_nodes_per_element);
Matrix<Real> J(natural_coords.rows(), node_coords.rows());
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> ncoord_p(natural_coords(p));
interpolation_element::computeDNDS(ncoord_p, dnds);
computeJMat(dnds, node_coords, J);
computeJacobian(J, jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Tensor3<Real> & J,
Vector<Real> & jacobians) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
computeJacobian(J(p), jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeJacobian(const Matrix<Real> & J,
Real & jacobians) {
if (J.rows() == J.cols()) {
jacobians = Math::det<element_property::spatial_dimension>(J.storage());
} else {
interpolation_element::computeSpecialJacobian(J, jacobians);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Tensor3<Real> & J,
const Tensor3<Real> & dnds,
Tensor3<Real> & shape_deriv) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> shape_deriv_p(shape_deriv(p));
computeShapeDerivatives(J(p), dnds(p), shape_deriv_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Matrix<Real> & J,
const Matrix<Real> & dnds,
Matrix<Real> & shape_deriv) {
Matrix<Real> inv_J(J.rows(), J.cols());
Math::inv<element_property::spatial_dimension>(J.storage(), inv_J.storage());
shape_deriv.mul<false, false>(inv_J, dnds);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeNormalsOnNaturalCoordinates(
const Matrix<Real> & coord, Matrix<Real> & f, Matrix<Real> & normals) {
UInt dimension = normals.rows();
UInt nb_points = coord.cols();
AKANTU_DEBUG_ASSERT((dimension - 1) ==
interpolation_property::natural_space_dimension,
"cannot extract a normal because of dimension mismatch "
<< dimension - 1 << " "
<< interpolation_property::natural_space_dimension);
Matrix<Real> J(dimension, interpolation_property::natural_space_dimension);
for (UInt p = 0; p < nb_points; ++p) {
interpolation_element::gradientOnNaturalCoordinates(coord(p), f, J);
if (dimension == 2) {
Math::normal2(J.storage(), normals(p).storage());
}
if (dimension == 3) {
Math::normal3(J(0).storage(), J(1).storage(), normals(p).storage());
}
}
}
/* ------------------------------------------------------------------------- */
/**
* In the non linear cases we need to iterate to find the natural coordinates
*@f$\xi@f$
* provided real coordinates @f$x@f$.
*
* We want to solve: @f$ x- \phi(\xi) = 0@f$ with @f$\phi(\xi) = \sum_I N_I(\xi)
*x_I@f$
* the mapping function which uses the nodal coordinates @f$x_I@f$.
*
* To that end we use the Newton method and the following series:
*
* @f$ \frac{\partial \phi(x_k)}{\partial \xi} \left( \xi_{k+1} - \xi_k \right)
*= x - \phi(x_k)@f$
*
* When we consider elements embedded in a dimension higher than them (2D
*triangle in a 3D space for example)
* @f$ J = \frac{\partial \phi(\xi_k)}{\partial \xi}@f$ is of dimension
*@f$dim_{space} \times dim_{elem}@f$ which
* is not invertible in most cases. Rather we can solve the problem:
*
* @f$ J^T J \left( \xi_{k+1} - \xi_k \right) = J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that
*
* @f$ d\xi = \xi_{k+1} - \xi_k = (J^T J)^{-1} J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that if the series converges we have:
*
* @f$ 0 = J^T \left( \phi(\xi_\infty) - x \right) @f$
*
* And we see that this is ill-posed only if @f$ J^T x = 0@f$ which means that
*the vector provided
* is normal to any tangent which means it is outside of the element itself.
*
* @param real_coords: the real coordinates the natural coordinates are sought
*for
* @param node_coords: the coordinates of the nodes forming the element
* @param natural_coords: output->the sought natural coordinates
* @param spatial_dimension: spatial dimension of the problem
*
**/
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Vector<Real> & real_coords, const Matrix<Real> & node_coords,
Vector<Real> & natural_coords, Real tolerance) {
UInt spatial_dimension = real_coords.size();
UInt dimension = natural_coords.size();
// matrix copy of the real_coords
Matrix<Real> mreal_coords(real_coords.storage(), spatial_dimension, 1);
// initial guess
// Matrix<Real> natural_guess(natural_coords.storage(), dimension, 1);
- natural_coords.clear();
+ natural_coords.zero();
// real space coordinates provided by initial guess
Matrix<Real> physical_guess(dimension, 1);
// objective function f = real_coords - physical_guess
Matrix<Real> f(dimension, 1);
// dnds computed on the natural_guess
// Matrix<Real> dnds(interpolation_element::nb_nodes_per_element,
// spatial_dimension);
// J Jacobian matrix computed on the natural_guess
Matrix<Real> J(spatial_dimension, dimension);
// G = J^t * J
Matrix<Real> G(spatial_dimension, spatial_dimension);
// Ginv = G^{-1}
Matrix<Real> Ginv(spatial_dimension, spatial_dimension);
// J = Ginv * J^t
Matrix<Real> F(spatial_dimension, dimension);
// dxi = \xi_{k+1} - \xi in the iterative process
Matrix<Real> dxi(spatial_dimension, 1);
/* --------------------------- */
/* init before iteration loop */
/* --------------------------- */
// do interpolation
auto update_f = [&f, &physical_guess, &natural_coords, &node_coords,
&mreal_coords, dimension]() {
Vector<Real> physical_guess_v(physical_guess.storage(), dimension);
interpolation_element::interpolateOnNaturalCoordinates(
natural_coords, node_coords, physical_guess_v);
// compute initial objective function value f = real_coords - physical_guess
f = mreal_coords;
f -= physical_guess;
// compute initial error
auto error = f.norm<L_2>();
return error;
};
auto inverse_map_error = update_f();
/* --------------------------- */
/* iteration loop */
/* --------------------------- */
while (tolerance < inverse_map_error) {
// compute J^t
interpolation_element::gradientOnNaturalCoordinates(natural_coords,
node_coords, J);
// compute G
G.mul<true, false>(J, J);
// inverse G
Ginv.inverse(G);
// compute F
F.mul<false, true>(Ginv, J);
// compute increment
dxi.mul<false, false>(F, f);
// update our guess
natural_coords += Vector<Real>(dxi(0));
inverse_map_error = update_f();
}
// memcpy(natural_coords.storage(), natural_guess.storage(), sizeof(Real) *
// natural_coords.size());
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Matrix<Real> & real_coords, const Matrix<Real> & node_coords,
Matrix<Real> & natural_coords, Real tolerance) {
UInt nb_points = real_coords.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> X(real_coords(p));
Vector<Real> ncoord_p(natural_coords(p));
inverseMap(X, node_coords, ncoord_p, tolerance);
}
}
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_CLASS_TMPL_HH__ */
+#endif /* AKANTU_ELEMENT_CLASS_TMPL_HH_ */
diff --git a/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh b/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh
index 4fff8a1d1..8145600a2 100644
--- a/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh
@@ -1,221 +1,223 @@
/**
* @file element_class_bernoulli_beam_inline_impl.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Mon Feb 19 2018
*
* @brief Specialization of the element_class class for the type
* _bernoulli_beam_2
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*
* @verbatim
--x-----q1----|----q2-----x---> x
-1 0 1
@endverbatim
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
#include "element_class_structural.hh"
//#include "aka_element_classes_info.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_HH__
-#define __AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_HH__
+#ifndef AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_HH_
+#define AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(_itp_bernoulli_beam_2,
_itp_lagrange_segment_2, 3,
2, 6);
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(_itp_bernoulli_beam_3,
_itp_lagrange_segment_2, 6,
4, 6);
AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY(_bernoulli_beam_2,
_gt_segment_2,
_itp_bernoulli_beam_2,
_segment_2, _ek_structural, 2,
_git_segment, 3);
AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY(_bernoulli_beam_3,
_gt_segment_2,
_itp_bernoulli_beam_3,
_segment_2, _ek_structural, 3,
_git_segment, 3);
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::computeShapes(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
Vector<Real> L(2);
InterpolationElement<_itp_lagrange_segment_2, _itk_lagrangian>::computeShapes(
natural_coords, L);
Matrix<Real> H(2, 4);
InterpolationElement<_itp_hermite_2, _itk_structural>::computeShapes(
natural_coords, real_coord, H);
// clang-format off
// u1 v1 t1 u2 v2 t2
N = {{L(0), 0 , 0 , L(1), 0 , 0 }, // u
{0 , H(0, 0), H(0, 1), 0 , H(0, 2), H(0, 3)}, // v
{0 , H(1, 0), H(1, 1), 0 , H(1, 2), H(1, 3)}}; // theta
// clang-format on
}
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::computeShapes(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
Vector<Real> L(2);
InterpolationElement<_itp_lagrange_segment_2, _itk_lagrangian>::computeShapes(
natural_coords, L);
Matrix<Real> H(2, 4);
InterpolationElement<_itp_hermite_2, _itk_structural>::computeShapes(
natural_coords, real_coord, H);
// clang-format off
// u1 v1 w1 x1 y1 z1 u2 v2 w2 x2 y2 z2
N = {{L(0), 0 , 0 , 0 , 0 , 0 , L(1), 0 , 0 , 0 , 0 , 0 }, // u
{0 , H(0, 0), 0 , 0 , H(0, 1), 0 , 0 , H(0, 2), 0 , 0 , H(0, 3), 0 }, // v
{0 , 0 , H(0, 0), 0 , 0 , H(0, 1), 0 , 0 , H(0, 2), 0 , 0 , H(0, 3)}, // w
{0 , 0 , 0 , L(0), 0 , 0 , 0 , 0 , 0 , L(1), 0 , 0 }, // thetax
{0 , H(1, 0), 0 , 0 , H(1, 1), 0 , 0 , H(1, 2), 0 , 0 , H(1, 3), 0 }, // thetay
{0 , 0 , H(1, 0), 0 , 0 , H(1, 1), 0 , 0 , H(1, 2), 0 , 0 , H(1, 3)}}; // thetaz
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & dnds) {
Matrix<Real> L(1, 2);
InterpolationElement<_itp_lagrange_segment_2, _itk_lagrangian>::computeDNDS(
natural_coords, L);
Matrix<Real> H(1, 4);
InterpolationElement<_itp_hermite_2, _itk_structural>::computeDNDS(
natural_coords, real_coord, H);
// Storing the derivatives in dnds
dnds.block(L, 0, 0);
dnds.block(H, 0, 2);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::arrangeInVoigt(
const Matrix<Real> & dnds, Matrix<Real> & B) {
auto L = dnds.block(0, 0, 1, 2); // Lagrange shape derivatives
auto H = dnds.block(0, 2, 1, 4); // Hermite shape derivatives
// clang-format off
// u1 v1 t1 u2 v2 t2
B = {{L(0, 0), 0, 0, L(0, 1), 0, 0 },
{0, H(0, 0), H(0, 1), 0, H(0, 2), H(0, 3)}};
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & dnds) {
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::computeDNDS(
natural_coords, real_coord, dnds);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::arrangeInVoigt(
const Matrix<Real> & dnds, Matrix<Real> & B) {
auto L = dnds.block(0, 0, 1, 2); // Lagrange shape derivatives
auto H = dnds.block(0, 2, 1, 4); // Hermite shape derivatives
// clang-format off
// u1 v1 w1 x1 y1 z1 u2 v2 w2 x2 y2 z2
B = {{L(0, 0), 0 , 0 , 0 , 0 , 0 , L(0, 1), 0 , 0 , 0 , 0 , 0 }, // eps
{0 , H(0, 0), 0 , 0 , 0 , H(0, 1), 0 , H(0, 2), 0 , 0 , 0 , H(0, 3)}, // chi strong axis
{0 , 0 ,-H(0, 0), 0 , H(0, 1), 0 , 0 , 0 ,-H(0, 2), 0 , H(0, 3), 0 }, // chi weak axis
{0 , 0 , 0 , L(0, 0), 0 , 0 , 0 , 0 , 0 , L(0, 1), 0 , 0 }}; // chi torsion
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void ElementClass<_bernoulli_beam_2>::computeRotationMatrix(
- Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> &) {
+ Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> & /*n*/) {
Vector<Real> x2 = X(1); // X2
Vector<Real> x1 = X(0); // X1
auto cs = (x2 - x1);
cs.normalize();
auto c = cs(0);
auto s = cs(1);
// clang-format off
/// Definition of the rotation matrix
R = {{ c, s, 0.},
{-s, c, 0.},
{ 0., 0., 1.}};
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void ElementClass<_bernoulli_beam_3>::computeRotationMatrix(
Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> & n) {
Vector<Real> x2 = X(1); // X2
Vector<Real> x1 = X(0); // X1
auto dim = X.rows();
auto x = (x2 - x1);
x.normalize();
auto x_n = x.crossProduct(n);
Matrix<Real> Pe = {{1., 0., 0.}, {0., -1., 0.}, {0., 0., 1.}};
Matrix<Real> Pg(dim, dim);
Pg(0) = x;
Pg(1) = x_n;
Pg(2) = n;
Pe *= Pg.inverse();
- R.clear();
+ R.zero();
/// Definition of the rotation matrix
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
R(i + dim, j + dim) = R(i, j) = Pe(i, j);
+ }
+ }
}
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_HH__ */
+#endif /* AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/element_classes/element_class_hermite_inline_impl.hh b/src/fe_engine/element_classes/element_class_hermite_inline_impl.hh
index 7905a92ae..cbb1c5949 100644
--- a/src/fe_engine/element_classes/element_class_hermite_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_hermite_inline_impl.hh
@@ -1,175 +1,175 @@
/**
* @file element_class_hermite_inline_impl.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Nov 10 2017
* @date last modification: Mon Feb 19 2018
*
* @brief Specialization of the element_class class for the type
* _hermite
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
terms of the GNU Lesser General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your option) any
later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
details.
*
* You should have received a copy of the GNU Lesser General Public License
along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*
* @verbatim
--x-----q1----|----q2-----x---> x
-1 0 1
@endverbatim
*
* @f[
* \begin{array}{ll}
* M_1(\xi) &= 1/4(\xi^{3}/-3\xi+2)\\
* M_2(\xi) &= -1/4(\xi^{3}-3\xi-2)
* \end{array}
*
* \begin{array}{ll}
* L_1(\xi) &= 1/4(\xi^{3}-\xi^{2}-\xi+1)\\
* L_2(\xi) &= 1/4(\xi^{3}+\xi^{2}-\xi-1)
* \end{array}
*
* \begin{array}{ll}
* M'_1(\xi) &= 3/4(\xi^{2}-1)\\
* M'_2(\xi) &= -3/4(\xi^{2}-1)
* \end{array}
*
* \begin{array}{ll}
* L'_1(\xi) &= 1/4(3\xi^{2}-2\xi-1)\\
* L'_2(\xi) &= 1/4(3\xi^{2}+2\xi-1)
* \end{array}
*@f]
*
*
*@f[
* \begin{array}{ll}
* N'_1(\xi) &= -1/2\\
* N'_2(\xi) &= 1/2
* \end{array}]
*
* \begin{array}{ll}
* -M''_1(\xi) &= -3\xi/2\\
* -M''_2(\xi) &= 3\xi/2\\
* \end{array}
*
* \begin{array}{ll}
* -L''_1(\xi) &= -1/2a(3\xi/a-1)\\
* -L''_2(\xi) &= -1/2a(3\xi/a+1)
* \end{array}
*@f]
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
#include "element_class_structural.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_HH__
-#define __AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_HH__
+#ifndef AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_HH_
+#define AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(_itp_hermite_2,
_itp_lagrange_segment_2, 2,
1, 4);
/* -------------------------------------------------------------------------- */
namespace {
namespace details {
inline Real computeLength(const Matrix<Real> & real_coord) {
Vector<Real> x1 = real_coord(0);
Vector<Real> x2 = real_coord(1);
return x1.distance(x2);
}
inline void computeShapes(const Vector<Real> & natural_coords, Real a,
Matrix<Real> & N) {
/// natural coordinate
Real xi = natural_coords(0);
// Cubic Hermite splines interpolating displacement
auto M1 = 1. / 4. * Math::pow<2>(xi - 1) * (xi + 2);
auto M2 = 1. / 4. * Math::pow<2>(xi + 1) * (2 - xi);
auto L1 = a / 4. * Math::pow<2>(xi - 1) * (xi + 1);
auto L2 = a / 4. * Math::pow<2>(xi + 1) * (xi - 1);
#if 1 // Version where we also interpolate the rotations
// Derivatives (with respect to x) of previous functions interpolating
// rotations
auto M1_ = 3. / (4. * a) * (xi * xi - 1);
auto M2_ = 3. / (4. * a) * (1 - xi * xi);
auto L1_ = 1 / 4. * (3 * xi * xi - 2 * xi - 1);
auto L2_ = 1 / 4. * (3 * xi * xi + 2 * xi - 1);
// clang-format off
// v1 t1 v2 t2
N = {{M1 , L1 , M2 , L2}, // displacement interpolation
{M1_, L1_, M2_, L2_}}; // rotation interpolation
// clang-format on
#else // Version where we only interpolate displacements
// clang-format off
// v1 t1 v2 t2
N = {{M1, L1, M2, L2}};
// clang-format on
#endif
}
/* ---------------------------------------------------------------------- */
inline void computeDNDS(const Vector<Real> & natural_coords, Real a,
Matrix<Real> & B) {
// natural coordinate
Real xi = natural_coords(0);
// Derivatives with respect to xi for rotations
- auto M1__ = 3. / 2. * xi;
- auto M2__ = 3. / 2. * (-xi);
- auto L1__ = a / 2. * (3 * xi - 1);
- auto L2__ = a / 2. * (3 * xi + 1);
+ auto M1 = 3. / 2. * xi;
+ auto M2 = 3. / 2. * (-xi);
+ auto L1 = a / 2. * (3 * xi - 1);
+ auto L2 = a / 2. * (3 * xi + 1);
- // v1 t1 v2 t2
- B = {{M1__, L1__, M2__, L2__}}; // computing curvature : {chi} = [B]{d}
+ // v1 t1 v2 t2
+ B = {{M1, L1, M2, L2}}; // computing curvature : {chi} = [B]{d}
B /= a; // to account for first order deriv w/r to x
}
} // namespace details
} // namespace
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_hermite_2, _itk_structural>::computeShapes(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
auto L = details::computeLength(real_coord);
details::computeShapes(natural_coords, L / 2, N);
}
/* -------------------------------------------------------------------------- */
template <>
inline void InterpolationElement<_itp_hermite_2, _itk_structural>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & B) {
auto L = details::computeLength(real_coord);
details::computeDNDS(natural_coords, L / 2, B);
}
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_HH__ */
+#endif /* AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.hh b/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.hh
index 489a88d17..2b5ce778f 100644
--- a/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.hh
@@ -1,213 +1,223 @@
/**
* @file element_class_kirchhoff_shell_inline_impl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 04 2014
* @date last modification: Wed Feb 21 2018
*
* @brief Element class Kirchhoff Shell
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class_structural.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_HH__
-#define __AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_HH__
+#ifndef AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_HH_
+#define AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(
_itp_discrete_kirchhoff_triangle_18, _itp_lagrange_triangle_3, 6, 6, 21);
AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY(
_discrete_kirchhoff_triangle_18, _gt_triangle_3,
_itp_discrete_kirchhoff_triangle_18, _triangle_3, _ek_structural, 3,
_git_triangle, 2);
/* -------------------------------------------------------------------------- */
namespace detail {
inline void computeBasisChangeMatrix(Matrix<Real> & P,
const Matrix<Real> & X) {
Vector<Real> X1 = X(0);
Vector<Real> X2 = X(1);
Vector<Real> X3 = X(2);
Vector<Real> a1 = X2 - X1;
Vector<Real> a2 = X3 - X1;
a1.normalize();
Vector<Real> e3 = a1.crossProduct(a2);
e3.normalize();
Vector<Real> e2 = e3.crossProduct(a1);
P(0) = a1;
P(1) = e2;
P(2) = e3;
P = P.transpose();
}
} // namespace detail
/* -------------------------------------------------------------------------- */
template <>
inline void
ElementClass<_discrete_kirchhoff_triangle_18>::computeRotationMatrix(
- Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> &) {
+ Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> & /*n*/) {
auto dim = X.rows();
Matrix<Real> P(dim, dim);
detail::computeBasisChangeMatrix(P, X);
- R.clear();
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
+ R.zero();
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
R(i + dim, j + dim) = R(i, j) = P(i, j);
+ }
+ }
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_discrete_kirchhoff_triangle_18>::computeShapes(
const Vector<Real> & /*natural_coords*/,
const Matrix<Real> & /*real_coord*/, Matrix<Real> & /*N*/) {}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_discrete_kirchhoff_triangle_18>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coordinates,
Matrix<Real> & B) {
auto dim = real_coordinates.cols();
Matrix<Real> P(dim, dim);
detail::computeBasisChangeMatrix(P, real_coordinates);
auto X = P * real_coordinates;
Vector<Real> X1 = X(0);
Vector<Real> X2 = X(1);
Vector<Real> X3 = X(2);
std::array<Vector<Real>, 3> A = {X2 - X1, X3 - X2, X1 - X3};
- std::array<Real, 3> L, C, S;
+ std::array<Real, 3> L;
+ std::array<Real, 3> C;
+ std::array<Real, 3> S;
// Setting all last coordinates to 0
std::for_each(A.begin(), A.end(), [](auto & a) { a(2) = 0; });
// Computing lengths
std::transform(A.begin(), A.end(), L.begin(),
[](auto & a) { return a.template norm<L_2>(); });
// Computing cosines
std::transform(A.begin(), A.end(), L.begin(), C.begin(),
[](auto & a, auto & l) { return a(0) / l; });
// Computing sines
std::transform(A.begin(), A.end(), L.begin(), S.begin(),
[](auto & a, auto & l) { return a(1) / l; });
// Natural coordinates
Real xi = natural_coords(0);
Real eta = natural_coords(1);
// Derivative of quadratic interpolation functions
Matrix<Real> dP = {{4 * (1 - 2 * xi - eta), 4 * eta, -4 * eta},
{-4 * xi, 4 * xi, 4 * (1 - xi - 2 * eta)}};
Matrix<Real> dNx1 = {
{3. / 2 * (dP(0, 0) * C[0] / L[0] - dP(0, 2) * C[2] / L[2]),
3. / 2 * (dP(0, 1) * C[1] / L[1] - dP(0, 0) * C[0] / L[0]),
3. / 2 * (dP(0, 2) * C[2] / L[2] - dP(0, 1) * C[1] / L[1])},
{3. / 2 * (dP(1, 0) * C[0] / L[0] - dP(1, 2) * C[2] / L[2]),
3. / 2 * (dP(1, 1) * C[1] / L[1] - dP(1, 0) * C[0] / L[0]),
3. / 2 * (dP(1, 2) * C[2] / L[2] - dP(1, 1) * C[1] / L[1])}};
Matrix<Real> dNx2 = {
// clang-format off
{-1 - 3. / 4 * (dP(0, 0) * C[0] * C[0] + dP(0, 2) * C[2] * C[2]),
1 - 3. / 4 * (dP(0, 1) * C[1] * C[1] + dP(0, 0) * C[0] * C[0]),
- 3. / 4 * (dP(0, 2) * C[2] * C[2] + dP(0, 1) * C[1] * C[1])},
{-1 - 3. / 4 * (dP(1, 0) * C[0] * C[0] + dP(1, 2) * C[2] * C[2]),
- 3. / 4 * (dP(1, 1) * C[1] * C[1] + dP(1, 0) * C[0] * C[0]),
1 - 3. / 4 * (dP(1, 2) * C[2] * C[2] + dP(1, 1) * C[1] * C[1])}};
// clang-format on
Matrix<Real> dNx3 = {
{-3. / 4 * (dP(0, 0) * C[0] * S[0] + dP(0, 2) * C[2] * S[2]),
-3. / 4 * (dP(0, 1) * C[1] * S[1] + dP(0, 0) * C[0] * S[0]),
-3. / 4 * (dP(0, 2) * C[2] * S[2] + dP(0, 1) * C[1] * S[1])},
{-3. / 4 * (dP(1, 0) * C[0] * S[0] + dP(1, 2) * C[2] * S[2]),
-3. / 4 * (dP(1, 1) * C[1] * S[1] + dP(1, 0) * C[0] * S[0]),
-3. / 4 * (dP(1, 2) * C[2] * S[2] + dP(1, 1) * C[1] * S[1])}};
Matrix<Real> dNy1 = {
{3. / 2 * (dP(0, 0) * S[0] / L[0] - dP(0, 2) * S[2] / L[2]),
3. / 2 * (dP(0, 1) * S[1] / L[1] - dP(0, 0) * S[0] / L[0]),
3. / 2 * (dP(0, 2) * S[2] / L[2] - dP(0, 1) * S[1] / L[1])},
{3. / 2 * (dP(1, 0) * S[0] / L[0] - dP(1, 2) * S[2] / L[2]),
3. / 2 * (dP(1, 1) * S[1] / L[1] - dP(1, 0) * S[0] / L[0]),
3. / 2 * (dP(1, 2) * S[2] / L[2] - dP(1, 1) * S[1] / L[1])}};
- Matrix<Real> dNy2 = dNx3;
+ const Matrix<Real> & dNy2 = dNx3;
Matrix<Real> dNy3 = {
// clang-format off
{-1 - 3. / 4 * (dP(0, 0) * S[0] * S[0] + dP(0, 2) * S[2] * S[2]),
1 - 3. / 4 * (dP(0, 1) * S[1] * S[1] + dP(0, 0) * S[0] * S[0]),
- 3. / 4 * (dP(0, 2) * S[2] * S[2] + dP(0, 1) * S[1] * S[1])},
{-1 - 3. / 4 * (dP(1, 0) * S[0] * S[0] + dP(1, 2) * S[2] * S[2]),
- 3. / 4 * (dP(1, 1) * S[1] * S[1] + dP(1, 0) * S[0] * S[0]),
1 - 3. / 4 * (dP(1, 2) * S[2] * S[2] + dP(1, 1) * S[1] * S[1])}};
// clang-format on
// Derivative of linear (membrane mode) functions
Matrix<Real> dNm(2, 3);
InterpolationElement<_itp_lagrange_triangle_3, _itk_lagrangian>::computeDNDS(
natural_coords, dNm);
UInt i = 0;
for (const Matrix<Real> & mat : {dNm, dNx1, dNx2, dNx3, dNy1, dNy2, dNy3}) {
B.block(mat, 0, i);
i += mat.cols();
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_discrete_kirchhoff_triangle_18,
_itk_structural>::arrangeInVoigt(const Matrix<Real> & dnds,
Matrix<Real> & B) {
- Matrix<Real> dNm(2, 3), dNx1(2, 3), dNx2(2, 3), dNx3(2, 3), dNy1(2, 3),
- dNy2(2, 3), dNy3(2, 3);
+ Matrix<Real> dNm(2, 3);
+ Matrix<Real> dNx1(2, 3);
+ Matrix<Real> dNx2(2, 3);
+ Matrix<Real> dNx3(2, 3);
+ Matrix<Real> dNy1(2, 3);
+ Matrix<Real> dNy2(2, 3);
+ Matrix<Real> dNy3(2, 3);
UInt i = 0;
+
for (Matrix<Real> * mat : {&dNm, &dNx1, &dNx2, &dNx3, &dNy1, &dNy2, &dNy3}) {
*mat = dnds.block(0, i, 2, 3);
i += mat->cols();
}
for (UInt i = 0; i < 3; ++i) {
// clang-format off
Matrix<Real> Bm = {{dNm(0, i), 0, 0, 0, 0, 0},
{0, dNm(1, i), 0, 0, 0, 0},
{dNm(1, i), dNm(0, i), 0, 0, 0, 0}};
Matrix<Real> Bf = {{0, 0, dNx1(0, i), -dNx3(0, i), dNx2(0, i), 0},
{0, 0, dNy1(1, i), -dNy3(1, i), dNy2(1, i), 0},
{0, 0, dNx1(1, i) + dNy1(0, i), -dNx3(1, i) - dNy3(0, i), dNx2(1, i) + dNy2(0, i), 0}};
// clang-format on
B.block(Bm, 0, i * 6);
B.block(Bf, 3, i * 6);
}
}
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_HH__ */
+#endif /* AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.hh b/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.hh
index 24c8f54a6..7183b1f64 100644
--- a/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.hh
@@ -1,163 +1,161 @@
/**
* @file element_class_pentahedron_6_inline_impl.hh
*
* @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
*
* @date creation: Mon Mar 14 2011
* @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _pentahedron_6
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*
* @verbatim
/z
|
|
| 1
| /|\
|/ | \
/ | \
/ | \
/ | \
4 2-----0
| \ / /
| \/ /
| \ /----------/y
| / \ /
|/ \ /
5---.--3
/
/
/
\x
x y z
* N0 -1 1 0
* N1 -1 0 1
* N2 -1 0 0
* N3 1 1 0
* N4 1 0 1
* N5 1 0 0
\endverbatim
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_pentahedron_6, _gt_pentahedron_6,
_itp_lagrange_pentahedron_6, _ek_regular,
3, _git_pentahedron, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_6>::computeShapes(
const vector_type & c, vector_type & N) {
/// Natural coordinates
N(0) = 0.5 * c(1) * (1 - c(0)); // N1(q)
N(1) = 0.5 * c(2) * (1 - c(0)); // N2(q)
N(2) = 0.5 * (1 - c(1) - c(2)) * (1 - c(0)); // N3(q)
N(3) = 0.5 * c(1) * (1 + c(0)); // N4(q)
N(4) = 0.5 * c(2) * (1 + c(0)); // N5(q)
N(5) = 0.5 * (1 - c(1) - c(2)) * (1 + c(0)); // N6(q)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_6>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
dnds(0, 0) = -0.5 * c(1);
dnds(0, 1) = -0.5 * c(2);
dnds(0, 2) = -0.5 * (1 - c(1) - c(2));
- dnds(0, 3) = 0.5 * c(1);
- dnds(0, 4) = 0.5 * c(2);
- dnds(0, 5) = 0.5 * (1 - c(1) - c(2));
+ dnds(0, 3) = 0.5 * c(1);
+ dnds(0, 4) = 0.5 * c(2);
+ dnds(0, 5) = 0.5 * (1 - c(1) - c(2));
dnds(1, 0) = 0.5 * (1 - c(0));
dnds(1, 1) = 0.0;
dnds(1, 2) = -0.5 * (1 - c(0));
dnds(1, 3) = 0.5 * (1 + c(0));
dnds(1, 4) = 0.0;
dnds(1, 5) = -0.5 * (1 + c(0));
dnds(2, 0) = 0.0;
dnds(2, 1) = 0.5 * (1 - c(0));
dnds(2, 2) = -0.5 * (1 - c(0));
dnds(2, 3) = 0.0;
dnds(2, 4) = 0.5 * (1 + c(0));
dnds(2, 5) = -0.5 * (1 + c(0));
}
/* -------------------------------------------------------------------------- */
// I have to duplicate this code since the Real * coords do not know their size
// in the Math module.
// If later we use eigen or Vector to implement this function
// there should be only one function in akantu::Math
// -> this is temporary for the release deadline which was so extended
inline Real triangle_inradius(const Real * coord1, const Real * coord2,
const Real * coord3) {
/**
* @f{eqnarray*}{
* r &=& A / s \\
* A &=& 1/4 * \sqrt{(a + b + c) * (a - b + c) * (a + b - c) (-a + b + c)} \\
* s &=& \frac{a + b + c}{2}
* @f}
*/
- Real a, b, c;
- a = Math::distance_3d(coord1, coord2);
- b = Math::distance_3d(coord2, coord3);
- c = Math::distance_3d(coord1, coord3);
+ auto a = Math::distance_3d(coord1, coord2);
+ auto b = Math::distance_3d(coord2, coord3);
+ auto c = Math::distance_3d(coord1, coord3);
- Real s;
- s = (a + b + c) * 0.5;
+ auto s = (a + b + c) * 0.5;
- return sqrt((s - a) * (s - b) * (s - c) / s);
+ return std::sqrt((s - a) * (s - b) * (s - c) / s);
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_pentahedron_6>::getInradius(const Matrix<Real> & coord) {
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Vector<Real> u4 = coord(4);
Vector<Real> u5 = coord(5);
- Real inradius_triangle_1 =
+ auto inradius_triangle_1 =
triangle_inradius(u0.storage(), u1.storage(), u2.storage());
- Real inradius_triangle_2 =
+ auto inradius_triangle_2 =
triangle_inradius(u3.storage(), u4.storage(), u5.storage());
- Real d1 = u3.distance(u0) * 0.5;
- Real d2 = u5.distance(u2) * 0.5;
- Real d3 = u4.distance(u1) * 0.5;
- Real p =
+ auto d1 = u3.distance(u0) * 0.5;
+ auto d2 = u5.distance(u2) * 0.5;
+ auto d3 = u4.distance(u1) * 0.5;
+ auto p =
2. * std::min({inradius_triangle_1, inradius_triangle_2, d1, d2, d3});
return p;
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.hh b/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.hh
index a0ce6f5e6..28b5e9459 100644
--- a/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.hh
@@ -1,186 +1,184 @@
/**
* @file element_class_quadrangle_8_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed May 18 2011
* @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the ElementClass for the _quadrangle_8
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
terms of the GNU Lesser General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your option) any
later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
details.
*
* You should have received a copy of the GNU Lesser General Public License
along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*
* @verbatim
\eta
^
|
(-1,1) (0,1) (1,1)
x-------x-------x
| | |
| | |
| | |
(-1,0)| | |(1,0)
----x---------------X-----> \xi
| | |
| | |
| | |
| | |
x-------x-------x
(-1,-1) (0,-1) (1,-1)
|
@endverbatim
*
* @f[
* \begin{array}{lll}
* N1 = (1 - \xi) (1 - \eta)(- 1 - \xi - \eta) / 4
* & \frac{\partial N1}{\partial \xi} = (1 - \eta)(2 \xi + \eta) / 4
* & \frac{\partial N1}{\partial \eta} = (1 - \xi)(\xi + 2 \eta) / 4 \\
* N2 = (1 + \xi) (1 - \eta)(- 1 + \xi - \eta) / 4 \\
* & \frac{\partial N2}{\partial \xi} = (1 - \eta)(2 \xi - \eta) / 4
* & \frac{\partial N2}{\partial \eta} = - (1 + \xi)(\xi - 2 \eta) / 4 \\
* N3 = (1 + \xi) (1 + \eta)(- 1 + \xi + \eta) / 4 \\
* & \frac{\partial N3}{\partial \xi} = (1 + \eta)(2 \xi + \eta) / 4
* & \frac{\partial N3}{\partial \eta} = (1 + \xi)(\xi + 2 \eta) / 4 \\
* N4 = (1 - \xi) (1 + \eta)(- 1 - \xi + \eta) / 4
* & \frac{\partial N4}{\partial \xi} = (1 + \eta)(2 \xi - \eta) / 4
* & \frac{\partial N4}{\partial \eta} = - (1 - \xi)(\xi - 2 \eta) / 4 \\
* N5 = (1 - \xi^2) (1 - \eta) / 2
* & \frac{\partial N1}{\partial \xi} = - \xi (1 - \eta)
* & \frac{\partial N1}{\partial \eta} = - (1 - \xi^2) / 2 \\
* N6 = (1 + \xi) (1 - \eta^2) / 2 \\
* & \frac{\partial N2}{\partial \xi} = (1 - \eta^2) / 2
* & \frac{\partial N2}{\partial \eta} = - \eta (1 + \xi) \\
* N7 = (1 - \xi^2) (1 + \eta) / 2 \\
* & \frac{\partial N3}{\partial \xi} = - \xi (1 + \eta)
* & \frac{\partial N3}{\partial \eta} = (1 - \xi^2) / 2 \\
* N8 = (1 - \xi) (1 - \eta^2) / 2
* & \frac{\partial N4}{\partial \xi} = - (1 - \eta^2) / 2
* & \frac{\partial N4}{\partial \eta} = - \eta (1 - \xi) \\
* \end{array}
* @f]
*
* @f{eqnarray*}{
* \xi_{q0} &=& 0 \qquad \eta_{q0} = 0
* @f}
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_quadrangle_8, _gt_quadrangle_8,
_itp_serendip_quadrangle_8, _ek_regular, 2,
_git_segment, 3);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_serendip_quadrangle_8>::computeShapes(
const vector_type & c, vector_type & N) {
/// Natural coordinates
const Real xi = c(0);
const Real eta = c(1);
N(0) = .25 * (1 - xi) * (1 - eta) * (-1 - xi - eta);
N(1) = .25 * (1 + xi) * (1 - eta) * (-1 + xi - eta);
N(2) = .25 * (1 + xi) * (1 + eta) * (-1 + xi + eta);
N(3) = .25 * (1 - xi) * (1 + eta) * (-1 - xi + eta);
N(4) = .5 * (1 - xi * xi) * (1 - eta);
N(5) = .5 * (1 + xi) * (1 - eta * eta);
N(6) = .5 * (1 - xi * xi) * (1 + eta);
N(7) = .5 * (1 - xi) * (1 - eta * eta);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_serendip_quadrangle_8>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
const Real xi = c(0);
const Real eta = c(1);
/// dN/dxi
dnds(0, 0) = .25 * (1 - eta) * (2 * xi + eta);
dnds(0, 1) = .25 * (1 - eta) * (2 * xi - eta);
dnds(0, 2) = .25 * (1 + eta) * (2 * xi + eta);
dnds(0, 3) = .25 * (1 + eta) * (2 * xi - eta);
dnds(0, 4) = -xi * (1 - eta);
dnds(0, 5) = .5 * (1 - eta * eta);
dnds(0, 6) = -xi * (1 + eta);
dnds(0, 7) = -.5 * (1 - eta * eta);
/// dN/deta
dnds(1, 0) = .25 * (1 - xi) * (2 * eta + xi);
dnds(1, 1) = .25 * (1 + xi) * (2 * eta - xi);
dnds(1, 2) = .25 * (1 + xi) * (2 * eta + xi);
dnds(1, 3) = .25 * (1 - xi) * (2 * eta - xi);
dnds(1, 4) = -.5 * (1 - xi * xi);
dnds(1, 5) = -eta * (1 + xi);
dnds(1, 6) = .5 * (1 - xi * xi);
dnds(1, 7) = -eta * (1 - xi);
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_quadrangle_8>::getInradius(const Matrix<Real> & coord) {
- Real a, b, h;
-
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Vector<Real> u4 = coord(4);
Vector<Real> u5 = coord(5);
Vector<Real> u6 = coord(6);
Vector<Real> u7 = coord(7);
- a = u0.distance(u4);
- b = u4.distance(u1);
- h = std::min(a, b);
+ auto a = u0.distance(u4);
+ auto b = u4.distance(u1);
+ auto h = std::min(a, b);
a = u1.distance(u5);
b = u5.distance(u2);
h = std::min(h, std::min(a, b));
a = u2.distance(u6);
b = u6.distance(u3);
h = std::min(h, std::min(a, b));
a = u3.distance(u7);
b = u7.distance(u0);
h = std::min(h, std::min(a, b));
return h;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_serendip_quadrangle_8>::computeSpecialJacobian(
const Matrix<Real> & J, Real & jac) {
Vector<Real> vprod(J.cols());
Matrix<Real> Jt(J.transpose(), true);
vprod.crossProduct(Jt(0), Jt(1));
jac = vprod.norm();
}
} // namespace akantu
diff --git a/src/fe_engine/element_type_conversion.hh b/src/fe_engine/element_type_conversion.hh
index f048d16a5..fc9f7da43 100644
--- a/src/fe_engine/element_type_conversion.hh
+++ b/src/fe_engine/element_type_conversion.hh
@@ -1,56 +1,57 @@
/**
* @file element_type_conversion.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Aug 11 2017
*
* @brief conversion between different types
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_TYPE_CONVERSION_HH__
-#define __AKANTU_ELEMENT_TYPE_CONVERSION_HH__
+#ifndef AKANTU_ELEMENT_TYPE_CONVERSION_HH_
+#define AKANTU_ELEMENT_TYPE_CONVERSION_HH_
namespace akantu {
-template <class InType, class OutType> OutType convertType(const InType &) {
+template <class InType, class OutType>
+OutType convertType(InType /*unused*/) {
return OutType();
}
template <>
inline InterpolationType
-convertType<ElementType, InterpolationType>(const ElementType & type) {
+convertType<ElementType, InterpolationType>(ElementType type) {
InterpolationType itp_type = _itp_not_defined;
#define GET_ITP(type) itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_ITP);
#undef GET_ITP
return itp_type;
}
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_TYPE_CONVERSION_HH__ */
+#endif /* AKANTU_ELEMENT_TYPE_CONVERSION_HH_ */
diff --git a/src/fe_engine/fe_engine.hh b/src/fe_engine/fe_engine.hh
index 8e4035ccb..8be4ae903 100644
--- a/src/fe_engine/fe_engine.hh
+++ b/src/fe_engine/fe_engine.hh
@@ -1,368 +1,368 @@
/**
* @file fe_engine.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief FEM class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "element_type_map.hh"
#include "mesh_events.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_FE_ENGINE_HH__
-#define __AKANTU_FE_ENGINE_HH__
+#ifndef AKANTU_FE_ENGINE_HH_
+#define AKANTU_FE_ENGINE_HH_
namespace akantu {
class Mesh;
class Integrator;
class ShapeFunctions;
class DOFManager;
class Element;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* The generic FEEngine class derived in a FEEngineTemplate class
* containing the
* shape functions and the integration method
*/
class FEEngine : protected Memory, public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- FEEngine(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
+ FEEngine(Mesh & mesh, UInt element_dimension = _all_dimensions,
const ID & id = "fem", MemoryID memory_id = 0);
~FEEngine() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// pre-compute all the shape functions, their derivatives and the jacobians
virtual void
- initShapeFunctions(const GhostType & ghost_type = _not_ghost) = 0;
+ initShapeFunctions(GhostType ghost_type = _not_ghost) = 0;
/// extract the nodal values and store them per element
template <typename T>
static void extractNodalToElementField(
const Mesh & mesh, const Array<T> & nodal_f, Array<T> & elemental_f,
- const ElementType & type, const GhostType & ghost_type = _not_ghost,
+ ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter);
/// filter a field
template <typename T>
static void
- filterElementalData(const Mesh & mesh, const Array<T> & quad_f,
- Array<T> & filtered_f, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ filterElementalData(const Mesh & mesh, const Array<T> & elem_f,
+ Array<T> & filtered_f, ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter);
/* ------------------------------------------------------------------------ */
/* Integration method bridges */
/* ------------------------------------------------------------------------ */
/// integrate f for all elements of type "type"
virtual void
integrate(const Array<Real> & f, Array<Real> & intf,
- UInt nb_degree_of_freedom, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ UInt nb_degree_of_freedom, ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate a scalar value f on all elements of type "type"
virtual Real
- integrate(const Array<Real> & f, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ integrate(const Array<Real> & f, ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate f for all integration points of type "type" but don't sum over
/// all integration points
virtual void integrateOnIntegrationPoints(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
- const ElementType & type, const GhostType & ghost_type = _not_ghost,
+ ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate one element scalar value on all elements of type "type"
- virtual Real integrate(const Vector<Real> & f, const ElementType & type,
+ virtual Real integrate(const Vector<Real> & f, ElementType type,
UInt index,
- const GhostType & ghost_type = _not_ghost) const = 0;
+ GhostType ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* compatibility with old FEEngine fashion */
/* ------------------------------------------------------------------------ */
/// get the number of integration points
virtual UInt
- getNbIntegrationPoints(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const = 0;
+ getNbIntegrationPoints(ElementType type,
+ GhostType ghost_type = _not_ghost) const = 0;
/// get the precomputed shapes
const virtual Array<Real> &
- getShapes(const ElementType & type, const GhostType & ghost_type = _not_ghost,
+ getShapes(ElementType type, GhostType ghost_type = _not_ghost,
UInt id = 0) const = 0;
/// get the derivatives of shapes
const virtual Array<Real> &
- getShapesDerivatives(const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ getShapesDerivatives(ElementType type,
+ GhostType ghost_type = _not_ghost,
UInt id = 0) const = 0;
/// get integration points
const virtual Matrix<Real> &
- getIntegrationPoints(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const = 0;
+ getIntegrationPoints(ElementType type,
+ GhostType ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* Shape method bridges */
/* ------------------------------------------------------------------------ */
/// Compute the gradient nablauq on the integration points of an element type
/// from nodal values u
virtual void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq,
- const UInt nb_degree_of_freedom, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ UInt nb_degree_of_freedom, ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Interpolate a nodal field u at the integration points of an element type
/// -> uq
virtual void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
- const ElementType & type, const GhostType & ghost_type = _not_ghost,
+ ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Interpolate a nodal field u at the integration points of many element
/// types -> uq
virtual void interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements = nullptr) const = 0;
/// pre multiplies a tensor by the shapes derivaties
virtual void
computeBtD(const Array<Real> & Ds, Array<Real> & BtDs,
- const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// left and right multiplies a tensor by the shapes derivaties
virtual void
computeBtDB(const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
- const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// left multiples a vector by the shape functions
virtual void
computeNtb(const Array<Real> & bs, Array<Real> & Ntbs,
- const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Compute the interpolation point position in the global coordinates for
/// many element types
virtual void computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & integration_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements = nullptr) const = 0;
/// Compute the interpolation point position in the global coordinates for an
/// element type
virtual void computeIntegrationPointsCoordinates(
- Array<Real> & integration_points_coordinates, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ Array<Real> & integration_points_coordinates, ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
virtual void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & integration_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// interpolate field at given position (interpolation_points) from given
/// values of this field at integration points (field)
virtual void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
- ElementTypeMapArray<Real> & result, const GhostType ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
virtual void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> &
integration_points_coordinates_inv_matrices,
- ElementTypeMapArray<Real> & result, const GhostType ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// interpolate on a phyiscal point inside an element
virtual void interpolate(const Vector<Real> & real_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const Element & element) const = 0;
/// compute the shape on a provided point
virtual void
computeShapes(const Vector<Real> & real_coords, UInt elem,
- const ElementType & type, Vector<Real> & shapes,
- const GhostType & ghost_type = _not_ghost) const = 0;
+ ElementType type, Vector<Real> & shapes,
+ GhostType ghost_type = _not_ghost) const = 0;
/// compute the shape derivatives on a provided point
virtual void
- computeShapeDerivatives(const Vector<Real> & real__coords, UInt element,
- const ElementType & type,
+ computeShapeDerivatives(const Vector<Real> & real_coords, UInt element,
+ ElementType type,
Matrix<Real> & shape_derivatives,
- const GhostType & ghost_type = _not_ghost) const = 0;
+ GhostType ghost_type = _not_ghost) const = 0;
/// assembles the lumped version of @f[ \int N^t rho N @f]
virtual void assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- ElementType type, const GhostType & ghost_type = _not_ghost) const = 0;
+ ElementType type, GhostType ghost_type = _not_ghost) const = 0;
/// assembles the matrix @f[ \int N^t rho N @f]
virtual void assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- ElementType type, const GhostType & ghost_type = _not_ghost) const = 0;
+ ElementType type, GhostType ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* Other methods */
/* ------------------------------------------------------------------------ */
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
- const GhostType & ghost_type = _not_ghost) = 0;
+ GhostType ghost_type = _not_ghost) = 0;
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
const Array<Real> & /*field*/,
- const GhostType & /*ghost_type*/ = _not_ghost) {
+ GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
const Array<Real> & /*field*/, Array<Real> & /*normal*/,
- const ElementType & /*type*/,
- const GhostType & /*ghost_type*/ = _not_ghost) const {
+ ElementType /*type*/,
+ GhostType /*ghost_type*/ = _not_ghost) const {
AKANTU_TO_IMPLEMENT();
}
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
private:
/// initialise the class
void init();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
using ElementTypesIteratorHelper =
ElementTypeMapArray<Real, ElementType>::ElementTypesIteratorHelper;
ElementTypesIteratorHelper elementTypes(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
/// get the dimension of the element handeled by this fe_engine object
AKANTU_GET_MACRO(ElementDimension, element_dimension, UInt);
/// get the mesh contained in the fem object
AKANTU_GET_MACRO(Mesh, mesh, const Mesh &);
/// get the mesh contained in the fem object
AKANTU_GET_MACRO_NOT_CONST(Mesh, mesh, Mesh &);
/// get the in-radius of an element
static inline Real getElementInradius(const Matrix<Real> & coord,
- const ElementType & type);
+ ElementType type);
/// get the normals on integration points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(NormalsOnIntegrationPoints,
normals_on_integration_points, Real);
/// get cohesive element type for a given facet type
static inline ElementType
- getCohesiveElementType(const ElementType & type_facet);
+ getCohesiveElementType(ElementType type_facet);
/// get igfem element type for a given regular type
static inline Vector<ElementType>
- getIGFEMElementTypes(const ElementType & type);
+ getIGFEMElementTypes(ElementType type);
/// get the interpolation element associated to an element type
static inline InterpolationType
- getInterpolationType(const ElementType & el_type);
+ getInterpolationType(ElementType el_type);
/// get the shape function class (probably useless: see getShapeFunction in
/// fe_engine_template.hh)
virtual const ShapeFunctions & getShapeFunctionsInterface() const = 0;
/// get the integrator class (probably useless: see getIntegrator in
/// fe_engine_template.hh)
virtual const Integrator & getIntegratorInterface() const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// spatial dimension of the problem
UInt element_dimension;
/// the mesh on which all computation are made
Mesh & mesh;
/// normals at integration points
ElementTypeMapArray<Real> normals_on_integration_points;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const FEEngine & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "fe_engine_inline_impl.hh"
#include "fe_engine_template.hh"
-#endif /* __AKANTU_FE_ENGINE_HH__ */
+#endif /* AKANTU_FE_ENGINE_HH_ */
diff --git a/src/fe_engine/fe_engine_inline_impl.hh b/src/fe_engine/fe_engine_inline_impl.hh
index 8ad876568..4e0e57288 100644
--- a/src/fe_engine/fe_engine_inline_impl.hh
+++ b/src/fe_engine/fe_engine_inline_impl.hh
@@ -1,192 +1,194 @@
/**
* @file fe_engine_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 20 2010
* @date last modification: Sun Aug 13 2017
*
* @brief Implementation of the inline functions of the FEEngine Class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include "element_type_conversion.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_FE_ENGINE_INLINE_IMPL_HH__
-#define __AKANTU_FE_ENGINE_INLINE_IMPL_HH__
+#ifndef AKANTU_FE_ENGINE_INLINE_IMPL_HH_
+#define AKANTU_FE_ENGINE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline Real FEEngine::getElementInradius(const Matrix<Real> & coord,
- const ElementType & type) {
+ ElementType type) {
Real inradius = 0;
#define GET_INRADIUS(type) inradius = ElementClass<type>::getInradius(coord);
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_INRADIUS);
#undef GET_INRADIUS
return inradius;
}
/* -------------------------------------------------------------------------- */
inline InterpolationType
-FEEngine::getInterpolationType(const ElementType & type) {
+FEEngine::getInterpolationType(ElementType type) {
return convertType<ElementType, InterpolationType>(type);
}
/* -------------------------------------------------------------------------- */
/// @todo rewrite this function in order to get the cohesive element
/// type directly from the facet
#if defined(AKANTU_COHESIVE_ELEMENT)
-inline ElementType FEEngine::getCohesiveElementType(const ElementType & type) {
+inline ElementType FEEngine::getCohesiveElementType(ElementType type) {
ElementType ctype;
#define GET_COHESIVE_TYPE(type) \
ctype = CohesiveFacetProperty<type>::cohesive_type;
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_COHESIVE_TYPE);
#undef GET_COHESIVE_TYPE
return ctype;
}
#else
inline ElementType
FEEngine::getCohesiveElementType(__attribute__((unused))
- const ElementType & type_facet) {
+ ElementType type_facet) {
return _not_defined;
}
#endif
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IGFEM)
} // akantu
#include "igfem_helper.hh"
namespace akantu {
inline Vector<ElementType>
-FEEngine::getIGFEMElementTypes(const ElementType & type) {
+FEEngine::getIGFEMElementTypes(ElementType type) {
#define GET_IGFEM_ELEMENT_TYPES(type) \
return IGFEMHelper::getIGFEMElementTypes<type>();
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(GET_IGFEM_ELEMENT_TYPES);
#undef GET_IGFEM_ELEMENT_TYPES
}
#endif
/* -------------------------------------------------------------------------- */
template <typename T>
void FEEngine::extractNodalToElementField(const Mesh & mesh,
const Array<T> & nodal_f,
Array<T> & elemental_f,
- const ElementType & type,
- const GhostType & ghost_type,
+ ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = nodal_f.getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
elemental_f.resize(nb_element);
T * nodal_f_val = nodal_f.storage();
T * f_val = elemental_f.storage();
UInt * el_conn;
for (UInt el = 0; el < nb_element; ++el) {
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
el_conn = conn_val + filter_elements(el) * nb_nodes_per_element;
- else
+ } else {
el_conn = conn_val + el * nb_nodes_per_element;
+ }
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = *(el_conn + n);
std::copy(nodal_f_val + node * nb_degree_of_freedom,
nodal_f_val + (node + 1) * nb_degree_of_freedom, f_val);
f_val += nb_degree_of_freedom;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void FEEngine::filterElementalData(const Mesh & mesh, const Array<T> & elem_f,
Array<T> & filtered_f,
- const ElementType & type,
- const GhostType & ghost_type,
+ ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0) {
filtered_f.resize(0);
return;
}
UInt nb_degree_of_freedom = elem_f.getNbComponent();
UInt nb_data_per_element = elem_f.size() / nb_element;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
filtered_f.resize(nb_element * nb_data_per_element);
T * elem_f_val = elem_f.storage();
T * f_val = filtered_f.storage();
UInt el_offset;
for (UInt el = 0; el < nb_element; ++el) {
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
el_offset = filter_elements(el);
- else
+ } else {
el_offset = el;
+ }
std::copy(elem_f_val +
el_offset * nb_data_per_element * nb_degree_of_freedom,
elem_f_val +
(el_offset + 1) * nb_data_per_element * nb_degree_of_freedom,
f_val);
f_val += nb_degree_of_freedom * nb_data_per_element;
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif /* __AKANTU_FE_ENGINE_INLINE_IMPL_HH__ */
+#endif /* AKANTU_FE_ENGINE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/fe_engine_template.hh b/src/fe_engine/fe_engine_template.hh
index df28a2e76..d53bc08dc 100644
--- a/src/fe_engine/fe_engine_template.hh
+++ b/src/fe_engine/fe_engine_template.hh
@@ -1,425 +1,426 @@
/**
* @file fe_engine_template.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jan 29 2018
*
* @brief templated class that calls integration and shape objects
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "integrator.hh"
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_FE_ENGINE_TEMPLATE_HH__
-#define __AKANTU_FE_ENGINE_TEMPLATE_HH__
+#ifndef AKANTU_FE_ENGINE_TEMPLATE_HH_
+#define AKANTU_FE_ENGINE_TEMPLATE_HH_
namespace akantu {
class DOFManager;
namespace fe_engine {
namespace details {
template <ElementKind> struct AssembleLumpedTemplateHelper;
template <ElementKind> struct AssembleFieldMatrixHelper;
} // namespace details
} // namespace fe_engine
template <ElementKind, typename> struct AssembleFieldMatrixStructHelper;
struct DefaultIntegrationOrderFunctor {
template <ElementType type> static inline constexpr int getOrder() {
return ElementClassProperty<type>::polynomial_degree;
}
};
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind = _ek_regular,
class IntegrationOrderFunctor = DefaultIntegrationOrderFunctor>
class FEEngineTemplate : public FEEngine {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using Integ = I<kind, IntegrationOrderFunctor>;
using Shape = S<kind>;
FEEngineTemplate(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
- ID id = "fem", MemoryID memory_id = 0);
+ const ID & id = "fem", MemoryID memory_id = 0);
~FEEngineTemplate() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// pre-compute all the shape functions, their derivatives and the jacobians
- void initShapeFunctions(const GhostType & ghost_type = _not_ghost) override;
+ void initShapeFunctions(GhostType ghost_type = _not_ghost) override;
void initShapeFunctions(const Array<Real> & nodes,
- const GhostType & ghost_type = _not_ghost);
+ GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Integration method bridges */
/* ------------------------------------------------------------------------ */
/// integrate f for all elements of type "type"
void
integrate(const Array<Real> & f, Array<Real> & intf,
- UInt nb_degree_of_freedom, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ UInt nb_degree_of_freedom, ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// integrate a scalar value on all elements of type "type"
Real
- integrate(const Array<Real> & f, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ integrate(const Array<Real> & f, ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// integrate one element scalar value on all elements of type "type"
- Real integrate(const Vector<Real> & f, const ElementType & type, UInt index,
- const GhostType & ghost_type = _not_ghost) const override;
+ Real integrate(const Vector<Real> & f, ElementType type, UInt index,
+ GhostType ghost_type = _not_ghost) const override;
/// integrate partially around an integration point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
void integrateOnIntegrationPoints(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
- const ElementType & type, const GhostType & ghost_type = _not_ghost,
+ ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate on a phyiscal point inside an element
void interpolate(const Vector<Real> & real_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const Element & element) const override;
/// get the number of integration points
UInt getNbIntegrationPoints(
- const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const override;
+ ElementType type,
+ GhostType ghost_type = _not_ghost) const override;
/// get shapes precomputed
- const Array<Real> & getShapes(const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ const Array<Real> & getShapes(ElementType type,
+ GhostType ghost_type = _not_ghost,
UInt id = 0) const override;
/// get the derivatives of shapes
const Array<Real> &
- getShapesDerivatives(const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ getShapesDerivatives(ElementType type,
+ GhostType ghost_type = _not_ghost,
UInt id = 0) const override;
/// get integration points
const inline Matrix<Real> & getIntegrationPoints(
- const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const override;
+ ElementType type,
+ GhostType ghost_type = _not_ghost) const override;
/* ------------------------------------------------------------------------ */
/* Shape method bridges */
/* ------------------------------------------------------------------------ */
/// compute the gradient of a nodal field on the integration points
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq,
- const UInt nb_degree_of_freedom, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ UInt nb_degree_of_freedom, ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate a nodal field on the integration points
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
- const ElementType & type, const GhostType & ghost_type = _not_ghost,
+ ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate a nodal field on the integration points given a
/// by_element_type
void interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements =
nullptr) const override;
/// pre multiplies a tensor by the shapes derivaties
void
computeBtD(const Array<Real> & Ds, Array<Real> & BtDs,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const override;
/// left and right multiplies a tensor by the shapes derivaties
void computeBtDB(
const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const override;
/// left multiples a vector by the shape functions
void computeNtb(const Array<Real> & bs, Array<Real> & Ntbs,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const override;
/// compute the position of integration points given by an element_type_map
/// from nodes position
inline void computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements =
nullptr) const override;
/// compute the position of integration points from nodes position
inline void computeIntegrationPointsCoordinates(
- Array<Real> & quadrature_points_coordinates, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ Array<Real> & quadrature_points_coordinates, ElementType type,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate field at given position (interpolation_points) from given
/// values of this field at integration points (field)
inline void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
- ElementTypeMapArray<Real> & result, const GhostType ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const override;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
inline void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
- ElementTypeMapArray<Real> & result, const GhostType ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const override;
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
inline void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter =
nullptr) const override;
/// find natural coords from real coords provided an element
void inverseMap(const Vector<Real> & real_coords, UInt element,
- const ElementType & type, Vector<Real> & natural_coords,
- const GhostType & ghost_type = _not_ghost) const;
+ ElementType type, Vector<Real> & natural_coords,
+ GhostType ghost_type = _not_ghost) const;
/// return true if the coordinates provided are inside the element, false
/// otherwise
inline bool contains(const Vector<Real> & real_coords, UInt element,
- const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ ElementType type,
+ GhostType ghost_type = _not_ghost) const;
/// compute the shape on a provided point
inline void
computeShapes(const Vector<Real> & real_coords, UInt element,
- const ElementType & type, Vector<Real> & shapes,
- const GhostType & ghost_type = _not_ghost) const override;
+ ElementType type, Vector<Real> & shapes,
+ GhostType ghost_type = _not_ghost) const override;
/// compute the shape derivatives on a provided point
inline void computeShapeDerivatives(
- const Vector<Real> & real__coords, UInt element, const ElementType & type,
+ const Vector<Real> & real_coords, UInt element, ElementType type,
Matrix<Real> & shape_derivatives,
- const GhostType & ghost_type = _not_ghost) const override;
+ GhostType ghost_type = _not_ghost) const override;
/* ------------------------------------------------------------------------ */
/* Other methods */
/* ------------------------------------------------------------------------ */
/// pre-compute normals on integration points
void computeNormalsOnIntegrationPoints(
- const GhostType & ghost_type = _not_ghost) override;
+ GhostType ghost_type = _not_ghost) override;
void computeNormalsOnIntegrationPoints(
const Array<Real> & field,
- const GhostType & ghost_type = _not_ghost) override;
+ GhostType ghost_type = _not_ghost) override;
void computeNormalsOnIntegrationPoints(
- const Array<Real> & field, Array<Real> & normal, const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const override;
+ const Array<Real> & field, Array<Real> & normal, ElementType type,
+ GhostType ghost_type = _not_ghost) const override;
template <ElementType type>
void computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
private:
// To avoid a weird full specialization of a method in a non specalized class
void
- computeNormalsOnIntegrationPointsPoint1(const Array<Real> &,
+ computeNormalsOnIntegrationPointsPoint1(const Array<Real> & /*unused*/,
Array<Real> & normal,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
public:
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
void assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- ElementType type, const GhostType & ghost_type) const override;
+ ElementType type, GhostType ghost_type) const override;
/// assemble a field as a matrix (ex. rho to mass matrix)
void assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- ElementType type, const GhostType & ghost_type) const override;
+ ElementType type, GhostType ghost_type) const override;
/// assemble a field as a lumped matrix (ex. rho in lumped mass)
// template <class Functor>
// void assembleFieldLumped(const Functor & field_funct, const ID & matrix_id,
// const ID & dof_id, DOFManager & dof_manager,
// ElementType type,
- // const GhostType & ghost_type) const;
+ // GhostType ghost_type) const;
// /// assemble a field as a matrix (ex. rho to mass matrix)
// template <class Functor>
// void assembleFieldMatrix(const Functor & field_funct, const ID & matrix_id,
// const ID & dof_id, DOFManager & dof_manager,
// ElementType type,
- // const GhostType & ghost_type) const;
+ // GhostType ghost_type) const;
// #ifdef AKANTU_STRUCTURAL_MECHANICS
// /// assemble a field as a matrix (ex. rho to mass matrix)
// void assembleFieldMatrix(const Array<Real> & field_1,
// UInt nb_degree_of_freedom, SparseMatrix & M,
// Array<Real> * n,
// ElementTypeMapArray<Real> & rotation_mat,
- // const ElementType & type,
- // const GhostType & ghost_type = _not_ghost)
+ // ElementType type,
+ // GhostType ghost_type = _not_ghost)
// const;
// /// compute shapes function in a matrix for structural elements
// void
- // computeShapesMatrix(const ElementType & type, UInt nb_degree_of_freedom,
+ // computeShapesMatrix(ElementType type, UInt nb_degree_of_freedom,
// UInt nb_nodes_per_element, Array<Real> * n, UInt id,
// UInt degree_to_interpolate, UInt degree_interpolated,
// const bool sign,
- // const GhostType & ghost_type = _not_ghost) const
+ // GhostType ghost_type = _not_ghost) const
// override;
// #endif
private:
friend struct fe_engine::details::AssembleLumpedTemplateHelper<kind>;
friend struct fe_engine::details::AssembleFieldMatrixHelper<kind>;
friend struct AssembleFieldMatrixStructHelper<kind, void>;
/// templated function to compute the scaling to assemble a lumped matrix
template <ElementType type>
void assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j
/// dV = \int \rho \varphi_i dV @f$
template <ElementType type>
void assembleLumpedRowSum(const Array<Real> & field, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// @f$ \tilde{M}_{i} = c * M_{ii} = \int_{V_e} \rho dV @f$
template <ElementType type>
void assembleLumpedDiagonalScaling(const Array<Real> & field,
const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// assemble a field as a matrix (ex. rho to mass matrix)
template <ElementType type>
void assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
#ifdef AKANTU_STRUCTURAL_MECHANICS
/// assemble a field as a matrix for structural elements (ex. rho to mass
/// matrix)
template <ElementType type>
void assembleFieldMatrix(const Array<Real> & field_1,
UInt nb_degree_of_freedom, SparseMatrix & M,
Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat,
__attribute__((unused))
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
#endif
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler interface */
/* ------------------------------------------------------------------------ */
public:
- void onElementsAdded(const Array<Element> &,
- const NewElementsEvent &) override;
- void onElementsRemoved(const Array<Element> &,
- const ElementTypeMapArray<UInt> &,
- const RemovedElementsEvent &) override;
- void onElementsChanged(const Array<Element> &, const Array<Element> &,
- const ElementTypeMapArray<UInt> &,
- const ChangedElementsEvent &) override;
+ void onElementsAdded(const Array<Element> & /*new_elements*/,
+ const NewElementsEvent & /*unused*/) override;
+ void onElementsRemoved(const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const RemovedElementsEvent & /*unused*/) override;
+ void onElementsChanged(const Array<Element> & /*unused*/,
+ const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const ChangedElementsEvent & /*unused*/) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the shape class (probably useless: see getShapeFunction)
const ShapeFunctions & getShapeFunctionsInterface() const override {
return shape_functions;
};
/// get the shape class
const Shape & getShapeFunctions() const { return shape_functions; };
/// get the integrator class (probably useless: see getIntegrator)
const Integrator & getIntegratorInterface() const override {
return integrator;
};
/// get the integrator class
const Integ & getIntegrator() const { return integrator; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
Integ integrator;
Shape shape_functions;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "fe_engine_template_tmpl.hh"
#include "fe_engine_template_tmpl_field.hh"
/* -------------------------------------------------------------------------- */
/* Shape Linked specialization */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "fe_engine_template_tmpl_struct.hh"
#endif
/* -------------------------------------------------------------------------- */
/* Shape IGFEM specialization */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IGFEM)
#include "fe_engine_template_tmpl_igfem.hh"
#endif
-#endif /* __AKANTU_FE_ENGINE_TEMPLATE_HH__ */
+#endif /* AKANTU_FE_ENGINE_TEMPLATE_HH_ */
diff --git a/src/fe_engine/fe_engine_template_cohesive.cc b/src/fe_engine/fe_engine_template_cohesive.cc
index 8a5e2ec66..ab5c78b34 100644
--- a/src/fe_engine/fe_engine_template_cohesive.cc
+++ b/src/fe_engine/fe_engine_template_cohesive.cc
@@ -1,131 +1,135 @@
/**
* @file fe_engine_template_cohesive.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Oct 31 2012
* @date last modification: Tue Feb 20 2018
*
* @brief Specialization of the FEEngineTemplate for cohesive element
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine_template.hh"
#include "integrator_gauss.hh"
#include "shape_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* compatibility functions */
/* -------------------------------------------------------------------------- */
template <>
Real FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
- integrate(const Array<Real> & f, const ElementType & type,
- const GhostType & ghost_type,
+ integrate(const Array<Real> & f, ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
UInt nb_element = mesh.getNbElement(type, ghost_type);
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
+ }
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == 1,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
#endif
Real integral = 0.;
#define INTEGRATE(type) \
integral = integrator.integrate<type>(f, ghost_type, filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INTEGRATE);
#undef INTEGRATE
AKANTU_DEBUG_OUT();
return integral;
}
/* -------------------------------------------------------------------------- */
template <>
void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
integrate(const Array<Real> & f, Array<Real> & intf,
- UInt nb_degree_of_freedom, const ElementType & type,
- const GhostType & ghost_type,
+ UInt nb_degree_of_freedom, ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const {
#ifndef AKANTU_NDEBUG
UInt nb_element = mesh.getNbElement(type, ghost_type);
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
+ }
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.size() == nb_element,
"The vector intf(" << intf.getID()
<< ") has not the good size.");
#endif
#define INTEGRATE(type) \
integrator.integrate<type>(f, intf, nb_degree_of_freedom, ghost_type, \
filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INTEGRATE);
#undef INTEGRATE
}
/* -------------------------------------------------------------------------- */
template <>
void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
- gradientOnIntegrationPoints(const Array<Real> &, Array<Real> &, const UInt,
- const ElementType &, const GhostType &,
- const Array<UInt> &) const {
+ gradientOnIntegrationPoints(
+ const Array<Real> & /* u */, Array<Real> & /* nablauq */,
+ UInt /* nb_degree_of_freedom */, ElementType /* type */,
+ GhostType /* ghost_type */,
+ const Array<UInt> & /* filter_elements */) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/fe_engine/fe_engine_template_tmpl.hh b/src/fe_engine/fe_engine_template_tmpl.hh
index 7d69abe75..e6d3f59ec 100644
--- a/src/fe_engine/fe_engine_template_tmpl.hh
+++ b/src/fe_engine/fe_engine_template_tmpl.hh
@@ -1,1402 +1,1421 @@
/**
* @file fe_engine_template_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Feb 15 2011
* @date last modification: Tue Feb 20 2018
*
* @brief Template implementation of FEEngineTemplate
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dof_manager.hh"
#include "fe_engine_template.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::FEEngineTemplate(
- Mesh & mesh, UInt spatial_dimension, ID id, MemoryID memory_id)
+ Mesh & mesh, UInt spatial_dimension, const ID & id, MemoryID memory_id)
: FEEngine(mesh, spatial_dimension, id, memory_id),
integrator(mesh, spatial_dimension, id, memory_id),
shape_functions(mesh, spatial_dimension, id, memory_id) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::~FEEngineTemplate() =
default;
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GradientOnIntegrationPointsHelper {
template <class S>
- static void call(const S &, Mesh &, const Array<Real> &, Array<Real> &,
- const UInt, const ElementType &, const GhostType &,
- const Array<UInt> &) {
+ static void call(const S & /*unused*/, Mesh & /*unused*/,
+ const Array<Real> & /*unused*/, Array<Real> & /*unused*/,
+ const UInt /*unused*/, ElementType /*unused*/,
+ GhostType /*unused*/,
+ const Array<UInt> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_GRADIENT(type) \
if (element_dimension == ElementClass<type>::getSpatialDimension()) \
shape_functions.template gradientOnIntegrationPoints<type>( \
u, nablauq, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GradientOnIntegrationPointsHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, Mesh & mesh, \
const Array<Real> & u, Array<Real> & nablauq, \
const UInt nb_degree_of_freedom, \
- const ElementType & type, const GhostType & ghost_type, \
+ ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
UInt element_dimension = mesh.getSpatialDimension(type); \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_GRADIENT, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER,
AKANTU_FE_ENGINE_LIST_GRADIENT_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER
#undef COMPUTE_GRADIENT
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
gradientOnIntegrationPoints(const Array<Real> & u, Array<Real> & nablauq,
const UInt nb_degree_of_freedom,
- const ElementType & type,
- const GhostType & ghost_type,
+ ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type, ghost_type);
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
+ }
UInt nb_points =
shape_functions.getIntegrationPoints(type, ghost_type).cols();
#ifndef AKANTU_NDEBUG
UInt element_dimension = mesh.getSpatialDimension(type);
AKANTU_DEBUG_ASSERT(u.size() == mesh.getNbNodes(),
"The vector u(" << u.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(u.getNbComponent() == nb_degree_of_freedom,
"The vector u("
<< u.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(
nablauq.getNbComponent() == nb_degree_of_freedom * element_dimension,
"The vector nablauq(" << nablauq.getID()
<< ") has not the good number of component.");
// AKANTU_DEBUG_ASSERT(nablauq.size() == nb_element * nb_points,
// "The vector nablauq(" << nablauq.getID()
// << ") has not the good size.");
#endif
nablauq.resize(nb_element * nb_points);
fe_engine::details::GradientOnIntegrationPointsHelper<kind>::call(
shape_functions, mesh, u, nablauq, nb_degree_of_freedom, type, ghost_type,
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::initShapeFunctions(
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
initShapeFunctions(mesh.getNodes(), ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::initShapeFunctions(
- const Array<Real> & nodes, const GhostType & ghost_type) {
+ const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
integrator.initIntegrator(nodes, type, ghost_type);
const auto & control_points = getIntegrationPoints(type, ghost_type);
shape_functions.initShapeFunctions(nodes, control_points, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateHelper {};
#define INTEGRATE(type) \
integrator.template integrate<type>(f, intf, nb_degree_of_freedom, \
ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_HELPER(kind) \
template <> struct IntegrateHelper<kind> { \
template <class I> \
static void call(const I & integrator, const Array<Real> & f, \
Array<Real> & intf, UInt nb_degree_of_freedom, \
- const ElementType & type, const GhostType & ghost_type, \
+ ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_INTEGRATE_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_element = mesh.getNbElement(type, ghost_type);
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
+ }
#ifndef AKANTU_NDEBUG
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
#endif
intf.resize(nb_element);
fe_engine::details::IntegrateHelper<kind>::call(integrator, f, intf,
nb_degree_of_freedom, type,
ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateScalarHelper {};
#define INTEGRATE(type) \
integral = \
integrator.template integrate<type>(f, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER(kind) \
template <> struct IntegrateScalarHelper<kind> { \
template <class I> \
static Real call(const I & integrator, const Array<Real> & f, \
- const ElementType & type, const GhostType & ghost_type, \
+ ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
Real integral = 0.; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
return integral; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
Real FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
- const Array<Real> & f, const ElementType & type,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ const Array<Real> & f, ElementType type,
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
// std::stringstream sstr; sstr << ghost_type;
// AKANTU_DEBUG_ASSERT(sstr.str() == nablauq.getTag(),
// "The vector " << nablauq.getID() << " is not taged " <<
// ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
+ }
UInt nb_quadrature_points = getNbIntegrationPoints(type, ghost_type);
AKANTU_DEBUG_ASSERT(
f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << ") has not the good size. (" << f.size()
<< "!=" << nb_quadrature_points * nb_element << ")");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == 1,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
#endif
Real integral = fe_engine::details::IntegrateScalarHelper<kind>::call(
integrator, f, type, ghost_type, filter_elements);
AKANTU_DEBUG_OUT();
return integral;
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateScalarOnOneElementHelper {};
#define INTEGRATE(type) \
res = integrator.template integrate<type>(f, index, ghost_type);
#define AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER(kind) \
template <> struct IntegrateScalarOnOneElementHelper<kind> { \
template <class I> \
static Real call(const I & integrator, const Vector<Real> & f, \
- const ElementType & type, UInt index, \
- const GhostType & ghost_type) { \
+ ElementType type, UInt index, \
+ GhostType ghost_type) { \
Real res = 0.; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
return res; \
} \
};
AKANTU_BOOST_ALL_KIND(
AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
Real FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
- const Vector<Real> & f, const ElementType & type, UInt index,
- const GhostType & ghost_type) const {
+ const Vector<Real> & f, ElementType type, UInt index,
+ GhostType ghost_type) const {
Real res = fe_engine::details::IntegrateScalarOnOneElementHelper<kind>::call(
integrator, f, type, index, ghost_type);
return res;
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateOnIntegrationPointsHelper {};
#define INTEGRATE(type) \
integrator.template integrateOnIntegrationPoints<type>( \
f, intf, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct IntegrateOnIntegrationPointsHelper<kind> { \
template <class I> \
static void call(const I & integrator, const Array<Real> & f, \
Array<Real> & intf, UInt nb_degree_of_freedom, \
- const ElementType & type, const GhostType & ghost_type, \
+ ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(
AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom,
- const ElementType & type,
- const GhostType & ghost_type,
+ ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_element = mesh.getNbElement(type, ghost_type);
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
+ }
UInt nb_quadrature_points = getNbIntegrationPoints(type);
#ifndef AKANTU_NDEBUG
// std::stringstream sstr; sstr << ghost_type;
// AKANTU_DEBUG_ASSERT(sstr.str() == nablauq.getTag(),
// "The vector " << nablauq.getID() << " is not taged " <<
// ghost_type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
#endif
intf.resize(nb_element * nb_quadrature_points);
fe_engine::details::IntegrateOnIntegrationPointsHelper<kind>::call(
integrator, f, intf, nb_degree_of_freedom, type, ghost_type,
filter_elements);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct InterpolateOnIntegrationPointsHelper {
template <class S>
- static void call(const S &, const Array<Real> &, Array<Real> &,
- const UInt, const ElementType &, const GhostType &,
- const Array<UInt> &) {
+ static void call(const S & /*unused*/, const Array<Real> & /*unused*/,
+ Array<Real> & /*unused*/, const UInt /*unused*/,
+ ElementType /*unused*/,
+ GhostType /*unused*/,
+ const Array<UInt> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define INTERPOLATE(type) \
shape_functions.template interpolateOnIntegrationPoints<type>( \
u, uq, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct InterpolateOnIntegrationPointsHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & u, \
Array<Real> & uq, const UInt nb_degree_of_freedom, \
- const ElementType & type, const GhostType & ghost_type, \
+ ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTERPOLATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER,
AKANTU_FE_ENGINE_LIST_INTERPOLATE_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER
#undef INTERPOLATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateOnIntegrationPoints(const Array<Real> & u, Array<Real> & uq,
const UInt nb_degree_of_freedom,
- const ElementType & type,
- const GhostType & ghost_type,
+ ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_points =
shape_functions.getIntegrationPoints(type, ghost_type).cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
+ }
#ifndef AKANTU_NDEBUG
AKANTU_DEBUG_ASSERT(u.size() == mesh.getNbNodes(),
"The vector u(" << u.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(u.getNbComponent() == nb_degree_of_freedom,
"The vector u("
<< u.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(uq.getNbComponent() == nb_degree_of_freedom,
"The vector uq("
<< uq.getID()
<< ") has not the good number of component.");
#endif
uq.resize(nb_element * nb_points);
fe_engine::details::InterpolateOnIntegrationPointsHelper<kind>::call(
shape_functions, u, uq, nb_degree_of_freedom, type, ghost_type,
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements) const {
AKANTU_DEBUG_IN();
const Array<UInt> * filter = nullptr;
for (auto ghost_type : ghost_types) {
- for (auto & type : uq.elementTypes(_all_dimensions, ghost_type, kind)) {
+ for (auto && type : uq.elementTypes(_all_dimensions, ghost_type, kind)) {
UInt nb_quad_per_element = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = 0;
- if (filter_elements) {
+ if (filter_elements != nullptr) {
filter = &((*filter_elements)(type, ghost_type));
nb_element = filter->size();
} else {
filter = &empty_filter;
nb_element = mesh.getNbElement(type, ghost_type);
}
UInt nb_tot_quad = nb_quad_per_element * nb_element;
Array<Real> & quad = uq(type, ghost_type);
quad.resize(nb_tot_quad);
interpolateOnIntegrationPoints(u, quad, quad.getNbComponent(), type,
ghost_type, *filter);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeBtDHelper {};
#define COMPUTE_BTD(type) \
shape_functions.template computeBtD<type>(Ds, BtDs, ghost_type, \
filter_elements);
#define AKANTU_SPECIALIZE_COMPUTE_BtD_HELPER(kind) \
template <> struct ComputeBtDHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & Ds, \
- Array<Real> & BtDs, const ElementType & type, \
- const GhostType & ghost_type, \
+ Array<Real> & BtDs, ElementType type, \
+ GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_BTD, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_COMPUTE_BtD_HELPER)
#undef AKANTU_SPECIALIZE_COMPUTE_BtD_HELPER
#undef COMPUTE_BTD
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeBtD(
- const Array<Real> & Ds, Array<Real> & BtDs, const ElementType & type,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ const Array<Real> & Ds, Array<Real> & BtDs, ElementType type,
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
fe_engine::details::ComputeBtDHelper<kind>::call(
shape_functions, Ds, BtDs, type, ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeBtDBHelper {};
#define COMPUTE_BTDB(type) \
shape_functions.template computeBtDB<type>(Ds, BtDBs, order_d, ghost_type, \
filter_elements);
#define AKANTU_SPECIALIZE_COMPUTE_BtDB_HELPER(kind) \
template <> struct ComputeBtDBHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & Ds, \
Array<Real> & BtDBs, UInt order_d, \
- const ElementType & type, const GhostType & ghost_type, \
+ ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_BTDB, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_COMPUTE_BtDB_HELPER)
#undef AKANTU_SPECIALIZE_COMPUTE_BtDB_HELPER
#undef COMPUTE_BTDB
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeBtDB(
const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
fe_engine::details::ComputeBtDBHelper<kind>::call(
shape_functions, Ds, BtDBs, order_d, type, ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeNtbHelper {};
#define COMPUTE_Ntb(type) \
shape_functions.template computeNtb<type>(bs, Ntbs, ghost_type, \
filter_elements);
#define AKANTU_SPECIALIZE_COMPUTE_Ntb_HELPER(kind) \
template <> struct ComputeNtbHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & bs, \
- Array<Real> & Ntbs, const ElementType & type, \
- const GhostType & ghost_type, \
+ Array<Real> & Ntbs, ElementType type, \
+ GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_Ntb, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_COMPUTE_Ntb_HELPER)
#undef AKANTU_SPECIALIZE_COMPUTE_Ntb_HELPER
#undef COMPUTE_Ntb
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeNtb(
- const Array<Real> & bs, Array<Real> & Ntbs, const ElementType & type,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ const Array<Real> & bs, Array<Real> & Ntbs, ElementType type,
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
fe_engine::details::ComputeNtbHelper<kind>::call(
shape_functions, bs, Ntbs, type, ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
interpolateOnIntegrationPoints(
nodes_coordinates, quadrature_points_coordinates, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
- Array<Real> & quadrature_points_coordinates, const ElementType & type,
- const GhostType & ghost_type,
+ Array<Real> & quadrature_points_coordinates, ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
interpolateOnIntegrationPoints(
nodes_coordinates, quadrature_points_coordinates, spatial_dimension, type,
ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_for_interpolation", getID(),
getMemoryID());
quadrature_points_coordinates.initialize(*this,
_nb_component = spatial_dimension);
computeIntegrationPointsCoordinates(quadrature_points_coordinates,
element_filter);
shape_functions.initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates,
interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, quadrature_points_coordinates,
element_filter);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
- ElementTypeMapArray<Real> & result, const GhostType ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
ElementTypeMapArray<Real> interpolation_points_coordinates_matrices(
"interpolation_points_coordinates_matrices", id, memory_id);
ElementTypeMapArray<Real> quad_points_coordinates_inv_matrices(
"quad_points_coordinates_inv_matrices", id, memory_id);
initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates,
interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, element_filter);
interpolateElementalFieldFromIntegrationPoints(
field, interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, result, ghost_type, element_filter);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
- ElementTypeMapArray<Real> & result, const GhostType ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
shape_functions.interpolateElementalFieldFromIntegrationPoints(
field, interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, result, ghost_type, element_filter);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct InterpolateHelper {
template <class S>
- static void call(const S &, const Vector<Real> &, UInt,
- const Matrix<Real> &, Vector<Real> &,
- const ElementType &, const GhostType &) {
+ static void call(const S & /*unused*/, const Vector<Real> & /*unused*/,
+ UInt /*unused*/, const Matrix<Real> & /*unused*/,
+ Vector<Real> & /*unused*/,
+ ElementType /*unused*/,
+ GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define INTERPOLATE(type) \
shape_functions.template interpolate<type>( \
real_coords, element, nodal_values, interpolated, ghost_type);
#define AKANTU_SPECIALIZE_INTERPOLATE_HELPER(kind) \
template <> struct InterpolateHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const Matrix<Real> & nodal_values, \
- Vector<Real> & interpolated, const ElementType & type, \
- const GhostType & ghost_type) { \
+ Vector<Real> & interpolated, ElementType type, \
+ GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTERPOLATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_INTERPOLATE_HELPER,
AKANTU_FE_ENGINE_LIST_INTERPOLATE)
#undef AKANTU_SPECIALIZE_INTERPOLATE_HELPER
#undef INTERPOLATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::interpolate(
const Vector<Real> & real_coords, const Matrix<Real> & nodal_values,
Vector<Real> & interpolated, const Element & element) const {
AKANTU_DEBUG_IN();
fe_engine::details::InterpolateHelper<kind>::call(
shape_functions, real_coords, element.element, nodal_values, interpolated,
element.type, element.ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
- computeNormalsOnIntegrationPoints(const GhostType & ghost_type) {
+ computeNormalsOnIntegrationPoints(GhostType ghost_type) {
AKANTU_DEBUG_IN();
computeNormalsOnIntegrationPoints(mesh.getNodes(), ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
AKANTU_DEBUG_IN();
// Real * coord = mesh.getNodes().storage();
UInt spatial_dimension = mesh.getSpatialDimension();
// allocate the normal arrays
normals_on_integration_points.initialize(
*this, _nb_component = spatial_dimension,
_spatial_dimension = element_dimension, _ghost_type = ghost_type,
_element_kind = kind);
// loop over the type to build the normals
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
auto & normals_on_quad = normals_on_integration_points(type, ghost_type);
computeNormalsOnIntegrationPoints(field, normals_on_quad, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeNormalsOnIntegrationPoints {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
- static void call(const FEEngineTemplate<I, S, k, IOF> &,
- const Array<Real> &, Array<Real> &, const ElementType &,
- const GhostType &) {
+ static void call(const FEEngineTemplate<I, S, k, IOF> & /*unused*/,
+ const Array<Real> & /*unused*/, Array<Real> & /*unused*/,
+ ElementType /*unused*/,
+ GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_NORMALS_ON_INTEGRATION_POINTS(type) \
fem.template computeNormalsOnIntegrationPoints<type>(field, normal, \
ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS(kind) \
template <> struct ComputeNormalsOnIntegrationPoints<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF> \
static void call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const Array<Real> & field, Array<Real> & normal, \
- const ElementType & type, const GhostType & ghost_type) { \
+ ElementType type, GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_NORMALS_ON_INTEGRATION_POINTS, \
kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS,
AKANTU_FE_ENGINE_LIST_COMPUTE_NORMALS_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS
#undef COMPUTE_NORMALS_ON_INTEGRATION_POINTS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
- const ElementType & type,
- const GhostType & ghost_type) const {
+ ElementType type,
+ GhostType ghost_type) const {
fe_engine::details::ComputeNormalsOnIntegrationPoints<kind>::call(
*this, field, normal, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
if (type == _point_1) {
computeNormalsOnIntegrationPointsPoint1(field, normal, ghost_type);
return;
}
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_points = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
normal.resize(nb_element * nb_points);
Array<Real>::matrix_iterator normals_on_quad =
normal.begin_reinterpret(spatial_dimension, nb_points, nb_element);
Array<Real> f_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, field, f_el, type, ghost_type);
const Matrix<Real> & quads =
integrator.template getIntegrationPoints<type>(ghost_type);
Array<Real>::matrix_iterator f_it =
f_el.begin(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem) {
ElementClass<type>::computeNormalsOnNaturalCoordinates(quads, *f_it,
*normals_on_quad);
++normals_on_quad;
++f_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
template <ElementKind kind> struct InverseMapHelper {
template <class S>
static void
call(const S & /*shape_functions*/, const Vector<Real> & /*real_coords*/,
- UInt /*element*/, const ElementType & /*type*/,
- Vector<Real> & /*natural_coords*/, const GhostType & /*ghost_type*/) {
+ UInt /*element*/, ElementType /*type*/,
+ Vector<Real> & /*natural_coords*/, GhostType /*ghost_type*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define INVERSE_MAP(type) \
shape_functions.template inverseMap<type>(real_coords, element, \
natural_coords, ghost_type);
#define AKANTU_SPECIALIZE_INVERSE_MAP_HELPER(kind) \
template <> struct InverseMapHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
- const ElementType & type, Vector<Real> & natural_coords, \
- const GhostType & ghost_type) { \
+ ElementType type, Vector<Real> & natural_coords, \
+ GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INVERSE_MAP, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_INVERSE_MAP_HELPER,
AKANTU_FE_ENGINE_LIST_INVERSE_MAP)
#undef AKANTU_SPECIALIZE_INVERSE_MAP_HELPER
#undef INVERSE_MAP
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::inverseMap(
- const Vector<Real> & real_coords, UInt element, const ElementType & type,
- Vector<Real> & natural_coords, const GhostType & ghost_type) const {
+ const Vector<Real> & real_coords, UInt element, ElementType type,
+ Vector<Real> & natural_coords, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
InverseMapHelper<kind>::call(shape_functions, real_coords, element, type,
natural_coords, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ContainsHelper {
template <class S>
- static void call(const S &, const Vector<Real> &, UInt,
- const ElementType &, const GhostType &) {
+ static void call(const S & /*unused*/, const Vector<Real> & /*unused*/,
+ UInt /*unused*/, ElementType /*unused*/,
+ GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define CONTAINS(type) \
contain = shape_functions.template contains<type>(real_coords, element, \
ghost_type);
#define AKANTU_SPECIALIZE_CONTAINS_HELPER(kind) \
template <> struct ContainsHelper<kind> { \
template <template <ElementKind> class S, ElementKind k> \
static bool call(const S<k> & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
- const ElementType & type, const GhostType & ghost_type) { \
+ ElementType type, GhostType ghost_type) { \
bool contain = false; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(CONTAINS, kind); \
return contain; \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_CONTAINS_HELPER,
AKANTU_FE_ENGINE_LIST_CONTAINS)
#undef AKANTU_SPECIALIZE_CONTAINS_HELPER
#undef CONTAINS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline bool FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::contains(
- const Vector<Real> & real_coords, UInt element, const ElementType & type,
- const GhostType & ghost_type) const {
+ const Vector<Real> & real_coords, UInt element, ElementType type,
+ GhostType ghost_type) const {
return fe_engine::details::ContainsHelper<kind>::call(
shape_functions, real_coords, element, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeShapesHelper {
template <class S>
- static void call(const S &, const Vector<Real> &, UInt, const ElementType,
- Vector<Real> &, const GhostType &) {
+ static void call(const S & /*unused*/, const Vector<Real> & /*unused*/,
+ UInt /*unused*/, const ElementType /*unused*/,
+ Vector<Real> & /*unused*/,
+ GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_SHAPES(type) \
shape_functions.template computeShapes<type>(real_coords, element, shapes, \
ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER(kind) \
template <> struct ComputeShapesHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType type, Vector<Real> & shapes, \
- const GhostType & ghost_type) { \
+ GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_SHAPES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER,
AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES)
#undef AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER
#undef COMPUTE_SHAPES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapes(
- const Vector<Real> & real_coords, UInt element, const ElementType & type,
- Vector<Real> & shapes, const GhostType & ghost_type) const {
+ const Vector<Real> & real_coords, UInt element, ElementType type,
+ Vector<Real> & shapes, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::ComputeShapesHelper<kind>::call(
shape_functions, real_coords, element, type, shapes, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeShapeDerivativesHelper {
template <class S>
static void call(__attribute__((unused)) const S & shape_functions,
__attribute__((unused)) const Vector<Real> & real_coords,
__attribute__((unused)) UInt element,
__attribute__((unused)) const ElementType type,
__attribute__((unused)) Matrix<Real> & shape_derivatives,
- __attribute__((unused)) const GhostType & ghost_type) {
+ __attribute__((unused)) GhostType ghost_type) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_SHAPE_DERIVATIVES(type) \
Matrix<Real> coords_mat(real_coords.storage(), shape_derivatives.rows(), 1); \
Tensor3<Real> shapesd_tensor(shape_derivatives.storage(), \
shape_derivatives.rows(), \
shape_derivatives.cols(), 1); \
shape_functions.template computeShapeDerivatives<type>( \
coords_mat, element, shapesd_tensor, ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER(kind) \
template <> struct ComputeShapeDerivativesHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType type, Matrix<Real> & shape_derivatives, \
- const GhostType & ghost_type) { \
+ GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_SHAPE_DERIVATIVES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER,
AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES_DERIVATIVES)
#undef AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER
#undef COMPUTE_SHAPE_DERIVATIVES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapeDerivatives(
- const Vector<Real> & real_coords, UInt element, const ElementType & type,
- Matrix<Real> & shape_derivatives, const GhostType & ghost_type) const {
+ const Vector<Real> & real_coords, UInt element, ElementType type,
+ Matrix<Real> & shape_derivatives, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::ComputeShapeDerivativesHelper<kind>::call(
shape_functions, real_coords, element, type, shape_derivatives,
ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetNbIntegrationPointsHelper {};
#define GET_NB_INTEGRATION_POINTS(type) \
nb_quad_points = integrator.template getNbIntegrationPoints<type>(ghost_type);
#define AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GetNbIntegrationPointsHelper<kind> { \
template <template <ElementKind, class> class I, ElementKind k, class IOF> \
static UInt call(const I<k, IOF> & integrator, const ElementType type, \
- const GhostType & ghost_type) { \
+ GhostType ghost_type) { \
UInt nb_quad_points = 0; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_NB_INTEGRATION_POINTS, kind); \
return nb_quad_points; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER
#undef GET_NB_INTEGRATION
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline UInt
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getNbIntegrationPoints(
- const ElementType & type, const GhostType & ghost_type) const {
+ ElementType type, GhostType ghost_type) const {
return fe_engine::details::GetNbIntegrationPointsHelper<kind>::call(
integrator, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetShapesHelper {};
#define GET_SHAPES(type) ret = &(shape_functions.getShapes(type, ghost_type));
#define AKANTU_SPECIALIZE_GET_SHAPES_HELPER(kind) \
template <> struct GetShapesHelper<kind> { \
template <class S> \
static const Array<Real> & call(const S & shape_functions, \
const ElementType type, \
- const GhostType & ghost_type) { \
+ GhostType ghost_type) { \
const Array<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_SHAPES, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_SHAPES_HELPER)
#undef AKANTU_SPECIALIZE_GET_SHAPES_HELPER
#undef GET_SHAPES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Array<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getShapes(
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
__attribute__((unused)) UInt id) const {
return fe_engine::details::GetShapesHelper<kind>::call(shape_functions, type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetShapesDerivativesHelper {
template <template <ElementKind> class S, ElementKind k>
- static const Array<Real> & call(const S<k> &, const ElementType &,
- const GhostType &, UInt) {
+ static const Array<Real> &
+ call(const S<k> & /*unused*/, ElementType /*unused*/,
+ GhostType /*unused*/, UInt /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define GET_SHAPES_DERIVATIVES(type) \
ret = &(shape_functions.getShapesDerivatives(type, ghost_type));
#define AKANTU_SPECIALIZE_GET_SHAPES_DERIVATIVES_HELPER(kind) \
template <> struct GetShapesDerivativesHelper<kind> { \
template <template <ElementKind> class S, ElementKind k> \
static const Array<Real> & \
call(const S<k> & shape_functions, const ElementType type, \
- const GhostType & ghost_type, __attribute__((unused)) UInt id) { \
+ GhostType ghost_type, __attribute__((unused)) UInt id) { \
const Array<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_SHAPES_DERIVATIVES, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_GET_SHAPES_DERIVATIVES_HELPER,
AKANTU_FE_ENGINE_LIST_GET_SHAPES_DERIVATIVES)
#undef AKANTU_SPECIALIZE_GET_SHAPE_DERIVATIVES_HELPER
#undef GET_SHAPES_DERIVATIVES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Array<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getShapesDerivatives(
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
__attribute__((unused)) UInt id) const {
return fe_engine::details::GetShapesDerivativesHelper<kind>::call(
shape_functions, type, ghost_type, id);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetIntegrationPointsHelper {};
#define GET_INTEGRATION_POINTS(type) \
ret = &(integrator.template getIntegrationPoints<type>(ghost_type));
#define AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GetIntegrationPointsHelper<kind> { \
template <template <ElementKind, class> class I, ElementKind k, class IOF> \
static const Matrix<Real> & call(const I<k, IOF> & integrator, \
const ElementType type, \
- const GhostType & ghost_type) { \
+ GhostType ghost_type) { \
const Matrix<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_INTEGRATION_POINTS, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER
#undef GET_INTEGRATION_POINTS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Matrix<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getIntegrationPoints(
- const ElementType & type, const GhostType & ghost_type) const {
+ ElementType type, GhostType ghost_type) const {
return fe_engine::details::GetIntegrationPointsHelper<kind>::call(
integrator, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::printself(
std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "FEEngineTemplate [" << std::endl;
stream << space << " + parent [" << std::endl;
FEEngine::printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << " + shape functions [" << std::endl;
shape_functions.printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << " + integrator [" << std::endl;
integrator.printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsAdded(
- const Array<Element> & new_elements, const NewElementsEvent &) {
+ const Array<Element> & new_elements, const NewElementsEvent & /*unused*/) {
integrator.onElementsAdded(new_elements);
shape_functions.onElementsAdded(new_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsRemoved(
- const Array<Element> &, const ElementTypeMapArray<UInt> &,
- const RemovedElementsEvent &) {}
+ const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const RemovedElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsChanged(
- const Array<Element> &, const Array<Element> &,
- const ElementTypeMapArray<UInt> &, const ChangedElementsEvent &) {}
+ const Array<Element> & /*unused*/, const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const ChangedElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPointsPoint1(
- const Array<Real> &, Array<Real> & normal,
- const GhostType & ghost_type) const {
+ const Array<Real> & /*unused*/, Array<Real> & normal,
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(mesh.getSpatialDimension() == 1,
"Mesh dimension must be 1 to compute normals on points!");
const auto type = _point_1;
auto spatial_dimension = mesh.getSpatialDimension();
// UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_points = getNbIntegrationPoints(type, ghost_type);
const auto & connectivity = mesh.getConnectivity(type, ghost_type);
auto nb_element = connectivity.size();
normal.resize(nb_element * nb_points);
auto normals_on_quad =
normal.begin_reinterpret(spatial_dimension, nb_points, nb_element);
const auto & segments = mesh.getElementToSubelement(type, ghost_type);
const auto & coords = mesh.getNodes();
const Mesh * mesh_segment;
- if (mesh.isMeshFacets())
+ if (mesh.isMeshFacets()) {
mesh_segment = &(mesh.getMeshParent());
- else
+ } else {
mesh_segment = &mesh;
+ }
for (UInt elem = 0; elem < nb_element; ++elem) {
UInt nb_segment = segments(elem).size();
AKANTU_DEBUG_ASSERT(
nb_segment > 0,
"Impossible to compute a normal on a point connected to 0 segments");
Real normal_value = 1;
if (nb_segment == 1) {
auto point = connectivity(elem);
const auto segment = segments(elem)[0];
const auto & segment_connectivity =
mesh_segment->getConnectivity(segment.type, segment.ghost_type);
Vector<UInt> segment_points = segment_connectivity.begin(
Mesh::getNbNodesPerElement(segment.type))[segment.element];
Real difference;
if (segment_points(0) == point) {
difference = coords(elem) - coords(segment_points(1));
} else {
difference = coords(elem) - coords(segment_points(0));
}
normal_value = difference / std::abs(difference);
}
for (UInt n(0); n < nb_points; ++n) {
(*normals_on_quad)(0, n) = normal_value;
}
++normals_on_quad;
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/fe_engine/fe_engine_template_tmpl_field.hh b/src/fe_engine/fe_engine_template_tmpl_field.hh
index b09253646..c217c5892 100644
--- a/src/fe_engine/fe_engine_template_tmpl_field.hh
+++ b/src/fe_engine/fe_engine_template_tmpl_field.hh
@@ -1,452 +1,455 @@
/**
* @file fe_engine_template_tmpl_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
* @date last modification: Thu Dec 07 2017
*
* @brief implementation of the assemble field s functions
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine_template.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH__
-#define __AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH__
+#ifndef AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH_
+#define AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Matrix lumping functions */
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
namespace {
template <class Functor>
void fillField(const Functor & field_funct, Array<Real> & field,
UInt nb_element, UInt nb_integration_points,
- const ElementType & type, const GhostType & ghost_type) {
+ ElementType type, GhostType ghost_type) {
UInt nb_degree_of_freedom = field.getNbComponent();
field.resize(nb_integration_points * nb_element);
auto field_it = field.begin_reinterpret(
nb_degree_of_freedom, nb_integration_points, nb_element);
Element el{type, 0, ghost_type};
for (; el.element < nb_element; ++el.element, ++field_it) {
field_funct(*field_it, el);
}
}
} // namespace
} // namespace details
} // namespace fe_engine
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct AssembleLumpedTemplateHelper {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
- static void
- call(const FEEngineTemplate<I, S, k, IOF> &,
- const std::function<void(Matrix<Real> &, const Element &)> &,
- const ID &, const ID &, DOFManager &, ElementType,
- const GhostType &) {
+ static void call(const FEEngineTemplate<I, S, k, IOF> & /*unused*/,
+ const std::function<void(Matrix<Real> &,
+ const Element &)> & /*unused*/,
+ const ID & /*unused*/, const ID & /*unused*/,
+ DOFManager & /*unused*/, ElementType /*unused*/,
+ GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define ASSEMBLE_LUMPED(type) \
fem.template assembleFieldLumped<type>(field_funct, lumped, dof_id, \
dof_manager, ghost_type)
#define AKANTU_SPECIALIZE_ASSEMBLE_HELPER(kind) \
template <> struct AssembleLumpedTemplateHelper<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF> \
static void \
call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const std::function<void(Matrix<Real> &, const Element &)> & \
field_funct, \
const ID & lumped, const ID & dof_id, DOFManager & dof_manager, \
- ElementType type, const GhostType & ghost_type) { \
+ ElementType type, GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_LUMPED, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_ASSEMBLE_HELPER,
AKANTU_FE_ENGINE_LIST_ASSEMBLE_FIELDS)
#undef AKANTU_SPECIALIZE_ASSEMBLE_HELPER
#undef AKANTU_SPECIALIZE_ASSEMBLE_HELPER_LIST_KIND
#undef ASSEMBLE_LUMPED
} // namespace details
} // namespace fe_engine
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IOF>
void FEEngineTemplate<I, S, kind, IOF>::assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- ElementType type, const GhostType & ghost_type) const {
+ ElementType type, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::AssembleLumpedTemplateHelper<kind>::call(
*this, field_funct, matrix_id, dof_id, dof_manager, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_degree_of_freedom = dof_manager.getDOFs(dof_id).getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_integration_points = this->getNbIntegrationPoints(type);
Array<Real> field(0, nb_degree_of_freedom);
fe_engine::details::fillField(field_funct, field, nb_element,
nb_integration_points, type, ghost_type);
switch (type) {
case _triangle_6:
case _quadrangle_8:
case _tetrahedron_10:
case _hexahedron_20:
case _pentahedron_15:
this->template assembleLumpedDiagonalScaling<type>(field, matrix_id, dof_id,
dof_manager, ghost_type);
break;
default:
this->template assembleLumpedRowSum<type>(field, matrix_id, dof_id,
dof_manager, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j dV =
* \int \rho \varphi_i dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
assembleLumpedRowSum(const Array<Real> & field, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt shapes_size = ElementClass<type>::getShapeSize();
UInt nb_degree_of_freedom = field.getNbComponent();
- Array<Real> * field_times_shapes =
+ auto * field_times_shapes =
new Array<Real>(0, shapes_size * nb_degree_of_freedom);
shape_functions.template computeNtb<type>(field, *field_times_shapes,
ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
- Array<Real> * int_field_times_shapes = new Array<Real>(
+ auto * int_field_times_shapes = new Array<Real>(
nb_element, shapes_size * nb_degree_of_freedom, "inte_rho_x_shapes");
integrator.template integrate<type>(
*field_times_shapes, *int_field_times_shapes,
nb_degree_of_freedom * shapes_size, ghost_type, empty_filter);
delete field_times_shapes;
dof_manager.assembleElementalArrayToLumpedMatrix(
dof_id, *int_field_times_shapes, matrix_id, type, ghost_type);
delete int_field_times_shapes;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = c * M_{ii} = \int_{V_e} \rho dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
assembleLumpedDiagonalScaling(const Array<Real> & field,
const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
- const ElementType & type_p1 = ElementClass<type>::getP1ElementType();
+ ElementType type_p1 = ElementClass<type>::getP1ElementType();
UInt nb_nodes_per_element_p1 = Mesh::getNbNodesPerElement(type_p1);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = field.getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
Vector<Real> nodal_factor(nb_nodes_per_element);
#define ASSIGN_WEIGHT_TO_NODES(corner, mid) \
{ \
for (UInt n = 0; n < nb_nodes_per_element_p1; n++) \
nodal_factor(n) = corner; \
for (UInt n = nb_nodes_per_element_p1; n < nb_nodes_per_element; n++) \
nodal_factor(n) = mid; \
}
if (type == _triangle_6)
ASSIGN_WEIGHT_TO_NODES(1. / 12., 1. / 4.);
if (type == _tetrahedron_10)
ASSIGN_WEIGHT_TO_NODES(1. / 32., 7. / 48.);
if (type == _quadrangle_8)
ASSIGN_WEIGHT_TO_NODES(
3. / 76.,
16. / 76.); /** coeff. derived by scaling
* the diagonal terms of the corresponding
* consistent mass computed with 3x3 gauss points;
* coeff. are (1./36., 8./36.) for 2x2 gauss points */
if (type == _hexahedron_20)
ASSIGN_WEIGHT_TO_NODES(
7. / 248., 16. / 248.); /** coeff. derived by scaling
* the diagonal terms of the corresponding
* consistent mass computed with 3x3x3 gauss
* points; coeff. are (1./40.,
* 1./15.) for 2x2x2 gauss points */
if (type == _pentahedron_15) {
// coefficients derived by scaling the diagonal terms of the corresponding
// consistent mass computed with 8 gauss points;
- for (UInt n = 0; n < nb_nodes_per_element_p1; n++)
+ for (UInt n = 0; n < nb_nodes_per_element_p1; n++) {
nodal_factor(n) = 51. / 2358.;
+ }
Real mid_triangle = 192. / 2358.;
Real mid_quadrangle = 300. / 2358.;
nodal_factor(6) = mid_triangle;
nodal_factor(7) = mid_triangle;
nodal_factor(8) = mid_triangle;
nodal_factor(9) = mid_quadrangle;
nodal_factor(10) = mid_quadrangle;
nodal_factor(11) = mid_quadrangle;
nodal_factor(12) = mid_triangle;
nodal_factor(13) = mid_triangle;
nodal_factor(14) = mid_triangle;
}
if (nb_element == 0) {
AKANTU_DEBUG_OUT();
return;
}
#undef ASSIGN_WEIGHT_TO_NODES
/// compute @f$ \int \rho dV = \rho V @f$ for each element
auto int_field = std::make_unique<Array<Real>>(
field.size(), nb_degree_of_freedom, "inte_rho_x");
integrator.template integrate<type>(field, *int_field, nb_degree_of_freedom,
ghost_type, empty_filter);
/// distribute the mass of the element to the nodes
auto lumped_per_node = std::make_unique<Array<Real>>(
nb_element, nb_degree_of_freedom * nb_nodes_per_element, "mass_per_node");
auto int_field_it = int_field->begin(nb_degree_of_freedom);
auto lumped_per_node_it =
lumped_per_node->begin(nb_degree_of_freedom, nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Vector<Real> l = (*lumped_per_node_it)(n);
l = *int_field_it;
l *= nodal_factor(n);
}
++int_field_it;
++lumped_per_node_it;
}
dof_manager.assembleElementalArrayToLumpedMatrix(dof_id, *lumped_per_node,
matrix_id, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct AssembleFieldMatrixHelper {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
- static void
- call(const FEEngineTemplate<I, S, k, IOF> &,
- const std::function<void(Matrix<Real> &, const Element &)> &,
- const ID &, const ID &, DOFManager &, ElementType,
- const GhostType &) {
+ static void call(const FEEngineTemplate<I, S, k, IOF> & /*unused*/,
+ const std::function<void(Matrix<Real> &,
+ const Element &)> & /*unused*/,
+ const ID & /*unused*/, const ID & /*unused*/,
+ DOFManager & /*unused*/, ElementType /*unused*/,
+ GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define ASSEMBLE_MATRIX(type) \
fem.template assembleFieldMatrix<type>(field_funct, matrix_id, dof_id, \
dof_manager, ghost_type)
#define AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER(kind) \
template <> struct AssembleFieldMatrixHelper<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF> \
static void \
call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const std::function<void(Matrix<Real> &, const Element &)> & \
field_funct, \
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager, \
- ElementType type, const GhostType & ghost_type) { \
+ ElementType type, GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_MATRIX, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER,
AKANTU_FE_ENGINE_LIST_ASSEMBLE_FIELDS)
#undef AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER
#undef ASSEMBLE_MATRIX
} // namespace details
} // namespace fe_engine
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IOF>
void FEEngineTemplate<I, S, kind, IOF>::assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- ElementType type, const GhostType & ghost_type) const {
+ ElementType type, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::AssembleFieldMatrixHelper<kind>::template call(
*this, field_funct, matrix_id, dof_id, dof_manager, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j dV =
* \int \rho \varphi_i dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt shapes_size = ElementClass<type>::getShapeSize();
UInt nb_degree_of_freedom = dof_manager.getDOFs(dof_id).getNbComponent();
UInt lmat_size = nb_degree_of_freedom * shapes_size;
UInt nb_element = mesh.getNbElement(type, ghost_type);
// \int N * N so degree 2 * degree of N
const UInt polynomial_degree =
2 * ElementClassProperty<type>::polynomial_degree;
// getting the integration points
Matrix<Real> integration_points =
integrator.template getIntegrationPoints<type, polynomial_degree>();
UInt nb_integration_points = integration_points.cols();
UInt vect_size = nb_integration_points * nb_element;
// getting the shapes on the integration points
Array<Real> shapes(0, shapes_size);
shape_functions.template computeShapesOnIntegrationPoints<type>(
mesh.getNodes(), integration_points, shapes, ghost_type);
// Extending the shape functions
/// \todo move this in the shape functions as Voigt format shapes to have the
/// code in common with the structural elements
Array<Real> modified_shapes(vect_size, lmat_size * nb_degree_of_freedom, 0.);
Array<Real> local_mat(vect_size, lmat_size * lmat_size);
auto mshapes_it = modified_shapes.begin(nb_degree_of_freedom, lmat_size);
auto shapes_it = shapes.begin(shapes_size);
for (UInt q = 0; q < vect_size; ++q, ++mshapes_it, ++shapes_it) {
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
for (UInt s = 0; s < shapes_size; ++s) {
(*mshapes_it)(d, s * nb_degree_of_freedom + d) = (*shapes_it)(s);
}
}
}
// getting the value to assemble on the integration points
Array<Real> field(vect_size, nb_degree_of_freedom);
fe_engine::details::fillField(field_funct, field, nb_element,
nb_integration_points, type, ghost_type);
// computing \rho * N
mshapes_it = modified_shapes.begin(nb_degree_of_freedom, lmat_size);
auto lmat = local_mat.begin(lmat_size, lmat_size);
auto field_it = field.begin_reinterpret(nb_degree_of_freedom, field.size());
for (UInt q = 0; q < vect_size; ++q, ++lmat, ++mshapes_it, ++field_it) {
const auto & rho = *field_it;
const auto & N = *mshapes_it;
auto & mat = *lmat;
Matrix<Real> Nt = N.transpose();
for (UInt d = 0; d < Nt.cols(); ++d) {
Nt(d) *= rho(d);
}
mat.template mul<false, false>(Nt, N);
}
// integrate the elemental values
Array<Real> int_field_times_shapes(nb_element, lmat_size * lmat_size,
"inte_rho_x_shapes");
this->integrator.template integrate<type, polynomial_degree>(
local_mat, int_field_times_shapes, lmat_size * lmat_size, ghost_type);
// assemble the elemental values to the matrix
dof_manager.assembleElementalMatricesToMatrix(
matrix_id, dof_id, int_field_times_shapes, type, ghost_type);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif /* __AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH__ */
+#endif /* AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH_ */
diff --git a/src/fe_engine/fe_engine_template_tmpl_struct.hh b/src/fe_engine/fe_engine_template_tmpl_struct.hh
index 3ac52df59..c0fe600ee 100644
--- a/src/fe_engine/fe_engine_template_tmpl_struct.hh
+++ b/src/fe_engine/fe_engine_template_tmpl_struct.hh
@@ -1,100 +1,101 @@
/**
* @file fe_engine_template_tmpl_struct.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 07 2014
* @date last modification: Tue Feb 20 2018
*
* @brief Template implementation of FEEngineTemplate for Structural Element
* Kinds
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_structural.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementKind kind, typename = void>
struct AssembleFieldMatrixStructHelper {};
template <ElementKind kind>
struct AssembleFieldMatrixStructHelper<
kind, typename std::enable_if<kind == _ek_structural>::type> {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
static void call(const FEEngineTemplate<I, S, k, IOF> & fem,
const Array<Real> & field_1, UInt nb_degree_of_freedom,
SparseMatrix & M, Array<Real> * n,
- ElementTypeMapArray<Real> & rotation_mat,
- const ElementType & type, const GhostType & ghost_type) {
+ ElementTypeMapArray<Real> & rotation_mat, ElementType type,
+ GhostType ghost_type) {
#define ASSEMBLE_MATRIX(type) \
fem.template assembleFieldMatrix<type>(field_1, nb_degree_of_freedom, M, n, \
rotation_mat, ghost_type)
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_MATRIX, _ek_structural);
#undef ASSEMBLE_MATRIX
}
};
// template <template <ElementKind, class> class I, template <ElementKind> class
// S,
// ElementKind kind, class IntegrationOrderFunctor>
// inline void
// FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
// const Array<Real> & field_1, UInt nb_degree_of_freedom, SparseMatrix & M,
// Array<Real> * n, ElementTypeMapArray<Real> & rotation_mat,
-// const ElementType & type, const GhostType & ghost_type) const {
+// ElementType type, GhostType ghost_type) const {
// AKANTU_DEBUG_IN();
// AssembleFieldMatrixStructHelper<kind>::template call(
// *this, field_1, nb_degree_of_freedom, M, n, rotation_mat, type,
// ghost_type);
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */ template <template <ElementKind, class> class I, template <ElementKind>
// class S,
// ElementKind kind, class IntegrationOrderFunctor>
// inline void
// FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapesMatrix(
-// const ElementType &, UInt, UInt, Array<Real> *, UInt, UInt, UInt,
-// const bool, const GhostType &) const {
+// ElementType, UInt, UInt, Array<Real> *, UInt, UInt, UInt,
+// const bool, GhostType) const {
// AKANTU_TO_IMPLEMENT();
// }
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
- const Array<Real> &, UInt, SparseMatrix &, Array<Real> *,
- ElementTypeMapArray<Real> &, const GhostType &) const {
+ const Array<Real> & /*unused*/, UInt /*unused*/, SparseMatrix & /*unused*/,
+ Array<Real> * /*unused*/, ElementTypeMapArray<Real> & /*unused*/,
+ GhostType /*unused*/) const {
AKANTU_TO_IMPLEMENT();
}
} // namespace akantu
diff --git a/src/fe_engine/gauss_integration_tmpl.hh b/src/fe_engine/gauss_integration_tmpl.hh
index 914bb4fcb..5145e2bca 100644
--- a/src/fe_engine/gauss_integration_tmpl.hh
+++ b/src/fe_engine/gauss_integration_tmpl.hh
@@ -1,278 +1,278 @@
/**
* @file gauss_integration_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 10 2016
* @date last modification: Wed Nov 29 2017
*
* @brief implementation of the gauss integration helpers
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_GAUSS_INTEGRATION_TMPL_HH__
-#define __AKANTU_GAUSS_INTEGRATION_TMPL_HH__
+#ifndef AKANTU_GAUSS_INTEGRATION_TMPL_HH_
+#define AKANTU_GAUSS_INTEGRATION_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* GaussIntegrationElement */
/* -------------------------------------------------------------------------- */
namespace _aka_gauss_helpers {
template <GaussIntegrationType type, UInt n>
struct GaussIntegrationNbPoints {
static const UInt nb_points = 0;
};
#if !defined(DOXYGEN)
template <UInt n> struct GaussIntegrationNbPoints<_git_not_defined, n> {
static const UInt nb_points = 0;
};
template <UInt n> struct GaussIntegrationNbPoints<_git_point, n> {
static const UInt nb_points = 1;
};
template <UInt n> struct GaussIntegrationNbPoints<_git_segment, n> {
- static const UInt nb_points = (n + 1) / 2 + ((n + 1) % 2 ? 1 : 0);
+ static const UInt nb_points = (n + 1) / 2 + (bool((n + 1) % 2) ? 1 : 0);
};
#define DECLARE_GAUSS_NB_POINTS(type, order, points) \
template <> struct GaussIntegrationNbPoints<type, order> { \
static const UInt nb_points = points; \
}
#define DECLARE_GAUSS_NB_POINTS_PENT(type, order, xo, yo) \
template <> struct GaussIntegrationNbPoints<type, order> { \
static const UInt x_order = xo; \
static const UInt yz_order = yo; \
static const UInt nb_points = 1; \
}
DECLARE_GAUSS_NB_POINTS(_git_triangle, 1, 1);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 2, 3);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 3, 4);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 4, 6);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 5, 7);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 1, 1);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 2, 4);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 3, 5);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 4, 15);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 5, 15);
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 1, 3,
2); // order 3 in x, order 2 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 2, 3,
2); // order 3 in x, order 2 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 3, 3,
3); // order 3 in x, order 3 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 4, 5,
5); // order 5 in x, order 5 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 5, 5,
5); // order 5 in x, order 5 in y and z
template <GaussIntegrationType type, UInt n, UInt on = n,
bool end_recurse = false>
struct GaussIntegrationNbPointsHelper {
static const UInt pnp = GaussIntegrationNbPoints<type, n>::nb_points;
static const UInt order = n;
static const UInt nb_points = pnp;
};
template <GaussIntegrationType type, UInt n, UInt on>
struct GaussIntegrationNbPointsHelper<type, n, on, true> {
static const UInt nb_points = 0;
};
#endif
/* ------------------------------------------------------------------------ */
/* Generic helper */
/* ------------------------------------------------------------------------ */
template <GaussIntegrationType type, UInt dimension, UInt n>
struct GaussIntegrationTypeDataHelper {
using git_np = GaussIntegrationNbPoints<type, n>;
using git_data = GaussIntegrationTypeData<type, git_np::nb_points>;
static UInt getNbQuadraturePoints() { return git_np::nb_points; }
- static const Matrix<Real> getQuadraturePoints() {
+ static Matrix<Real> getQuadraturePoints() {
return Matrix<Real>(git_data::quad_positions, dimension,
git_np::nb_points);
}
- static const Vector<Real> getWeights() {
+ static Vector<Real> getWeights() {
return Vector<Real>(git_data::quad_weights, git_np::nb_points);
}
};
#if !defined(DOXYGEN)
/* ------------------------------------------------------------------------ */
/* helper for _segment _quadrangle _hexahedron */
/* ------------------------------------------------------------------------ */
template <UInt dimension, UInt dp>
struct GaussIntegrationTypeDataHelper<_git_segment, dimension, dp> {
using git_np = GaussIntegrationNbPoints<_git_segment, dp>;
using git_data = GaussIntegrationTypeData<_git_segment, git_np::nb_points>;
static UInt getNbQuadraturePoints() {
return Math::pow<dimension>(git_np::nb_points);
}
- static const Matrix<Real> getQuadraturePoints() {
+ static Matrix<Real> getQuadraturePoints() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad = git_np::nb_points;
Matrix<Real> quads(dimension, tot_nquad);
Vector<Real> pos(git_data::quad_positions, nquad);
UInt offset = 1;
for (UInt d = 0; d < dimension; ++d) {
for (UInt n = 0, q = 0; n < tot_nquad; ++n, q += offset) {
UInt rq = q % tot_nquad + q / tot_nquad;
quads(d, rq) = pos(n % nquad);
}
offset *= nquad;
}
return quads;
}
- static const Vector<Real> getWeights() {
+ static Vector<Real> getWeights() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad = git_np::nb_points;
Vector<Real> quads_weights(tot_nquad, 1.);
Vector<Real> weights(git_data::quad_weights, nquad);
UInt offset = 1;
for (UInt d = 0; d < dimension; ++d) {
for (UInt n = 0, q = 0; n < tot_nquad; ++n, q += offset) {
UInt rq = q % tot_nquad + q / tot_nquad;
quads_weights(rq) *= weights(n % nquad);
}
offset *= nquad;
}
return quads_weights;
}
};
/* ------------------------------------------------------------------------ */
/* helper for _pentahedron */
/* ------------------------------------------------------------------------ */
template <UInt dimension, UInt dp>
struct GaussIntegrationTypeDataHelper<_git_pentahedron, dimension, dp> {
using git_info = GaussIntegrationNbPoints<_git_pentahedron, dp>;
using git_np_seg =
GaussIntegrationNbPoints<_git_segment, git_info::x_order>;
using git_np_tri =
GaussIntegrationNbPoints<_git_triangle, git_info::yz_order>;
using git_data_seg =
GaussIntegrationTypeData<_git_segment, git_np_seg::nb_points>;
using git_data_tri =
GaussIntegrationTypeData<_git_triangle, git_np_tri::nb_points>;
static UInt getNbQuadraturePoints() {
return git_np_seg::nb_points * git_np_tri::nb_points;
}
- static const Matrix<Real> getQuadraturePoints() {
+ static Matrix<Real> getQuadraturePoints() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad_seg = git_np_seg::nb_points;
UInt nquad_tri = git_np_tri::nb_points;
Matrix<Real> quads(dimension, tot_nquad);
Matrix<Real> pos_seg_w(git_data_seg::quad_positions, 1, nquad_seg);
Matrix<Real> pos_tri_w(git_data_tri::quad_positions, 2, nquad_tri);
for (UInt ns = 0, q = 0; ns < nquad_seg; ++ns) {
Vector<Real> pos_seg = pos_seg_w(ns);
for (UInt nt = 0; nt < nquad_tri; ++nt, ++q) {
Vector<Real> pos_tri = pos_tri_w(nt);
Vector<Real> quad = quads(q);
quad(_x) = pos_seg(_x);
quad(_y) = pos_tri(_x);
quad(_z) = pos_tri(_y);
}
}
return quads;
}
- static const Vector<Real> getWeights() {
+ static Vector<Real> getWeights() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad_seg = git_np_seg::nb_points;
UInt nquad_tri = git_np_tri::nb_points;
Vector<Real> quads_weights(tot_nquad);
Vector<Real> weight_seg(git_data_seg::quad_weights, nquad_seg);
Vector<Real> weight_tri(git_data_tri::quad_weights, nquad_tri);
for (UInt ns = 0, q = 0; ns < nquad_seg; ++ns) {
for (UInt nt = 0; nt < nquad_tri; ++nt, ++q) {
quads_weights(q) = weight_seg(ns) * weight_tri(nt);
}
}
return quads_weights;
}
};
#endif
} // namespace _aka_gauss_helpers
template <ElementType element_type, UInt n>
-const Matrix<Real>
+Matrix<Real>
GaussIntegrationElement<element_type, n>::getQuadraturePoints() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
using interpolation_property = InterpolationProperty<itp_type>;
using data_helper = _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n>;
Matrix<Real> tmp(data_helper::getQuadraturePoints());
return tmp;
}
/* -------------------------------------------------------------------------- */
template <ElementType element_type, UInt n>
-const Vector<Real> GaussIntegrationElement<element_type, n>::getWeights() {
+Vector<Real> GaussIntegrationElement<element_type, n>::getWeights() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
using interpolation_property = InterpolationProperty<itp_type>;
using data_helper = _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n>;
Vector<Real> tmp(data_helper::getWeights());
return tmp;
}
/* -------------------------------------------------------------------------- */
template <ElementType element_type, UInt n>
UInt GaussIntegrationElement<element_type, n>::getNbQuadraturePoints() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
using interpolation_property = InterpolationProperty<itp_type>;
using data_helper = _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n>;
return data_helper::getNbQuadraturePoints();
}
} // namespace akantu
-#endif /* __AKANTU_GAUSS_INTEGRATION_TMPL_HH__ */
+#endif /* AKANTU_GAUSS_INTEGRATION_TMPL_HH_ */
diff --git a/src/fe_engine/integration_point.hh b/src/fe_engine/integration_point.hh
index 72fc39f54..4e8037213 100644
--- a/src/fe_engine/integration_point.hh
+++ b/src/fe_engine/integration_point.hh
@@ -1,169 +1,170 @@
/**
* @file integration_point.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Jun 17 2015
* @date last modification: Wed Nov 08 2017
*
* @brief definition of the class IntegrationPoint
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_types.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_QUADRATURE_POINT_H
#define AKANTU_QUADRATURE_POINT_H
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
class IntegrationPoint;
extern const IntegrationPoint IntegrationPointNull;
/* -------------------------------------------------------------------------- */
class IntegrationPoint : public Element {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using position_type = Vector<Real>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationPoint(const Element & element, UInt num_point = 0,
UInt nb_quad_per_element = 0)
: Element(element), num_point(num_point),
global_num(element.element * nb_quad_per_element + num_point),
position(nullptr, 0){};
IntegrationPoint(ElementType type = _not_defined, UInt element = 0,
UInt num_point = 0, GhostType ghost_type = _not_ghost)
: Element{type, element, ghost_type}, num_point(num_point),
position(nullptr, 0){};
IntegrationPoint(UInt element, UInt num_point, UInt global_num,
const position_type & position, ElementType type,
GhostType ghost_type = _not_ghost)
: Element{type, element, ghost_type}, num_point(num_point),
global_num(global_num), position(nullptr, 0) {
this->position.shallowCopy(position);
};
IntegrationPoint(const IntegrationPoint & quad)
: Element(quad), num_point(quad.num_point), global_num(quad.global_num),
position(nullptr, 0) {
position.shallowCopy(quad.position);
};
virtual ~IntegrationPoint() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
inline bool operator==(const IntegrationPoint & quad) const {
return Element::operator==(quad) && this->num_point == quad.num_point;
}
inline bool operator!=(const IntegrationPoint & quad) const {
return Element::operator!=(quad) || (num_point != quad.num_point) ||
(global_num != quad.global_num);
}
bool operator<(const IntegrationPoint & rhs) const {
bool res = Element::operator<(rhs) ||
(Element::operator==(rhs) && this->num_point < rhs.num_point);
return res;
}
inline IntegrationPoint & operator=(const IntegrationPoint & q) {
if (this != &q) {
element = q.element;
type = q.type;
ghost_type = q.ghost_type;
num_point = q.num_point;
global_num = q.global_num;
position.shallowCopy(q.position);
}
return *this;
}
/// get the position of the integration point
AKANTU_GET_MACRO(Position, position, const position_type &);
/// set the position of the integration point
void setPosition(const position_type & position) {
this->position.shallowCopy(position);
}
/// deep copy of the position of the integration point
void copyPosition(const position_type & position) {
this->position.deepCopy(position);
}
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
+ for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
+ }
stream << space << "IntegrationPoint [";
stream << *static_cast<const Element *>(this);
stream << ", " << num_point << "(" << global_num << ")"
<< "]";
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
/// number of quadrature point in the element
UInt num_point;
/// global number of the quadrature point
UInt global_num{0};
// TODO might be temporary: however this class should be tought maybe...
std::string material_id;
private:
/// position of the quadrature point
position_type position;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const IntegrationPoint & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AKANTU_QUADRATURE_POINT_H */
diff --git a/src/fe_engine/integrator.hh b/src/fe_engine/integrator.hh
index 31c302236..ac6f4bc0e 100644
--- a/src/fe_engine/integrator.hh
+++ b/src/fe_engine/integrator.hh
@@ -1,138 +1,139 @@
/**
* @file integrator.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief interface for integrator classes
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_INTEGRATOR_HH__
-#define __AKANTU_INTEGRATOR_HH__
+#ifndef AKANTU_INTEGRATOR_HH_
+#define AKANTU_INTEGRATOR_HH_
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Integrator : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Integrator(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "integrator", const MemoryID & memory_id = 0)
: Memory(id, memory_id), mesh(mesh),
_spatial_dimension(spatial_dimension),
jacobians("jacobians", id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
~Integrator() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// empty method
template <ElementType type>
inline void precomputeJacobiansOnQuadraturePoints(__attribute__((unused))
GhostType ghost_type) {}
/// empty method
void integrateOnElement(const Array<Real> & /*f*/, Real * /*intf*/,
UInt /*nb_degree_of_freedom*/,
const Element & /*elem*/,
GhostType /*ghost_type*/) const {};
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
+ for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
+ }
stream << space << "Integrator [" << std::endl;
jacobians.printself(stream, indent + 1);
stream << space << "]" << std::endl;
};
/* ------------------------------------------------------------------------ */
public:
- virtual void onElementsAdded(const Array<Element> &) {}
+ virtual void onElementsAdded(const Array<Element> & /*unused*/) {}
virtual void
- onElementsRemoved(const Array<Element> &,
+ onElementsRemoved(const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & new_numbering) {
jacobians.onElementsRemoved(new_numbering);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// access to the jacobians
- Array<Real> & getJacobians(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) {
+ Array<Real> & getJacobians(ElementType type,
+ GhostType ghost_type = _not_ghost) {
return jacobians(type, ghost_type);
};
/// access to the jacobians const
const Array<Real> &
- getJacobians(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const {
+ getJacobians(ElementType type,
+ GhostType ghost_type = _not_ghost) const {
return jacobians(type, ghost_type);
};
AKANTU_GET_MACRO(Jacobians, jacobians, const ElementTypeMapArray<Real> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// mesh associated to the integrator
const Mesh & mesh;
// spatial dimension of the elements to consider
UInt _spatial_dimension;
/// jacobians for all elements
ElementTypeMapArray<Real> jacobians;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "integrator_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Integrator & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AKANTU_INTEGRATOR_HH__ */
+#endif /* AKANTU_INTEGRATOR_HH_ */
diff --git a/src/fe_engine/integrator_gauss.hh b/src/fe_engine/integrator_gauss.hh
index 23d341210..f822a5b41 100644
--- a/src/fe_engine/integrator_gauss.hh
+++ b/src/fe_engine/integrator_gauss.hh
@@ -1,205 +1,204 @@
/**
* @file integrator_gauss.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Gauss integration facilities
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_INTEGRATOR_GAUSS_HH__
-#define __AKANTU_INTEGRATOR_GAUSS_HH__
+#ifndef AKANTU_INTEGRATOR_GAUSS_HH_
+#define AKANTU_INTEGRATOR_GAUSS_HH_
namespace akantu {
namespace integrator {
namespace details {
template <ElementKind> struct GaussIntegratorComputeJacobiansHelper;
} // namespace details
} // namespace integrator
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss : public Integrator {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegratorGauss(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "integrator_gauss",
const MemoryID & memory_id = 0);
~IntegratorGauss() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
- void initIntegrator(const Array<Real> & nodes, const ElementType & type,
- const GhostType & ghost_type);
+ void initIntegrator(const Array<Real> & nodes, ElementType type,
+ GhostType ghost_type);
template <ElementType type>
inline void initIntegrator(const Array<Real> & nodes,
- const GhostType & ghost_type);
+ GhostType ghost_type);
/// integrate f on the element "elem" of type "type"
template <ElementType type>
inline void integrateOnElement(const Array<Real> & f, Real * intf,
- UInt nb_degree_of_freedom, const UInt elem,
- const GhostType & ghost_type) const;
+ UInt nb_degree_of_freedom, UInt elem,
+ GhostType ghost_type) const;
/// integrate f for all elements of type "type"
template <ElementType type>
void integrate(const Array<Real> & in_f, Array<Real> & intf,
- UInt nb_degree_of_freedom, const GhostType & ghost_type,
+ UInt nb_degree_of_freedom, GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate scalar field in_f
template <ElementType type, UInt polynomial_degree>
Real integrate(const Array<Real> & in_f,
- const GhostType & ghost_type = _not_ghost) const;
+ GhostType ghost_type = _not_ghost) const;
/// integrate partially around a quadrature point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
template <ElementType type>
Real integrate(const Vector<Real> & in_f, UInt index,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// integrate scalar field in_f
template <ElementType type>
- Real integrate(const Array<Real> & in_f, const GhostType & ghost_type,
+ Real integrate(const Array<Real> & in_f, GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate a field without using the pre-computed values
template <ElementType type, UInt polynomial_degree>
void integrate(const Array<Real> & in_f, Array<Real> & intf,
- UInt nb_degree_of_freedom, const GhostType & ghost_type) const;
+ UInt nb_degree_of_freedom, GhostType ghost_type) const;
/// integrate partially around a quadrature point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
template <ElementType type>
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
- const GhostType & ghost_type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// return a matrix with quadrature points natural coordinates
template <ElementType type>
- const Matrix<Real> & getIntegrationPoints(const GhostType & ghost_type) const;
+ const Matrix<Real> & getIntegrationPoints(GhostType ghost_type) const;
/// return number of quadrature points
template <ElementType type>
- UInt getNbIntegrationPoints(const GhostType & ghost_type) const;
+ UInt getNbIntegrationPoints(GhostType ghost_type) const;
template <ElementType type, UInt n> Matrix<Real> getIntegrationPoints() const;
template <ElementType type, UInt n>
Vector<Real> getIntegrationWeights() const;
protected:
friend struct integrator::details::GaussIntegratorComputeJacobiansHelper<
kind>;
template <ElementType type>
void computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
- Array<Real> & jacobians, const GhostType & ghost_type,
+ Array<Real> & jacobians, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
- Array<Real> & jacobians, const ElementType & type,
- const GhostType & ghost_type,
+ Array<Real> & jacobians, ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// precompute jacobians on elements of type "type"
template <ElementType type>
void precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
- const GhostType & ghost_type);
+ GhostType ghost_type);
// multiply the jacobians by the integration weights and stores the results in
// jacobians
template <ElementType type, UInt polynomial_degree>
void multiplyJacobiansByWeights(
Array<Real> & jacobians,
const Array<UInt> & filter_elements = empty_filter) const;
/// compute the vector of quadrature points natural coordinates
template <ElementType type>
- void computeQuadraturePoints(const GhostType & ghost_type);
+ void computeQuadraturePoints(GhostType ghost_type);
/// check that the jacobians are not negative
template <ElementType type>
- void checkJacobians(const GhostType & ghost_type) const;
+ void checkJacobians(GhostType ghost_type) const;
/// internal integrate partially around a quadrature point (@f$ intf_q = f_q *
/// J_q *
/// w_q @f$)
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
const Array<Real> & jacobians,
UInt nb_element) const;
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, const Array<Real> & jacobians,
UInt nb_element) const;
public:
/// compute the jacobians on quad points for a given element
template <ElementType type>
- void
- computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
- const Matrix<Real> & integration_points,
- Vector<Real> & jacobians) const;
+ void computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
+ const Matrix<Real> & quad,
+ Vector<Real> & jacobians) const;
public:
void onElementsAdded(const Array<Element> & elements) override;
template <ElementType type>
void onElementsAddedByType(const Array<UInt> & new_elements,
- const GhostType & ghost_type);
+ GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// integrate the field f with the jacobian jac -> inte
inline void integrate(Real * f, Real * jac, Real * inte,
UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const;
private:
/// ElementTypeMap of the quadrature points
ElementTypeMap<Matrix<Real>> quadrature_points;
};
} // namespace akantu
#include "integrator_gauss_inline_impl.hh"
-#endif /* __AKANTU_INTEGRATOR_GAUSS_HH__ */
+#endif /* AKANTU_INTEGRATOR_GAUSS_HH_ */
diff --git a/src/fe_engine/integrator_gauss_inline_impl.hh b/src/fe_engine/integrator_gauss_inline_impl.hh
index cabbbc66c..efc9bd9a9 100644
--- a/src/fe_engine/integrator_gauss_inline_impl.hh
+++ b/src/fe_engine/integrator_gauss_inline_impl.hh
@@ -1,759 +1,766 @@
/**
* @file integrator_gauss_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
* @date last modification: Tue Feb 20 2018
*
* @brief inline function of gauss integrator
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "mesh_iterators.hh"
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace debug {
struct IntegratorGaussException : public Exception {};
} // namespace debug
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::integrateOnElement(
const Array<Real> & f, Real * intf, UInt nb_degree_of_freedom,
- const UInt elem, const GhostType & ghost_type) const {
+ const UInt elem, GhostType ghost_type) const {
Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points = ElementClass<type>::getNbQuadraturePoints();
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f do not have the good number of component.");
Real * f_val = f.storage() + elem * f.getNbComponent();
Real * jac_val = jac_loc.storage() + elem * nb_quadrature_points;
integrate(f_val, jac_val, intf, nb_degree_of_freedom, nb_quadrature_points);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
- const Vector<Real> & in_f, UInt index, const GhostType & ghost_type) const {
+ const Vector<Real> & in_f, UInt index, GhostType ghost_type) const {
const Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points =
GaussIntegrationElement<type>::getNbQuadraturePoints();
AKANTU_DEBUG_ASSERT(in_f.size() == nb_quadrature_points,
"The vector f do not have nb_quadrature_points entries.");
Real * jac_val = jac_loc.storage() + index * nb_quadrature_points;
Real intf;
integrate(in_f.storage(), jac_val, &intf, 1, nb_quadrature_points);
return intf;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
Real * f, Real * jac, Real * inte, UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const {
- memset(inte, 0, nb_degree_of_freedom * sizeof(Real));
+ std::fill_n(inte, nb_degree_of_freedom, 0.);
Real * cjac = jac;
for (UInt q = 0; q < nb_quadrature_points; ++q) {
for (UInt dof = 0; dof < nb_degree_of_freedom; ++dof) {
inte[dof] += *f * *cjac;
++f;
}
++cjac;
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline const Matrix<Real> &
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationPoints(
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_ASSERT(
quadrature_points.exists(type, ghost_type),
"Quadrature points for type "
<< quadrature_points.printType(type, ghost_type)
<< " have not been initialized."
<< " Did you use 'computeQuadraturePoints' function ?");
return quadrature_points(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline UInt
IntegratorGauss<kind, IntegrationOrderFunctor>::getNbIntegrationPoints(
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_ASSERT(
quadrature_points.exists(type, ghost_type),
"Quadrature points for type "
<< quadrature_points.printType(type, ghost_type)
<< " have not been initialized."
<< " Did you use 'computeQuadraturePoints' function ?");
return quadrature_points(type, ghost_type).cols();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
inline Matrix<Real>
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationPoints() const {
return GaussIntegrationElement<type,
polynomial_degree>::getQuadraturePoints();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
inline Vector<Real>
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationWeights() const {
return GaussIntegrationElement<type, polynomial_degree>::getWeights();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
IntegratorGauss<kind, IntegrationOrderFunctor>::computeQuadraturePoints(
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
Matrix<Real> & quads = quadrature_points(type, ghost_type);
const UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
quads =
GaussIntegrationElement<type, polynomial_degree>::getQuadraturePoints();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & quad,
Vector<Real> & jacobians) const {
// jacobian
ElementClass<type>::computeJacobian(quad, node_coords, jacobians);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
IntegratorGauss<kind, IntegrationOrderFunctor>::IntegratorGauss(
const Mesh & mesh, UInt spatial_dimension, const ID & id,
const MemoryID & memory_id)
: Integrator(mesh, spatial_dimension, id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::checkJacobians(
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->quadrature_points(type, ghost_type).cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
Real * jacobians_val = jacobians(type, ghost_type).storage();
for (UInt i = 0; i < nb_element * nb_quadrature_points;
++i, ++jacobians_val) {
- if (*jacobians_val < 0)
+ if (*jacobians_val < 0) {
AKANTU_CUSTOM_EXCEPTION_INFO(debug::IntegratorGaussException{},
"Negative jacobian computed,"
<< " possible problem in the element "
"node ordering (Quadrature Point "
<< i % nb_quadrature_points << ":"
<< i / nb_quadrature_points << ":"
<< type << ":" << ghost_type << ")");
+ }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
- Array<Real> & jacobians, const GhostType & ghost_type,
+ Array<Real> & jacobians, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = quad_points.cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
auto jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
auto jacobians_begin = jacobians_it;
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
auto x_it = x_el.begin(spatial_dimension, nb_nodes_per_element);
nb_element = x_el.size();
// Matrix<Real> local_coord(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
const Matrix<Real> & x = *x_it;
if (filter_elements != empty_filter) {
jacobians_it = jacobians_begin + filter_elements(elem);
}
Vector<Real> & J = *jacobians_it;
computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
if (filter_elements == empty_filter) {
++jacobians_it;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
template <>
template <ElementType type>
void IntegratorGauss<_ek_structural, DefaultIntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
- Array<Real> & jacobians, const GhostType & ghost_type,
+ Array<Real> & jacobians, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
const UInt spatial_dimension = mesh.getSpatialDimension();
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const UInt nb_quadrature_points = quad_points.cols();
const UInt nb_dofs = ElementClass<type>::getNbDegreeOfFreedom();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
auto jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
auto jacobians_begin = jacobians_it;
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
auto x_it = x_el.begin(spatial_dimension, nb_nodes_per_element);
nb_element = x_el.size();
const bool has_extra_normal =
mesh.hasData<Real>("extra_normal", type, ghost_type);
- Array<Real>::const_vector_iterator extra_normal, extra_normal_begin;
+ Array<Real>::const_vector_iterator extra_normal;
+ Array<Real>::const_vector_iterator extra_normal_begin;
if (has_extra_normal) {
extra_normal = mesh.getData<Real>("extra_normal", type, ghost_type)
.begin(spatial_dimension);
extra_normal_begin = extra_normal;
}
// Matrix<Real> local_coord(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
if (filter_elements != empty_filter) {
jacobians_it = jacobians_begin + filter_elements(elem);
extra_normal = extra_normal_begin + filter_elements(elem);
}
const Matrix<Real> & X = *x_it;
Vector<Real> & J = *jacobians_it;
Matrix<Real> R(nb_dofs, nb_dofs);
- if (has_extra_normal)
+ if (has_extra_normal) {
ElementClass<type>::computeRotationMatrix(R, X, *extra_normal);
- else
+ } else {
ElementClass<type>::computeRotationMatrix(R, X, Vector<Real>(X.rows()));
+ }
// Extracting relevant lines
auto x = (R.block(0, 0, spatial_dimension, spatial_dimension) * X)
.block(0, 0, ElementClass<type>::getNaturalSpaceDimension(),
ElementClass<type>::getNbNodesPerElement());
computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
if (filter_elements == empty_filter) {
++jacobians_it;
++extra_normal;
}
}
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
template <>
template <ElementType type>
void IntegratorGauss<_ek_cohesive, DefaultIntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
- Array<Real> & jacobians, const GhostType & ghost_type,
+ Array<Real> & jacobians, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = quad_points.cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
auto jacobians_begin =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
auto x_it = x_el.begin(spatial_dimension, nb_nodes_per_element);
UInt nb_nodes_per_subelement = nb_nodes_per_element / 2;
Matrix<Real> x(spatial_dimension, nb_nodes_per_subelement);
nb_element = x_el.size();
UInt l_el = 0;
auto compute = [&](const auto & el) {
Vector<Real> J(jacobians_begin[el]);
Matrix<Real> X(x_it[l_el]);
++l_el;
- for (UInt n = 0; n < nb_nodes_per_subelement; ++n)
+ for (UInt n = 0; n < nb_nodes_per_subelement; ++n) {
Vector<Real>(x(n)) =
(Vector<Real>(X(n)) + Vector<Real>(X(n + nb_nodes_per_subelement))) /
2.;
+ }
- if (type == _cohesive_1d_2)
+ if (type == _cohesive_1d_2) {
J(0) = 1;
- else
+ } else {
this->computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
+ }
};
for_each_element(nb_element, filter_elements, compute);
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & jacobians_tmp = jacobians.alloc(0, 1, type, ghost_type);
this->computeJacobiansOnIntegrationPoints<type>(
nodes, quadrature_points(type, ghost_type), jacobians_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
void IntegratorGauss<kind, IntegrationOrderFunctor>::multiplyJacobiansByWeights(
Array<Real> & jacobians, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points =
GaussIntegrationElement<type, polynomial_degree>::getNbQuadraturePoints();
Vector<Real> weights =
GaussIntegrationElement<type, polynomial_degree>::getWeights();
auto && view = make_view(jacobians, nb_quadrature_points);
if (filter_elements != empty_filter) {
auto J_it = view.begin();
for (auto el : filter_elements) {
Vector<Real> J(J_it[el]);
J *= weights;
}
} else {
for (auto & J : make_view(jacobians, nb_quadrature_points)) {
J *= weights;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
const Array<Real> & jacobians, UInt nb_element) const {
AKANTU_DEBUG_IN();
intf.resize(nb_element);
- if (nb_element == 0)
+ if (nb_element == 0) {
return;
+ }
UInt nb_points = jacobians.size() / nb_element;
Array<Real>::const_matrix_iterator J_it;
Array<Real>::matrix_iterator inte_it;
Array<Real>::const_matrix_iterator f_it;
f_it = in_f.begin_reinterpret(nb_degree_of_freedom, nb_points, nb_element);
inte_it = intf.begin_reinterpret(nb_degree_of_freedom, 1, nb_element);
J_it = jacobians.begin_reinterpret(nb_points, 1, nb_element);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Matrix<Real> & f = *f_it;
const Matrix<Real> & J = *J_it;
Matrix<Real> & inte_f = *inte_it;
inte_f.mul<false, false>(f, J);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
const Array<Real> & jac_loc = jacobians(type, ghost_type);
if (filter_elements != empty_filter) {
UInt nb_element = filter_elements.size();
- Array<Real> * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
+ auto * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
this->integrate(in_f, intf, nb_degree_of_freedom, *filtered_J, nb_element);
delete filtered_J;
} else {
UInt nb_element = mesh.getNbElement(type, ghost_type);
this->integrate(in_f, intf, nb_degree_of_freedom, jac_loc, nb_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
Matrix<Real> quads = this->getIntegrationPoints<type, polynomial_degree>();
Array<Real> jacobians;
this->computeJacobiansOnIntegrationPoints<type>(mesh.getNodes(), quads,
jacobians, ghost_type);
this->multiplyJacobiansByWeights<type, polynomial_degree>(jacobians);
this->integrate(in_f, intf, nb_degree_of_freedom, jacobians,
mesh.getNbElement(type, ghost_type));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
- const Array<Real> & in_f, const GhostType & ghost_type) const {
+ const Array<Real> & in_f, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
Array<Real> intfv(0, 1);
integrate<type, polynomial_degree>(in_f, intfv, 1, ghost_type);
Real res = Math::reduce(intfv);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
- const Array<Real> & in_f, const GhostType & ghost_type,
+ const Array<Real> & in_f, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
Array<Real> intfv(0, 1);
integrate<type>(in_f, intfv, 1, ghost_type, filter_elements);
Real res = Math::reduce(intfv);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom,
const Array<Real> & jacobians,
UInt nb_element) const {
AKANTU_DEBUG_IN();
UInt nb_points = jacobians.size() / nb_element;
intf.resize(nb_element * nb_points);
auto J_it = jacobians.begin();
auto f_it = in_f.begin(nb_degree_of_freedom);
auto inte_it = intf.begin(nb_degree_of_freedom);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Real & J = *J_it;
const Vector<Real> & f = *f_it;
Vector<Real> & inte_f = *inte_it;
inte_f = f;
inte_f *= J;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom,
- const GhostType & ghost_type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
const Array<Real> & jac_loc = this->jacobians(type, ghost_type);
if (filter_elements != empty_filter) {
UInt nb_element = filter_elements.size();
- Array<Real> * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
+ auto * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
this->integrateOnIntegrationPoints(in_f, intf, nb_degree_of_freedom,
*filtered_J, nb_element);
} else {
UInt nb_element = mesh.getNbElement(type, ghost_type);
this->integrateOnIntegrationPoints(in_f, intf, nb_degree_of_freedom,
jac_loc, nb_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
IntegratorGauss<kind, IntegrationOrderFunctor>::onElementsAddedByType(
- const Array<UInt> & elements, const GhostType & ghost_type) {
+ const Array<UInt> & elements, GhostType ghost_type) {
const auto & nodes = mesh.getNodes();
if (not quadrature_points.exists(type, ghost_type)) {
computeQuadraturePoints<type>(ghost_type);
}
- if (not jacobians.exists(type, ghost_type))
+ if (not jacobians.exists(type, ghost_type)) {
jacobians.alloc(0, 1, type, ghost_type);
+ }
this->computeJacobiansOnIntegrationPoints(
nodes, quadrature_points(type, ghost_type), jacobians(type, ghost_type),
type, ghost_type, elements);
constexpr UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
multiplyJacobiansByWeights<type, polynomial_degree>(
this->jacobians(type, ghost_type), elements);
}
/* -------------------------------------------------------------------------- */
namespace integrator {
namespace details {
template <ElementKind kind> struct IntegratorOnElementsAddedHelper {};
#define ON_ELEMENT_ADDED(type) \
integrator.template onElementsAddedByType<type>(elements, ghost_type);
#define AKANTU_SPECIALIZE_ON_ELEMENT_ADDED_HELPER(kind) \
template <> struct IntegratorOnElementsAddedHelper<kind> { \
template <class I> \
static void call(I & integrator, const Array<UInt> & elements, \
- const ElementType & type, const GhostType & ghost_type) { \
+ ElementType type, GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ON_ELEMENT_ADDED, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_ON_ELEMENT_ADDED_HELPER)
#undef AKANTU_SPECIALIZE_ON_ELEMENT_ADDED_HELPER
#undef ON_ELEMENT_ADDED
} // namespace details
} // namespace integrator
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::onElementsAdded(
const Array<Element> & new_elements) {
for (auto elements_range : MeshElementsByTypes(new_elements)) {
auto type = elements_range.getType();
auto ghost_type = elements_range.getGhostType();
- if (mesh.getSpatialDimension(type) != _spatial_dimension)
+ if (mesh.getSpatialDimension(type) != _spatial_dimension) {
continue;
-
- if (mesh.getKind(type) != kind)
+ }
+
+ if (mesh.getKind(type) != kind) {
continue;
+ }
integrator::details::IntegratorOnElementsAddedHelper<kind>::call(
*this, elements_range.getElements(), type, ghost_type);
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::initIntegrator(
- const Array<Real> & nodes, const GhostType & ghost_type) {
+ const Array<Real> & nodes, GhostType ghost_type) {
computeQuadraturePoints<type>(ghost_type);
precomputeJacobiansOnQuadraturePoints<type>(nodes, ghost_type);
checkJacobians<type>(ghost_type);
constexpr UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
multiplyJacobiansByWeights<type, polynomial_degree>(
this->jacobians(type, ghost_type));
}
namespace integrator {
namespace details {
template <ElementKind kind> struct GaussIntegratorInitHelper {};
#define INIT_INTEGRATOR(type) \
_int.template initIntegrator<type>(nodes, ghost_type)
#define AKANTU_GAUSS_INTERGRATOR_INIT_HELPER(kind) \
template <> struct GaussIntegratorInitHelper<kind> { \
template <ElementKind k, class IOF> \
static void call(IntegratorGauss<k, IOF> & _int, \
- const Array<Real> & nodes, const ElementType & type, \
- const GhostType & ghost_type) { \
+ const Array<Real> & nodes, ElementType type, \
+ GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INIT_INTEGRATOR, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_GAUSS_INTERGRATOR_INIT_HELPER)
#undef AKANTU_GAUSS_INTERGRATOR_INIT_HELPER
#undef INIT_INTEGRATOR
} // namespace details
} // namespace integrator
template <ElementKind kind, class IntegrationOrderFunctor>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::initIntegrator(
- const Array<Real> & nodes, const ElementType & type,
- const GhostType & ghost_type) {
+ const Array<Real> & nodes, ElementType type, GhostType ghost_type) {
integrator::details::GaussIntegratorInitHelper<kind>::call(*this, nodes, type,
ghost_type);
}
namespace integrator {
namespace details {
template <ElementKind kind> struct GaussIntegratorComputeJacobiansHelper {};
#define AKANTU_COMPUTE_JACOBIANS(type) \
_int.template computeJacobiansOnIntegrationPoints<type>( \
nodes, quad_points, jacobians, ghost_type, filter_elements);
#define AKANTU_GAUSS_INTERGRATOR_COMPUTE_JACOBIANS(kind) \
template <> struct GaussIntegratorComputeJacobiansHelper<kind> { \
template <ElementKind k, class IOF> \
static void \
call(const IntegratorGauss<k, IOF> & _int, const Array<Real> & nodes, \
const Matrix<Real> & quad_points, Array<Real> & jacobians, \
- const ElementType & type, const GhostType & ghost_type, \
+ ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(AKANTU_COMPUTE_JACOBIANS, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_GAUSS_INTERGRATOR_COMPUTE_JACOBIANS)
#undef AKANTU_GAUSS_INTERGRATOR_COMPUTE_JACOBIANS
#undef AKANTU_COMPUTE_JACOBIANS
} // namespace details
} // namespace integrator
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
- Array<Real> & jacobians, const ElementType & type,
- const GhostType & ghost_type,
+ Array<Real> & jacobians, ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
integrator::details::GaussIntegratorComputeJacobiansHelper<kind>::call(
*this, nodes, quad_points, jacobians, type, ghost_type, filter_elements);
}
} // namespace akantu
diff --git a/src/fe_engine/interpolation_element_tmpl.hh b/src/fe_engine/interpolation_element_tmpl.hh
index fbe43a8a8..74bf1d54b 100644
--- a/src/fe_engine/interpolation_element_tmpl.hh
+++ b/src/fe_engine/interpolation_element_tmpl.hh
@@ -1,72 +1,72 @@
/**
* @file interpolation_element_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 06 2013
* @date last modification: Wed Nov 29 2017
*
* @brief interpolation property description
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_INTERPOLATION_ELEMENT_TMPL_HH__
-#define __AKANTU_INTERPOLATION_ELEMENT_TMPL_HH__
+#ifndef AKANTU_INTERPOLATION_ELEMENT_TMPL_HH_
+#define AKANTU_INTERPOLATION_ELEMENT_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Regular Elements */
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_not_defined, _itk_not_defined, 0,
0);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_point_1,
_itk_lagrangian, 1, 0);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_segment_2,
_itk_lagrangian, 2, 1);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_segment_3,
_itk_lagrangian, 3, 1);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_triangle_3,
_itk_lagrangian, 3, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_triangle_6,
_itk_lagrangian, 6, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_tetrahedron_4,
_itk_lagrangian, 4, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_tetrahedron_10,
_itk_lagrangian, 10, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_quadrangle_4,
_itk_lagrangian, 4, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_serendip_quadrangle_8,
_itk_lagrangian, 8, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_hexahedron_8,
_itk_lagrangian, 8, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_serendip_hexahedron_20,
_itk_lagrangian, 20, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_pentahedron_6,
_itk_lagrangian, 6, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_pentahedron_15,
_itk_lagrangian, 15, 3);
} // namespace akantu
-#endif /* __AKANTU_INTERPOLATION_ELEMENT_TMPL_HH__ */
+#endif /* AKANTU_INTERPOLATION_ELEMENT_TMPL_HH_ */
diff --git a/src/fe_engine/shape_cohesive.hh b/src/fe_engine/shape_cohesive.hh
index 00bc6ab2d..3b282c839 100644
--- a/src/fe_engine/shape_cohesive.hh
+++ b/src/fe_engine/shape_cohesive.hh
@@ -1,184 +1,184 @@
/**
* @file shape_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Feb 15 2011
* @date last modification: Tue Feb 20 2018
*
* @brief shape functions for cohesive elements description
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_COHESIVE_HH__
-#define __AKANTU_SHAPE_COHESIVE_HH__
+#ifndef AKANTU_SHAPE_COHESIVE_HH_
+#define AKANTU_SHAPE_COHESIVE_HH_
namespace akantu {
struct CohesiveReduceFunctionMean {
inline Real operator()(Real u_plus, Real u_minus) {
return .5 * (u_plus + u_minus);
}
};
struct CohesiveReduceFunctionOpening {
inline Real operator()(Real u_plus, Real u_minus) {
return (u_plus - u_minus);
}
};
template <> class ShapeLagrange<_ek_cohesive> : public ShapeLagrangeBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "shape_cohesive",
const MemoryID & memory_id = 0);
~ShapeLagrange() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
- const ElementType & type,
- const GhostType & ghost_type);
+ ElementType type,
+ GhostType ghost_type);
/// extract the nodal values and store them per element
template <ElementType type, class ReduceFunction>
void extractNodalToElementField(
const Array<Real> & nodal_f, Array<Real> & elemental_f,
- const GhostType & ghost_type = _not_ghost,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// computes the shape functions derivatives for given interpolation points
template <ElementType type>
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shape_derivatives, const GhostType & ghost_type,
+ Array<Real> & shape_derivatives, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shape_derivatives, const ElementType & type,
- const GhostType & ghost_type,
+ Array<Real> & shape_derivatives, ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const override;
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// pre compute all shape derivatives on the element integration points from
/// natural coordinates
template <ElementType type>
void precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type, class ReduceFunction>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
- const GhostType ghost_type = _not_ghost,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
- const GhostType ghost_type = _not_ghost,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const {
interpolateOnIntegrationPoints<type, CohesiveReduceFunctionMean>(
u, uq, nb_degree_of_freedom, ghost_type, filter_elements);
}
/// compute the gradient of u on the integration points in the natural
/// coordinates
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const {
variationOnIntegrationPoints<type, CohesiveReduceFunctionMean>(
u, nablauq, nb_degree_of_freedom, ghost_type, filter_elements);
}
/* ------------------------------------------------------------------------ */
template <ElementType type>
void computeBtD(const Array<Real> & /*Ds*/, Array<Real> & /*BtDs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
template <ElementType type>
void computeBtDB(const Array<Real> & /*Ds*/, Array<Real> & /*BtDBs*/,
- UInt /*order_d*/, GhostType /*ghost_type*/,
+ UInt /*order_d*/, GhostType/*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
/// multiply a field by shape functions
template <ElementType type>
void
computeNtb(const Array<Real> & /*bs*/, Array<Real> & /*Ntbs*/,
- const GhostType & /*ghost_type*/,
+ GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/ = empty_filter) const {
AKANTU_TO_IMPLEMENT();
}
/* ------------------------------------------------------------------------ */
/// compute the gradient of u on the integration points
template <ElementType type, class ReduceFunction>
void variationOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// compute the normals to the field u on integration points
template <ElementType type, class ReduceFunction>
void computeNormalsOnIntegrationPoints(
const Array<Real> & u, Array<Real> & normals_u,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
};
/// standard output stream operator
template <class ShapeFunction>
inline std::ostream & operator<<(std::ostream & stream,
const ShapeCohesive<ShapeFunction> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "shape_cohesive_inline_impl.hh"
-#endif /* __AKANTU_SHAPE_COHESIVE_HH__ */
+#endif /* AKANTU_SHAPE_COHESIVE_HH_ */
diff --git a/src/fe_engine/shape_cohesive_inline_impl.hh b/src/fe_engine/shape_cohesive_inline_impl.hh
index 2f879e0e0..fc7134bac 100644
--- a/src/fe_engine/shape_cohesive_inline_impl.hh
+++ b/src/fe_engine/shape_cohesive_inline_impl.hh
@@ -1,330 +1,332 @@
/**
* @file shape_cohesive_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 03 2012
* @date last modification: Mon Feb 19 2018
*
* @brief ShapeCohesive inline implementation
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_iterators.hh"
#include "shape_cohesive.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_COHESIVE_INLINE_IMPL_HH__
-#define __AKANTU_SHAPE_COHESIVE_INLINE_IMPL_HH__
+#ifndef AKANTU_SHAPE_COHESIVE_INLINE_IMPL_HH_
+#define AKANTU_SHAPE_COHESIVE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline ShapeLagrange<_ek_cohesive>::ShapeLagrange(const Mesh & mesh,
UInt spatial_dimension,
const ID & id,
const MemoryID & memory_id)
: ShapeLagrangeBase(mesh, spatial_dimension, _ek_cohesive, id, memory_id) {}
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
/* -------------------------------------------------------------------------- */
inline void ShapeLagrange<_ek_cohesive>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- const ElementType & type, const GhostType & ghost_type) {
+ ElementType type, GhostType ghost_type) {
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_cohesive>::computeShapeDerivativesOnIntegrationPoints(
- const Array<Real> &, const Matrix<Real> & integration_points,
- Array<Real> & shape_derivatives, const GhostType & ghost_type,
+ const Array<Real> & /*unused*/, const Matrix<Real> & integration_points,
+ Array<Real> & shape_derivatives, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
UInt spatial_dimension = ElementClass<type>::getNaturalSpaceDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
AKANTU_DEBUG_ASSERT(shape_derivatives.getNbComponent() == size_of_shapesd,
"The shapes_derivatives array does not have the correct "
<< "number of component");
shape_derivatives.resize(nb_element * nb_points);
Real * shapesd_val = shape_derivatives.storage();
auto compute = [&](const auto & el) {
auto ptr = shapesd_val + el * nb_points * size_of_shapesd;
Tensor3<Real> B(ptr, spatial_dimension, nb_nodes_per_element, nb_points);
ElementClass<type>::computeDNDS(integration_points, B);
};
for_each_element(nb_element, filter_elements, compute);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void
ShapeLagrange<_ek_cohesive>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shape_derivatives, const ElementType & type,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ Array<Real> & shape_derivatives, ElementType type,
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
#define AKANTU_COMPUTE_SHAPES(type) \
computeShapeDerivativesOnIntegrationPoints<type>( \
nodes, integration_points, shape_derivatives, ghost_type, \
filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(AKANTU_COMPUTE_SHAPES);
#undef AKANTU_COMPUTE_SHAPES
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_cohesive>::precomputeShapesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapes = ElementClass<type>::getShapeSize();
Array<Real> & shapes_tmp =
shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
this->computeShapesOnIntegrationPoints<type>(nodes, natural_coords,
shapes_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_cohesive>::precomputeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
Array<Real> & shapes_derivatives_tmp =
shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
this->computeShapeDerivativesOnIntegrationPoints<type>(
nodes, natural_coords, shapes_derivatives_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::extractNodalToElementField(
const Array<Real> & nodal_f, Array<Real> & elemental_f,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_itp_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_degree_of_freedom = nodal_f.getNbComponent();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
const auto & conn_array = this->mesh.getConnectivity(type, ghost_type);
auto conn = conn_array.begin(conn_array.getNbComponent() / 2, 2);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
elemental_f.resize(nb_element);
Array<Real>::matrix_iterator u_it =
elemental_f.begin(nb_degree_of_freedom, nb_nodes_per_itp_element);
ReduceFunction reduce_function;
auto compute = [&](const auto & el) {
Matrix<Real> & u = *u_it;
Matrix<UInt> el_conn(conn[el]);
// compute the average/difference of the nodal field loaded from cohesive
// element
for (UInt n = 0; n < el_conn.rows(); ++n) {
UInt node_plus = el_conn(n, 0);
UInt node_minus = el_conn(n, 1);
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
Real u_plus = nodal_f(node_plus, d);
Real u_minus = nodal_f(node_minus, d);
u(d, n) = reduce_function(u_plus, u_minus);
}
}
++u_it;
};
for_each_element(nb_element, filter_elements, compute);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(this->shapes.exists(itp_type, ghost_type),
"No shapes for the type "
<< this->shapes.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
this->extractNodalToElementField<type, ReduceFunction>(in_u, u_el, ghost_type,
filter_elements);
this->template interpolateElementalFieldOnIntegrationPoints<type>(
u_el, out_uq, ghost_type, shapes(itp_type, ghost_type), filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::variationOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(
this->shapes_derivatives.exists(itp_type, ghost_type),
"No shapes for the type "
<< this->shapes_derivatives.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
this->extractNodalToElementField<type, ReduceFunction>(in_u, u_el, ghost_type,
filter_elements);
this->template gradientElementalFieldOnIntegrationPoints<type>(
u_el, nablauq, ghost_type, shapes_derivatives(itp_type, ghost_type),
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::computeNormalsOnIntegrationPoints(
- const Array<Real> & u, Array<Real> & normals_u, GhostType ghost_type,
- const Array<UInt> & filter_elements) const {
+ const Array<Real> & u, Array<Real> & normals_u,
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
UInt nb_points = this->integration_points(type, ghost_type).cols();
UInt spatial_dimension = this->mesh.getSpatialDimension();
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
+ }
normals_u.resize(nb_points * nb_element);
Array<Real> tangents_u(0, (spatial_dimension * (spatial_dimension - 1)));
if (spatial_dimension > 1) {
tangents_u.resize(nb_element * nb_points);
this->template variationOnIntegrationPoints<type, ReduceFunction>(
u, tangents_u, spatial_dimension, ghost_type, filter_elements);
}
Real * tangent = tangents_u.storage();
if (spatial_dimension == 3) {
for (auto & normal : make_view(normals_u, spatial_dimension)) {
Math::vectorProduct3(tangent, tangent + spatial_dimension,
normal.storage());
normal /= normal.norm();
tangent += spatial_dimension * 2;
}
} else if (spatial_dimension == 2) {
for (auto & normal : make_view(normals_u, spatial_dimension)) {
Vector<Real> a1(tangent, spatial_dimension);
normal(0) = -a1(1);
normal(1) = a1(0);
normal.normalize();
tangent += spatial_dimension;
}
} else if (spatial_dimension == 1) {
const auto facet_type = Mesh::getFacetType(type);
const auto & mesh_facets = mesh.getMeshFacets();
const auto & facets = mesh_facets.getSubelementToElement(type, ghost_type);
const auto & segments =
mesh_facets.getElementToSubelement(facet_type, ghost_type);
Real values[2];
for (auto el : arange(nb_element)) {
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
el = filter_elements(el);
+ }
for (UInt p = 0; p < 2; ++p) {
Element facet = facets(el, p);
Element segment = segments(facet.element)[0];
Vector<Real> barycenter(values + p, 1);
mesh.getBarycenter(segment, barycenter);
}
Real difference = values[0] - values[1];
AKANTU_DEBUG_ASSERT(difference != 0.,
"Error in normal computation for cohesive elements");
normals_u(el) = difference / std::abs(difference);
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif /* __AKANTU_SHAPE_COHESIVE_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SHAPE_COHESIVE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/shape_functions.cc b/src/fe_engine/shape_functions.cc
index b8224e57e..a35173c9a 100644
--- a/src/fe_engine/shape_functions.cc
+++ b/src/fe_engine/shape_functions.cc
@@ -1,236 +1,241 @@
/**
* @file shape_functions.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
* @date last modification: Wed Oct 11 2017
*
* @brief implementation of th shape functions interface
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ShapeFunctions::ShapeFunctions(const Mesh & mesh, UInt spatial_dimension,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), shapes("shapes_generic", id, memory_id),
shapes_derivatives("shapes_derivatives_generic", id, memory_id),
mesh(mesh), _spatial_dimension(spatial_dimension) {}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void
ShapeFunctions::initElementalFieldInterpolationFromIntegrationPoints(
const Array<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const Array<Real> & quadrature_points_coordinates,
- const GhostType & ghost_type, const Array<UInt> & element_filter) const {
+ GhostType ghost_type, const Array<UInt> & element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
UInt nb_element_filter;
- if (element_filter == empty_filter)
+ if (element_filter == empty_filter) {
nb_element_filter = nb_element;
- else
+ } else {
nb_element_filter = element_filter.size();
+ }
UInt nb_quad_per_element =
GaussIntegrationElement<type>::getNbQuadraturePoints();
UInt nb_interpolation_points_per_elem =
interpolation_points_coordinates.size() / nb_element;
AKANTU_DEBUG_ASSERT(interpolation_points_coordinates.size() % nb_element == 0,
"Number of interpolation points should be a multiple of "
"total number of elements");
- if (!quad_points_coordinates_inv_matrices.exists(type, ghost_type))
+ if (!quad_points_coordinates_inv_matrices.exists(type, ghost_type)) {
quad_points_coordinates_inv_matrices.alloc(
nb_element_filter, nb_quad_per_element * nb_quad_per_element, type,
ghost_type);
- else
+ } else {
quad_points_coordinates_inv_matrices(type, ghost_type)
.resize(nb_element_filter);
+ }
- if (!interpolation_points_coordinates_matrices.exists(type, ghost_type))
+ if (!interpolation_points_coordinates_matrices.exists(type, ghost_type)) {
interpolation_points_coordinates_matrices.alloc(
nb_element_filter,
nb_interpolation_points_per_elem * nb_quad_per_element, type,
ghost_type);
- else
+ } else {
interpolation_points_coordinates_matrices(type, ghost_type)
.resize(nb_element_filter);
+ }
Array<Real> & quad_inv_mat =
quad_points_coordinates_inv_matrices(type, ghost_type);
Array<Real> & interp_points_mat =
interpolation_points_coordinates_matrices(type, ghost_type);
Matrix<Real> quad_coord_matrix(nb_quad_per_element, nb_quad_per_element);
Array<Real>::const_matrix_iterator quad_coords_it =
quadrature_points_coordinates.begin_reinterpret(
spatial_dimension, nb_quad_per_element, nb_element_filter);
Array<Real>::const_matrix_iterator points_coords_begin =
interpolation_points_coordinates.begin_reinterpret(
spatial_dimension, nb_interpolation_points_per_elem, nb_element);
Array<Real>::matrix_iterator inv_quad_coord_it =
quad_inv_mat.begin(nb_quad_per_element, nb_quad_per_element);
Array<Real>::matrix_iterator int_points_mat_it = interp_points_mat.begin(
nb_interpolation_points_per_elem, nb_quad_per_element);
/// loop over the elements of the current material and element type
for (UInt el = 0; el < nb_element_filter;
++el, ++inv_quad_coord_it, ++int_points_mat_it, ++quad_coords_it) {
/// matrix containing the quadrature points coordinates
const Matrix<Real> & quad_coords = *quad_coords_it;
/// matrix to store the matrix inversion result
Matrix<Real> & inv_quad_coord_matrix = *inv_quad_coord_it;
/// insert the quad coordinates in a matrix compatible with the
/// interpolation
buildElementalFieldInterpolationMatrix<type>(quad_coords,
quad_coord_matrix);
/// invert the interpolation matrix
inv_quad_coord_matrix.inverse(quad_coord_matrix);
/// matrix containing the interpolation points coordinates
const Matrix<Real> & points_coords =
points_coords_begin[element_filter(el)];
/// matrix to store the interpolation points coordinates
/// compatible with these functions
Matrix<Real> & inv_points_coord_matrix = *int_points_mat_it;
/// insert the quad coordinates in a matrix compatible with the
/// interpolation
buildElementalFieldInterpolationMatrix<type>(points_coords,
inv_points_coord_matrix);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ShapeFunctions::initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
for (auto ghost_type : ghost_types) {
auto types_iterable = mesh.elementTypes(spatial_dimension, ghost_type);
- if (element_filter) {
+ if (element_filter != nullptr) {
types_iterable =
element_filter->elementTypes(spatial_dimension, ghost_type);
}
for (auto type : types_iterable) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
- if (nb_element == 0)
+ if (nb_element == 0) {
continue;
+ }
const Array<UInt> * elem_filter;
- if (element_filter)
+ if (element_filter != nullptr) {
elem_filter = &((*element_filter)(type, ghost_type));
- else
+ } else {
elem_filter = &(empty_filter);
+ }
#define AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS(type) \
this->initElementalFieldInterpolationFromIntegrationPoints<type>( \
interpolation_points_coordinates(type, ghost_type), \
interpolation_points_coordinates_matrices, \
quad_points_coordinates_inv_matrices, \
quadrature_points_coordinates(type, ghost_type), ghost_type, \
*elem_filter)
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(
AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS);
#undef AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ShapeFunctions::interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
- ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
auto types_iterable = mesh.elementTypes(spatial_dimension, ghost_type);
if (element_filter != nullptr) {
types_iterable =
element_filter->elementTypes(spatial_dimension, ghost_type);
}
for (auto type : types_iterable) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0) {
continue;
}
const Array<UInt> * elem_filter;
if (element_filter != nullptr) {
elem_filter = &((*element_filter)(type, ghost_type));
} else {
elem_filter = &(empty_filter);
}
#define AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS(type) \
interpolateElementalFieldFromIntegrationPoints<type>( \
field(type, ghost_type), \
interpolation_points_coordinates_matrices(type, ghost_type), \
quad_points_coordinates_inv_matrices(type, ghost_type), result, \
ghost_type, *elem_filter)
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(
AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS);
#undef AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/fe_engine/shape_functions.hh b/src/fe_engine/shape_functions.hh
index b24153176..2c17873ce 100644
--- a/src/fe_engine/shape_functions.hh
+++ b/src/fe_engine/shape_functions.hh
@@ -1,214 +1,215 @@
/**
* @file shape_functions.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief shape function class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_FUNCTIONS_HH__
-#define __AKANTU_SHAPE_FUNCTIONS_HH__
+#ifndef AKANTU_SHAPE_FUNCTIONS_HH_
+#define AKANTU_SHAPE_FUNCTIONS_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
class ShapeFunctions : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeFunctions(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "shape", const MemoryID & memory_id = 0);
~ShapeFunctions() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
+ for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
+ }
stream << space << "Shapes [" << std::endl;
integration_points.printself(stream, indent + 1);
// shapes.printself(stream, indent + 1);
// shapes_derivatives.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/// set the integration points for a given element
template <ElementType type>
void setIntegrationPointsByType(const Matrix<Real> & integration_points,
- const GhostType & ghost_type);
+ GhostType ghost_type);
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * element_filter) const;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
- ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const;
protected:
/// interpolate nodal values stored by element on the integration points
template <ElementType type>
void interpolateElementalFieldOnIntegrationPoints(
- const Array<Real> & u_el, Array<Real> & uq, const GhostType & ghost_type,
+ const Array<Real> & u_el, Array<Real> & uq, GhostType ghost_type,
const Array<Real> & shapes,
const Array<UInt> & filter_elements = empty_filter) const;
/// gradient of nodal values stored by element on the control points
template <ElementType type>
void gradientElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & out_nablauq,
- const GhostType & ghost_type, const Array<Real> & shapes_derivatives,
+ GhostType ghost_type, const Array<Real> & shapes_derivatives,
const Array<UInt> & filter_elements) const;
protected:
/// By element versions of non-templated eponym methods
template <ElementType type>
inline void interpolateElementalFieldFromIntegrationPoints(
const Array<Real> & field,
const Array<Real> & interpolation_points_coordinates_matrices,
const Array<Real> & quad_points_coordinates_inv_matrices,
- ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const Array<UInt> & element_filter) const;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
template <ElementType type>
inline void initElementalFieldInterpolationFromIntegrationPoints(
const Array<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const Array<Real> & quadrature_points_coordinates,
- const GhostType & ghost_type, const Array<UInt> & element_filter) const;
+ GhostType ghost_type, const Array<UInt> & element_filter) const;
/// build matrix for the interpolation of field form integration points
template <ElementType type>
inline void buildElementalFieldInterpolationMatrix(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order =
ElementClassProperty<type>::polynomial_degree) const;
/// build the so called interpolation matrix (first collumn is 1, then the
/// other collumns are the traansposed coordinates)
- inline void buildInterpolationMatrix(const Matrix<Real> & coordinates,
+ static inline void buildInterpolationMatrix(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix,
- UInt integration_order) const;
+ UInt integration_order);
public:
- virtual void onElementsAdded(const Array<Element> &) {
+ virtual void onElementsAdded(const Array<Element> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
- virtual void onElementsRemoved(const Array<Element> &,
- const ElementTypeMapArray<UInt> &) {
+ virtual void onElementsRemoved(const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the size of the shapes returned by the element class
- static inline UInt getShapeSize(const ElementType & type);
+ static inline UInt getShapeSize(ElementType type);
/// get the size of the shapes derivatives returned by the element class
- static inline UInt getShapeDerivativesSize(const ElementType & type);
+ static inline UInt getShapeDerivativesSize(ElementType type);
inline const Matrix<Real> &
- getIntegrationPoints(const ElementType & type,
- const GhostType & ghost_type) const {
+ getIntegrationPoints(ElementType type,
+ GhostType ghost_type) const {
return integration_points(type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get a the shapes vector
inline const Array<Real> &
- getShapes(const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ getShapes(ElementType el_type,
+ GhostType ghost_type = _not_ghost) const;
/// get a the shapes derivatives vector
inline const Array<Real> &
- getShapesDerivatives(const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ getShapesDerivatives(ElementType el_type,
+ GhostType ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// shape functions for all elements
ElementTypeMapArray<Real, InterpolationType> shapes;
/// shape functions derivatives for all elements
ElementTypeMapArray<Real, InterpolationType> shapes_derivatives;
/// associated mesh
const Mesh & mesh;
// spatial dimension of the elements to consider
UInt _spatial_dimension;
/// shape functions for all elements
ElementTypeMap<Matrix<Real>> integration_points;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ShapeFunctions & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "shape_functions_inline_impl.hh"
-#endif /* __AKANTU_SHAPE_FUNCTIONS_HH__ */
+#endif /* AKANTU_SHAPE_FUNCTIONS_HH_ */
diff --git a/src/fe_engine/shape_functions_inline_impl.hh b/src/fe_engine/shape_functions_inline_impl.hh
index aa724c4a4..14f870227 100644
--- a/src/fe_engine/shape_functions_inline_impl.hh
+++ b/src/fe_engine/shape_functions_inline_impl.hh
@@ -1,400 +1,414 @@
/**
* @file shape_functions_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Oct 27 2010
* @date last modification: Tue Feb 20 2018
*
* @brief ShapeFunctions inline implementation
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_HH__
-#define __AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_HH__
+#ifndef AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_HH_
+#define AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline const Array<Real> &
-ShapeFunctions::getShapes(const ElementType & el_type,
- const GhostType & ghost_type) const {
+ShapeFunctions::getShapes(ElementType el_type,
+ GhostType ghost_type) const {
return shapes(FEEngine::getInterpolationType(el_type), ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const Array<Real> &
-ShapeFunctions::getShapesDerivatives(const ElementType & el_type,
- const GhostType & ghost_type) const {
+ShapeFunctions::getShapesDerivatives(ElementType el_type,
+ GhostType ghost_type) const {
return shapes_derivatives(FEEngine::getInterpolationType(el_type),
ghost_type);
}
/* -------------------------------------------------------------------------- */
-inline UInt ShapeFunctions::getShapeSize(const ElementType & type) {
+inline UInt ShapeFunctions::getShapeSize(ElementType type) {
AKANTU_DEBUG_IN();
UInt shape_size = 0;
#define GET_SHAPE_SIZE(type) shape_size = ElementClass<type>::getShapeSize()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SHAPE_SIZE); // ,
#undef GET_SHAPE_SIZE
AKANTU_DEBUG_OUT();
return shape_size;
}
/* -------------------------------------------------------------------------- */
-inline UInt ShapeFunctions::getShapeDerivativesSize(const ElementType & type) {
+inline UInt ShapeFunctions::getShapeDerivativesSize(ElementType type) {
AKANTU_DEBUG_IN();
UInt shape_derivatives_size = 0;
#define GET_SHAPE_DERIVATIVES_SIZE(type) \
shape_derivatives_size = ElementClass<type>::getShapeDerivativesSize()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SHAPE_DERIVATIVES_SIZE); // ,
#undef GET_SHAPE_DERIVATIVES_SIZE
AKANTU_DEBUG_OUT();
return shape_derivatives_size;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeFunctions::setIntegrationPointsByType(const Matrix<Real> & points,
- const GhostType & ghost_type) {
- if (not this->integration_points.exists(type, ghost_type))
+ GhostType ghost_type) {
+ if (not this->integration_points.exists(type, ghost_type)) {
this->integration_points(type, ghost_type).shallowCopy(points);
+ }
}
/* -------------------------------------------------------------------------- */
inline void
ShapeFunctions::buildInterpolationMatrix(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix,
- UInt integration_order) const {
+ UInt integration_order) {
switch (integration_order) {
case 1: {
- for (UInt i = 0; i < coordinates.cols(); ++i)
+ for (UInt i = 0; i < coordinates.cols(); ++i) {
coordMatrix(i, 0) = 1;
+ }
break;
}
case 2: {
UInt nb_quadrature_points = coordMatrix.cols();
for (UInt i = 0; i < coordinates.cols(); ++i) {
coordMatrix(i, 0) = 1;
- for (UInt j = 1; j < nb_quadrature_points; ++j)
+ for (UInt j = 1; j < nb_quadrature_points; ++j) {
coordMatrix(i, j) = coordinates(j - 1, i);
+ }
}
break;
}
default: {
AKANTU_TO_IMPLEMENT();
break;
}
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix(
- const Matrix<Real> &, Matrix<Real> &, UInt) const {
+ const Matrix<Real> & /*unused*/, Matrix<Real> & /*unused*/,
+ UInt /*unused*/) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_segment_2>(
- const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
- UInt integration_order) const {
+ const Matrix<Real> & /*unused*/ coordinates,
+ Matrix<Real> & /*unused*/ coordMatrix,
+ UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_segment_3>(
- const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
- UInt integration_order) const {
+ const Matrix<Real> & /*unused*/ coordinates,
+ Matrix<Real> & /*unused*/ coordMatrix,
+ UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_triangle_3>(
- const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
- UInt integration_order) const {
+ const Matrix<Real> & /*unused*/ coordinates,
+ Matrix<Real> & /*unused*/ coordMatrix,
+ UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_triangle_6>(
- const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
- UInt integration_order) const {
+ const Matrix<Real> & /*unused*/ coordinates,
+ Matrix<Real> & /*unused*/ coordMatrix,
+ UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_tetrahedron_4>(
- const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
- UInt integration_order) const {
+ const Matrix<Real> & /*unused*/ coordinates,
+ Matrix<Real> & /*unused*/ coordMatrix,
+ UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_tetrahedron_10>(
- const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
- UInt integration_order) const {
+ const Matrix<Real> & /*unused*/ coordinates,
+ Matrix<Real> & /*unused*/ coordMatrix,
+ UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/**
* @todo Write a more efficient interpolation for quadrangles by
* dropping unnecessary quadrature points
*
*/
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_quadrangle_4>(
- const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
- UInt integration_order) const {
+ const Matrix<Real> & /*unused*/ coordinates,
+ Matrix<Real> & /*unused*/ coordMatrix,
+ UInt /*unused*/ integration_order) const {
if (integration_order !=
ElementClassProperty<_quadrangle_4>::polynomial_degree) {
AKANTU_TO_IMPLEMENT();
} else {
for (UInt i = 0; i < coordinates.cols(); ++i) {
Real x = coordinates(0, i);
Real y = coordinates(1, i);
coordMatrix(i, 0) = 1;
coordMatrix(i, 1) = x;
coordMatrix(i, 2) = y;
coordMatrix(i, 3) = x * y;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_quadrangle_8>(
- const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
- UInt integration_order) const {
+ const Matrix<Real> & /*unused*/ coordinates,
+ Matrix<Real> & /*unused*/ coordMatrix,
+ UInt /*unused*/ integration_order) const {
if (integration_order !=
ElementClassProperty<_quadrangle_8>::polynomial_degree) {
AKANTU_TO_IMPLEMENT();
} else {
for (UInt i = 0; i < coordinates.cols(); ++i) {
// UInt j = 0;
Real x = coordinates(0, i);
Real y = coordinates(1, i);
coordMatrix(i, 0) = 1;
coordMatrix(i, 1) = x;
coordMatrix(i, 2) = y;
coordMatrix(i, 3) = x * y;
// for (UInt e = 0; e <= 2; ++e) {
// for (UInt n = 0; n <= 2; ++n) {
// coordMatrix(i, j) = std::pow(x, e) * std::pow(y, n);
// ++j;
// }
// }
}
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::interpolateElementalFieldFromIntegrationPoints(
const Array<Real> & field,
const Array<Real> & interpolation_points_coordinates_matrices,
const Array<Real> & quad_points_coordinates_inv_matrices,
- ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
+ ElementTypeMapArray<Real> & result, GhostType ghost_type,
const Array<UInt> & element_filter) const {
AKANTU_DEBUG_IN();
auto nb_element = this->mesh.getNbElement(type, ghost_type);
auto nb_quad_per_element =
GaussIntegrationElement<type>::getNbQuadraturePoints();
auto nb_interpolation_points_per_elem =
interpolation_points_coordinates_matrices.getNbComponent() /
nb_quad_per_element;
- if (not result.exists(type, ghost_type))
+ if (not result.exists(type, ghost_type)) {
result.alloc(nb_element * nb_interpolation_points_per_elem,
field.getNbComponent(), type, ghost_type);
+ }
- if (element_filter != empty_filter)
+ if (element_filter != empty_filter) {
nb_element = element_filter.size();
+ }
Matrix<Real> coefficients(nb_quad_per_element, field.getNbComponent());
auto & result_vec = result(type, ghost_type);
auto field_it = field.begin_reinterpret(field.getNbComponent(),
nb_quad_per_element, nb_element);
auto interpolation_points_coordinates_it =
interpolation_points_coordinates_matrices.begin(
nb_interpolation_points_per_elem, nb_quad_per_element);
auto result_begin = result_vec.begin_reinterpret(
field.getNbComponent(), nb_interpolation_points_per_elem,
result_vec.size() / nb_interpolation_points_per_elem);
auto inv_quad_coord_it = quad_points_coordinates_inv_matrices.begin(
nb_quad_per_element, nb_quad_per_element);
/// loop over the elements of the current filter and element type
for (UInt el = 0; el < nb_element; ++el, ++field_it, ++inv_quad_coord_it,
++interpolation_points_coordinates_it) {
/**
* matrix containing the inversion of the quadrature points'
* coordinates
*/
const auto & inv_quad_coord_matrix = *inv_quad_coord_it;
/**
* multiply it by the field values over quadrature points to get
* the interpolation coefficients
*/
coefficients.mul<false, true>(inv_quad_coord_matrix, *field_it);
/// matrix containing the points' coordinates
const auto & coord = *interpolation_points_coordinates_it;
/// multiply the coordinates matrix by the coefficients matrix and store the
/// result
Matrix<Real> res(result_begin[element_filter(el)]);
res.mul<true, true>(coefficients, coord);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::interpolateElementalFieldOnIntegrationPoints(
- const Array<Real> & u_el, Array<Real> & uq, const GhostType & ghost_type,
+ const Array<Real> & u_el, Array<Real> & uq, GhostType ghost_type,
const Array<Real> & shapes, const Array<UInt> & filter_elements) const {
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_nodes_per_element = ElementClass<type>::getShapeSize();
auto nb_points = shapes.size() / mesh.getNbElement(type, ghost_type);
auto nb_degree_of_freedom = u_el.getNbComponent() / nb_nodes_per_element;
Array<Real>::const_matrix_iterator N_it;
Array<Real> * filtered_N = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filtered_N = new Array<Real>(0, shapes.getNbComponent());
FEEngine::filterElementalData(mesh, shapes, *filtered_N, type, ghost_type,
filter_elements);
N_it = filtered_N->begin_reinterpret(nb_nodes_per_element, nb_points,
nb_element);
} else {
N_it =
shapes.begin_reinterpret(nb_nodes_per_element, nb_points, nb_element);
}
uq.resize(nb_element * nb_points);
auto u_it = u_el.begin(nb_degree_of_freedom, nb_nodes_per_element);
auto inter_u_it =
uq.begin_reinterpret(nb_degree_of_freedom, nb_points, nb_element);
for (UInt el = 0; el < nb_element; ++el, ++N_it, ++u_it, ++inter_u_it) {
const auto & u = *u_it;
const auto & N = *N_it;
auto & inter_u = *inter_u_it;
inter_u.template mul<false, false>(u, N);
}
delete filtered_N;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeFunctions::gradientElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & out_nablauq,
- const GhostType & ghost_type, const Array<Real> & shapes_derivatives,
+ GhostType ghost_type, const Array<Real> & shapes_derivatives,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
auto nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
auto nb_points = integration_points(type, ghost_type).cols();
auto element_dimension = ElementClass<type>::getNaturalSpaceDimension();
auto nb_degree_of_freedom = u_el.getNbComponent() / nb_nodes_per_element;
auto nb_element = mesh.getNbElement(type, ghost_type);
Array<Real>::const_matrix_iterator B_it;
Array<Real> * filtered_B = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filtered_B = new Array<Real>(0, shapes_derivatives.getNbComponent());
FEEngine::filterElementalData(mesh, shapes_derivatives, *filtered_B, type,
ghost_type, filter_elements);
B_it = filtered_B->begin(element_dimension, nb_nodes_per_element);
} else {
B_it = shapes_derivatives.begin(element_dimension, nb_nodes_per_element);
}
out_nablauq.resize(nb_element * nb_points);
auto u_it = u_el.begin(nb_degree_of_freedom, nb_nodes_per_element);
auto nabla_u_it = out_nablauq.begin(nb_degree_of_freedom, element_dimension);
for (UInt el = 0; el < nb_element; ++el, ++u_it) {
const auto & u = *u_it;
for (UInt q = 0; q < nb_points; ++q, ++B_it, ++nabla_u_it) {
const auto & B = *B_it;
auto & nabla_u = *nabla_u_it;
nabla_u.template mul<false, true>(u, B);
}
}
delete filtered_B;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/shape_lagrange.hh b/src/fe_engine/shape_lagrange.hh
index b11740508..ad931716e 100644
--- a/src/fe_engine/shape_lagrange.hh
+++ b/src/fe_engine/shape_lagrange.hh
@@ -1,172 +1,172 @@
/**
* @file shape_lagrange.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
* @date last modification: Mon Jan 29 2018
*
* @brief lagrangian shape functions class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_base.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_LAGRANGE_HH__
-#define __AKANTU_SHAPE_LAGRANGE_HH__
+#ifndef AKANTU_SHAPE_LAGRANGE_HH_
+#define AKANTU_SHAPE_LAGRANGE_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Shape> class ShapeCohesive;
class ShapeIGFEM;
template <ElementKind kind> class ShapeLagrange : public ShapeLagrangeBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "shape_lagrange",
const MemoryID & memory_id = 0);
~ShapeLagrange() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialization function for structural elements not yet implemented
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
- const ElementType & type,
- const GhostType & ghost_type);
+ ElementType type,
+ GhostType ghost_type);
/// computes the shape functions derivatives for given interpolation points
template <ElementType type>
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shape_derivatives, const GhostType & ghost_type,
+ Array<Real> & shape_derivatives, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shape_derivatives, const ElementType & type,
- const GhostType & ghost_type,
+ Array<Real> & shape_derivatives, ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements) const override;
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
- const GhostType & ghost_type);
+ GhostType ghost_type);
/// pre compute all shape derivatives on the element integration points from
/// natural coordinates
template <ElementType type>
void
precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
- const GhostType & ghost_type);
+ GhostType ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
const Array<Real> & shapes, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// interpolate on physical point
template <ElementType type>
void interpolate(const Vector<Real> & real_coords, UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// compute the gradient of u on the integration points
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void computeBtD(const Array<Real> & Ds, Array<Real> & BtDs,
GhostType ghost_type,
const Array<UInt> & filter_elements) const;
template <ElementType type>
void computeBtDB(const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// multiply a field by shape functions @f$ fts_{ij} = f_i * \varphi_j @f$
template <ElementType type>
void computeNtb(const Array<Real> & bs, Array<Real> & Ntbs,
GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// find natural coords from real coords provided an element
template <ElementType type>
void inverseMap(const Vector<Real> & real_coords, UInt element,
Vector<Real> & natural_coords,
- const GhostType & ghost_type = _not_ghost) const;
+ GhostType ghost_type = _not_ghost) const;
/// return true if the coordinates provided are inside the element, false
/// otherwise
template <ElementType type>
bool contains(const Vector<Real> & real_coords, UInt elem,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
/// compute the shape on a provided point
template <ElementType type>
void computeShapes(const Vector<Real> & real_coords, UInt elem,
- Vector<Real> & shapes, const GhostType & ghost_type) const;
+ Vector<Real> & shapes, GhostType ghost_type) const;
/// compute the shape derivatives on a provided point
template <ElementType type>
void computeShapeDerivatives(const Matrix<Real> & real_coords, UInt elem,
Tensor3<Real> & shapes,
- const GhostType & ghost_type) const;
+ GhostType ghost_type) const;
protected:
/// compute the shape derivatives on integration points for a given element
template <ElementType type>
inline void
computeShapeDerivativesOnCPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_inline_impl.hh"
-#endif /* __AKANTU_SHAPE_LAGRANGE_HH__ */
+#endif /* AKANTU_SHAPE_LAGRANGE_HH_ */
diff --git a/src/fe_engine/shape_lagrange_base.cc b/src/fe_engine/shape_lagrange_base.cc
index a225dd6af..f0faa46ef 100644
--- a/src/fe_engine/shape_lagrange_base.cc
+++ b/src/fe_engine/shape_lagrange_base.cc
@@ -1,166 +1,172 @@
/**
* @file shape_lagrange_base.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
* @date last modification: Tue Feb 20 2018
*
* @brief common par for the shape lagrange
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_base.hh"
#include "mesh_iterators.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
ShapeLagrangeBase::ShapeLagrangeBase(const Mesh & mesh, UInt spatial_dimension,
- const ElementKind & kind, const ID & id,
+ ElementKind kind, const ID & id,
const MemoryID & memory_id)
: ShapeFunctions(mesh, spatial_dimension, id, memory_id), _kind(kind) {}
/* -------------------------------------------------------------------------- */
ShapeLagrangeBase::~ShapeLagrangeBase() = default;
/* -------------------------------------------------------------------------- */
#define AKANTU_COMPUTE_SHAPES(type) \
_this.template computeShapesOnIntegrationPoints<type>( \
nodes, integration_points, shapes, ghost_type, filter_elements)
namespace shape_lagrange {
namespace details {
template <ElementKind kind> struct Helper {
template <class S>
- static void call(const S &, const Array<Real> &, const Matrix<Real> &,
- Array<Real> &, const ElementType &, const GhostType &,
- const Array<UInt> &) {
+ static void call(const S & /*unused*/, const Array<Real> & /*unused*/,
+ const Matrix<Real> & /*unused*/,
+ Array<Real> & /*unused*/, ElementType /*unused*/,
+ GhostType /*unused*/,
+ const Array<UInt> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#if !defined(DOXYGEN)
#define AKANTU_COMPUTE_SHAPES_KIND(kind) \
template <> struct Helper<kind> { \
template <class S> \
static void call(const S & _this, const Array<Real> & nodes, \
const Matrix<Real> & integration_points, \
- Array<Real> & shapes, const ElementType & type, \
- const GhostType & ghost_type, \
+ Array<Real> & shapes, ElementType type, \
+ GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(AKANTU_COMPUTE_SHAPES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_COMPUTE_SHAPES_KIND,
AKANTU_FE_ENGINE_LIST_LAGRANGE_BASE)
} // namespace details
} // namespace shape_lagrange
#endif
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shapes, const ElementType & type,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ Array<Real> & shapes, ElementType type,
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
auto kind = Mesh::getKind(type);
#define AKANTU_COMPUTE_SHAPES_KIND_SWITCH(kind) \
shape_lagrange::details::Helper<kind>::call( \
*this, nodes, integration_points, shapes, type, ghost_type, \
filter_elements);
AKANTU_BOOST_LIST_SWITCH(
AKANTU_COMPUTE_SHAPES_KIND_SWITCH,
BOOST_PP_LIST_TO_SEQ(AKANTU_FE_ENGINE_LIST_LAGRANGE_BASE), kind);
#undef AKANTU_COMPUTE_SHAPES
#undef AKANTU_COMPUTE_SHAPES_KIND
#undef AKANTU_COMPUTE_SHAPES_KIND_SWITCH
}
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::onElementsAdded(const Array<Element> & new_elements) {
AKANTU_DEBUG_IN();
const auto & nodes = mesh.getNodes();
for (auto elements_range : MeshElementsByTypes(new_elements)) {
auto type = elements_range.getType();
auto ghost_type = elements_range.getGhostType();
- if (mesh.getSpatialDimension(type) != _spatial_dimension)
+ if (mesh.getSpatialDimension(type) != _spatial_dimension) {
continue;
+ }
- if (mesh.getKind(type) != _kind)
+ if (mesh.getKind(type) != _kind) {
continue;
+ }
- auto & elements = elements_range.getElements();
+ const auto & elements = elements_range.getElements();
auto itp_type = FEEngine::getInterpolationType(type);
if (not shapes.exists(itp_type, ghost_type)) {
auto size_of_shapes = this->getShapeSize(type);
this->shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
}
const auto & natural_coords = integration_points(type, ghost_type);
computeShapesOnIntegrationPoints(nodes, natural_coords,
shapes(itp_type, ghost_type), type,
ghost_type, elements);
- if (_spatial_dimension != mesh.getSpatialDimension())
+ if (_spatial_dimension != mesh.getSpatialDimension()) {
continue;
-
+ }
+
if (not this->shapes_derivatives.exists(itp_type, ghost_type)) {
auto size_of_shapesd = this->getShapeDerivativesSize(type);
this->shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
}
computeShapeDerivativesOnIntegrationPoints(
nodes, natural_coords, shapes_derivatives(itp_type, ghost_type), type,
ghost_type, elements);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::onElementsRemoved(
- const Array<Element> &, const ElementTypeMapArray<UInt> & new_numbering) {
+ const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & new_numbering) {
this->shapes.onElementsRemoved(new_numbering);
this->shapes_derivatives.onElementsRemoved(new_numbering);
}
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Shapes Lagrange [" << std::endl;
ShapeFunctions::printself(stream, indent + 1);
shapes.printself(stream, indent + 1);
shapes_derivatives.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/fe_engine/shape_lagrange_base.hh b/src/fe_engine/shape_lagrange_base.hh
index b608a67ef..095822a12 100644
--- a/src/fe_engine/shape_lagrange_base.hh
+++ b/src/fe_engine/shape_lagrange_base.hh
@@ -1,91 +1,91 @@
/**
* @file shape_lagrange_base.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
* @date last modification: Wed Nov 08 2017
*
* @brief Base class for the shape lagrange
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_LAGRANGE_BASE_HH__
-#define __AKANTU_SHAPE_LAGRANGE_BASE_HH__
+#ifndef AKANTU_SHAPE_LAGRANGE_BASE_HH_
+#define AKANTU_SHAPE_LAGRANGE_BASE_HH_
namespace akantu {
class ShapeLagrangeBase : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrangeBase(const Mesh & mesh, UInt spatial_dimension,
- const ElementKind & kind, const ID & id = "shape_lagrange",
+ ElementKind kind, const ID & id = "shape_lagrange",
const MemoryID & memory_id = 0);
~ShapeLagrangeBase() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// computes the shape functions for given interpolation points
virtual void computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shapes, const ElementType & type,
- const GhostType & ghost_type,
+ Array<Real> & shapes, ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// computes the shape functions derivatives for given interpolation points
virtual void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shape_derivatives, const ElementType & type,
- const GhostType & ghost_type,
+ Array<Real> & shape_derivatives, ElementType type,
+ GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
template <ElementType type>
void computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shapes, const GhostType & ghost_type,
+ Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
public:
void onElementsAdded(const Array<Element> & elements) override;
void
onElementsRemoved(const Array<Element> & elements,
const ElementTypeMapArray<UInt> & new_numbering) override;
protected:
/// The kind to consider
ElementKind _kind;
};
} // namespace akantu
#include "shape_lagrange_base_inline_impl.hh"
-#endif /* __AKANTU_SHAPE_LAGRANGE_BASE_HH__ */
+#endif /* AKANTU_SHAPE_LAGRANGE_BASE_HH_ */
diff --git a/src/fe_engine/shape_lagrange_base_inline_impl.hh b/src/fe_engine/shape_lagrange_base_inline_impl.hh
index a1df4f823..d809c5fd1 100644
--- a/src/fe_engine/shape_lagrange_base_inline_impl.hh
+++ b/src/fe_engine/shape_lagrange_base_inline_impl.hh
@@ -1,83 +1,85 @@
/**
* @file shape_lagrange_base_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
* @date last modification: Wed Oct 11 2017
*
* @brief A Documented file.
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_base.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_HH__
-#define __AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_HH__
+#ifndef AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_HH_
+#define AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrangeBase::computeShapesOnIntegrationPoints(
- const Array<Real> &, const Matrix<Real> & integration_points,
- Array<Real> & shapes, const GhostType & ghost_type,
+ const Array<Real> & /*unused*/, const Matrix<Real> & integration_points,
+ Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
shapes.resize(nb_element * nb_points);
#if !defined(AKANTU_NDEBUG)
UInt size_of_shapes = ElementClass<type>::getShapeSize();
AKANTU_DEBUG_ASSERT(shapes.getNbComponent() == size_of_shapes,
"The shapes array does not have the correct "
<< "number of component");
#endif
auto shapes_it = shapes.begin_reinterpret(
ElementClass<type>::getNbNodesPerInterpolationElement(), nb_points,
nb_element);
auto shapes_begin = shapes_it;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
for (UInt elem = 0; elem < nb_element; ++elem) {
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
shapes_it = shapes_begin + filter_elements(elem);
+ }
Matrix<Real> & N = *shapes_it;
ElementClass<type>::computeShapes(integration_points, N);
- if (filter_elements == empty_filter)
+ if (filter_elements == empty_filter) {
++shapes_it;
+ }
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif /* __AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/shape_lagrange_inline_impl.hh b/src/fe_engine/shape_lagrange_inline_impl.hh
index bea4cd555..c536c317c 100644
--- a/src/fe_engine/shape_lagrange_inline_impl.hh
+++ b/src/fe_engine/shape_lagrange_inline_impl.hh
@@ -1,537 +1,540 @@
/**
* @file shape_lagrange_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 27 2010
* @date last modification: Tue Feb 20 2018
*
* @brief ShapeLagrange inline implementation
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "aka_voigthelper.hh"
#include "fe_engine.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_HH__
-#define __AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_HH__
+#ifndef AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_HH_
+#define AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
if (ElementClass<type>::getNaturalSpaceDimension() == \
mesh.getSpatialDimension() || \
kind != _ek_regular) \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
template <ElementKind kind>
inline void ShapeLagrange<kind>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- const ElementType & type, const GhostType & ghost_type) {
+ ElementType type, GhostType ghost_type) {
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
#undef INIT_SHAPE_FUNCTIONS
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
inline void ShapeLagrange<kind>::computeShapeDerivativesOnCPointsByElement(
const Matrix<Real> & node_coords, const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const {
AKANTU_DEBUG_IN();
// compute dnds
Tensor3<Real> dnds(node_coords.rows(), node_coords.cols(),
natural_coords.cols());
ElementClass<type>::computeDNDS(natural_coords, dnds);
// compute jacobian
Tensor3<Real> J(node_coords.rows(), natural_coords.rows(),
natural_coords.cols());
ElementClass<type>::computeJMat(dnds, node_coords, J);
// compute dndx
ElementClass<type>::computeShapeDerivatives(J, dnds, shapesd);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::inverseMap(const Vector<Real> & real_coords,
UInt elem, Vector<Real> & natural_coords,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
ElementClass<type>::inverseMap(real_coords, nodes_coord, natural_coords);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
bool ShapeLagrange<kind>::contains(const Vector<Real> & real_coords, UInt elem,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> natural_coords(spatial_dimension);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
return ElementClass<type>::contains(natural_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolate(const Vector<Real> & real_coords,
UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
UInt nb_shapes = ElementClass<type>::getShapeSize();
Vector<Real> shapes(nb_shapes);
computeShapes<type>(real_coords, elem, shapes, ghost_type);
ElementClass<type>::interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapes(const Vector<Real> & real_coords,
UInt elem, Vector<Real> & shapes,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> natural_coords(spatial_dimension);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
ElementClass<type>::computeShapes(natural_coords, shapes);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapeDerivatives(
const Matrix<Real> & real_coords, UInt elem, Tensor3<Real> & shapesd,
- const GhostType & ghost_type) const {
+ GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_points = real_coords.cols();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
AKANTU_DEBUG_ASSERT(mesh.getSpatialDimension() == shapesd.size(0) &&
nb_nodes_per_element == shapesd.size(1),
"Shape size doesn't match");
AKANTU_DEBUG_ASSERT(nb_points == shapesd.size(2),
"Number of points doesn't match shapes size");
Matrix<Real> natural_coords(spatial_dimension, nb_points);
// Creates the matrix of natural coordinates
for (UInt i = 0; i < nb_points; i++) {
Vector<Real> real_point = real_coords(i);
Vector<Real> natural_point = natural_coords(i);
inverseMap<type>(real_point, elem, natural_point, ghost_type);
}
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
computeShapeDerivativesOnCPointsByElement<type>(nodes_coord, natural_coords,
shapesd);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
ShapeLagrange<kind>::ShapeLagrange(const Mesh & mesh, UInt spatial_dimension,
const ID & id, const MemoryID & memory_id)
: ShapeLagrangeBase(mesh, spatial_dimension, kind, id, memory_id) {}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shape_derivatives, const GhostType & ghost_type,
+ Array<Real> & shape_derivatives, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
AKANTU_DEBUG_ASSERT(shape_derivatives.getNbComponent() == size_of_shapesd,
"The shapes_derivatives array does not have the correct "
<< "number of component");
shape_derivatives.resize(nb_element * nb_points);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
Real * shapesd_val = shape_derivatives.storage();
Array<Real>::matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
+ }
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
- if (filter_elements != empty_filter)
+ if (filter_elements != empty_filter) {
shapesd_val = shape_derivatives.storage() +
filter_elements(elem) * size_of_shapesd * nb_points;
+ }
Matrix<Real> & X = *x_it;
Tensor3<Real> B(shapesd_val, spatial_dimension, nb_nodes_per_element,
nb_points);
computeShapeDerivativesOnCPointsByElement<type>(X, integration_points, B);
- if (filter_elements == empty_filter)
+ if (filter_elements == empty_filter) {
shapesd_val += size_of_shapesd * nb_points;
+ }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
void ShapeLagrange<kind>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shape_derivatives, const ElementType & type,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ Array<Real> & shape_derivatives, ElementType type,
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
#define AKANTU_COMPUTE_SHAPES(type) \
computeShapeDerivativesOnIntegrationPoints<type>( \
nodes, integration_points, shape_derivatives, ghost_type, \
filter_elements);
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(AKANTU_COMPUTE_SHAPES);
#undef AKANTU_COMPUTE_SHAPES
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::precomputeShapesOnIntegrationPoints(
- const Array<Real> & nodes, const GhostType & ghost_type) {
+ const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapes = ElementClass<type>::getShapeSize();
Array<Real> & shapes_tmp =
shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
this->computeShapesOnIntegrationPoints<type>(nodes, natural_coords,
shapes_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::precomputeShapeDerivativesOnIntegrationPoints(
- const Array<Real> & nodes, const GhostType & ghost_type) {
+ const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
Array<Real> & shapes_derivatives_tmp =
shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
this->computeShapeDerivativesOnIntegrationPoints<type>(
nodes, natural_coords, shapes_derivatives_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
const Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->interpolateElementalFieldOnIntegrationPoints<type>(
u_el, out_uq, ghost_type, shapes, filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(shapes.exists(itp_type, ghost_type),
"No shapes for the type "
<< shapes.printType(itp_type, ghost_type));
this->interpolateOnIntegrationPoints<type>(in_u, out_uq, nb_degree_of_freedom,
shapes(itp_type, ghost_type),
ghost_type, filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::gradientOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_nablauq,
UInt nb_degree_of_freedom, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(
shapes_derivatives.exists(itp_type, ghost_type),
"No shapes derivatives for the type "
<< shapes_derivatives.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->gradientElementalFieldOnIntegrationPoints<type>(
u_el, out_nablauq, ghost_type, shapes_derivatives(itp_type, ghost_type),
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeBtD(
const Array<Real> & Ds, Array<Real> & BtDs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
const auto & shapes_derivatives =
this->shapes_derivatives(itp_type, ghost_type);
auto spatial_dimension = mesh.getSpatialDimension();
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> shapes_derivatives_filtered(0,
shapes_derivatives.getNbComponent());
auto && view =
make_view(shapes_derivatives, spatial_dimension, nb_nodes_per_element);
auto B_it = view.begin();
auto B_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes_derivatives,
shapes_derivatives_filtered, type, ghost_type,
filter_elements);
auto && view = make_view(shapes_derivatives_filtered, spatial_dimension,
nb_nodes_per_element);
B_it = view.begin();
B_end = view.end();
}
for (auto && values :
zip(range(B_it, B_end),
make_view(Ds, Ds.getNbComponent() / spatial_dimension,
spatial_dimension),
make_view(BtDs, BtDs.getNbComponent() / nb_nodes_per_element,
nb_nodes_per_element))) {
const auto & B = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D = std::get<2>(values);
// transposed due to the storage layout of B
Bt_D.template mul<false, false>(D, B);
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeBtDB(
const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
const auto & shapes_derivatives =
this->shapes_derivatives(itp_type, ghost_type);
constexpr auto dim = ElementClass<type>::getSpatialDimension();
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> shapes_derivatives_filtered(0,
shapes_derivatives.getNbComponent());
auto && view = make_view(shapes_derivatives, dim, nb_nodes_per_element);
auto B_it = view.begin();
auto B_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes_derivatives,
shapes_derivatives_filtered, type, ghost_type,
filter_elements);
auto && view =
make_view(shapes_derivatives_filtered, dim, nb_nodes_per_element);
B_it = view.begin();
B_end = view.end();
}
if (order_d == 4) {
UInt tangent_size = VoigtHelper<dim>::size;
Matrix<Real> B(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> Bt_D(dim * nb_nodes_per_element, tangent_size);
for (auto && values :
zip(range(B_it, B_end), make_view(Ds, tangent_size, tangent_size),
make_view(BtDBs, dim * nb_nodes_per_element,
dim * nb_nodes_per_element))) {
const auto & Bfull = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D_B = std::get<2>(values);
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(Bfull, B,
nb_nodes_per_element);
Bt_D.template mul<true, false>(B, D);
Bt_D_B.template mul<false, false>(Bt_D, B);
}
} else if (order_d == 2) {
Matrix<Real> Bt_D(nb_nodes_per_element, dim);
for (auto && values :
zip(range(B_it, B_end), make_view(Ds, dim, dim),
make_view(BtDBs, nb_nodes_per_element, nb_nodes_per_element))) {
const auto & B = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D_B = std::get<2>(values);
Bt_D.template mul<true, false>(B, D);
Bt_D_B.template mul<false, false>(Bt_D, B);
}
}
}
template <>
template <>
inline void ShapeLagrange<_ek_regular>::computeBtDB<_point_1>(
const Array<Real> & /*Ds*/, Array<Real> & /*BtDBs*/, UInt /*order_d*/,
GhostType /*ghost_type*/, const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeNtb(
const Array<Real> & bs, Array<Real> & Ntbs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
Ntbs.resize(bs.size());
UInt size_of_shapes = ElementClass<type>::getShapeSize();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
UInt nb_degree_of_freedom = bs.getNbComponent();
Array<Real> shapes_filtered(0, size_of_shapes);
auto && view = make_view(shapes(itp_type, ghost_type), 1, size_of_shapes);
auto N_it = view.begin();
auto N_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes(itp_type, ghost_type),
shapes_filtered, type, ghost_type,
filter_elements);
auto && view = make_view(shapes_filtered, 1, size_of_shapes);
N_it = view.begin();
N_end = view.end();
}
for (auto && values :
zip(make_view(bs, nb_degree_of_freedom, 1), range(N_it, N_end),
make_view(Ntbs, nb_degree_of_freedom, size_of_shapes))) {
const auto & b = std::get<0>(values);
const auto & N = std::get<1>(values);
auto & Ntb = std::get<2>(values);
Ntb.template mul<false, false>(b, N);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif /* __AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/shape_structural.hh b/src/fe_engine/shape_structural.hh
index df433cf9e..c6b606939 100644
--- a/src/fe_engine/shape_structural.hh
+++ b/src/fe_engine/shape_structural.hh
@@ -1,177 +1,172 @@
/**
* @file shape_structural.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
* @date last modification: Tue Feb 20 2018
*
* @brief shape class for element with different set of shapes functions
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_STRUCTURAL_HH__
-#define __AKANTU_SHAPE_STRUCTURAL_HH__
+#ifndef AKANTU_SHAPE_STRUCTURAL_HH_
+#define AKANTU_SHAPE_STRUCTURAL_HH_
namespace akantu {
template <ElementKind kind> class ShapeStructural : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
// Ctors/Dtors should be explicitely implemented for _ek_structural
public:
ShapeStructural(Mesh & mesh, UInt spatial_dimension,
const ID & id = "shape_structural",
const MemoryID & memory_id = 0);
~ShapeStructural() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override {
- std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
- ;
+ std::string space(indent, AKANTU_INDENT);
stream << space << "ShapesStructural [" << std::endl;
rotation_matrices.printself(stream, indent + 1);
ShapeFunctions::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/// compute shape functions on given integration points
template <ElementType type>
void computeShapesOnIntegrationPoints(
const Array<Real> &, const Matrix<Real> & integration_points,
- Array<Real> & shapes, const GhostType & ghost_type,
+ Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// initialization function for structural elements
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
- const ElementType & type,
- const GhostType & ghost_type);
+ ElementType type, GhostType ghost_type);
/// precompute the rotation matrices for the elements dofs
template <ElementType type>
void precomputeRotationMatrices(const Array<Real> & nodes,
- const GhostType & ghost_type);
+ GhostType ghost_type);
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
- const GhostType & ghost_type);
+ GhostType ghost_type);
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
- void
- precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
- const GhostType & ghost_type);
+ void precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
+ GhostType ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type>
void interpolateOnIntegrationPoints(
- const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
- const GhostType & ghost_type = _not_ghost,
+ const Array<Real> & u, Array<Real> & uq, UInt nb_dof,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// compute the gradient of u on the integration points
template <ElementType type>
void gradientOnIntegrationPoints(
- const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
- const GhostType & ghost_type = _not_ghost,
+ const Array<Real> & u, Array<Real> & nablauq, UInt nb_dof,
+ GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// interpolate on physical point
template <ElementType type>
void interpolate(const Vector<Real> & /*real_coords*/, UInt /*elem*/,
const Matrix<Real> & /*nodal_values*/,
Vector<Real> & /*interpolated*/,
- const GhostType & /*ghost_type*/) const {
+ GhostType /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the shapes on a provided point
template <ElementType type>
void computeShapes(const Vector<Real> & /*real_coords*/, UInt /*elem*/,
Vector<Real> & /*shapes*/,
- const GhostType & /*ghost_type*/) const {
+ GhostType /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the shape derivatives on a provided point
template <ElementType type>
void computeShapeDerivatives(const Matrix<Real> & /*real_coords*/,
UInt /*elem*/, Tensor3<Real> & /*shapes*/,
- const GhostType & /*ghost_type*/) const {
+ GhostType /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
}
/// get the rotations vector
inline const Array<Real> &
- getRotations(const ElementType & el_type,
- __attribute__((unused))
- const GhostType & ghost_type = _not_ghost) const {
+ getRotations(ElementType el_type, __attribute__((unused))
+ GhostType ghost_type = _not_ghost) const {
return rotation_matrices(el_type);
}
/* ------------------------------------------------------------------------ */
template <ElementType type>
void computeBtD(const Array<Real> & /*Ds*/, Array<Real> & /*BtDs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
template <ElementType type>
void computeBtDB(const Array<Real> & /*Ds*/, Array<Real> & /*BtDBs*/,
UInt /*order_d*/, GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
/// multiply a field by shape functions
template <ElementType type>
void
computeNtb(const Array<Real> & /*bs*/, Array<Real> & /*Ntbs*/,
- const GhostType & /*ghost_type*/,
+ GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/ = empty_filter) const {
AKANTU_TO_IMPLEMENT();
}
protected:
ElementTypeMapArray<Real> rotation_matrices;
};
} // namespace akantu
#include "shape_structural_inline_impl.hh"
-#endif /* __AKANTU_SHAPE_STRUCTURAL_HH__ */
+#endif /* AKANTU_SHAPE_STRUCTURAL_HH_ */
diff --git a/src/fe_engine/shape_structural_inline_impl.hh b/src/fe_engine/shape_structural_inline_impl.hh
index 303231cc5..bb29be0c5 100644
--- a/src/fe_engine/shape_structural_inline_impl.hh
+++ b/src/fe_engine/shape_structural_inline_impl.hh
@@ -1,432 +1,433 @@
/**
* @file shape_structural_inline_impl.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 11 2017
* @date last modification: Wed Feb 21 2018
*
* @brief ShapeStructural inline implementation
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_iterators.hh"
#include "shape_structural.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_HH__
-#define __AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_HH__
+#ifndef AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_HH_
+#define AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_HH_
namespace akantu {
namespace {
/// Extract nodal coordinates per elements
template <ElementType type>
- std::unique_ptr<Array<Real>>
- getNodesPerElement(const Mesh & mesh, const Array<Real> & nodes,
- const GhostType & ghost_type) {
+ std::unique_ptr<Array<Real>> getNodesPerElement(const Mesh & mesh,
+ const Array<Real> & nodes,
+ GhostType ghost_type) {
const auto dim = ElementClass<type>::getSpatialDimension();
const auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nodes_per_element =
std::make_unique<Array<Real>>(0, dim * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, *nodes_per_element, type,
ghost_type);
return nodes_per_element;
}
} // namespace
template <ElementKind kind>
inline void ShapeStructural<kind>::initShapeFunctions(
const Array<Real> & /* unused */, const Matrix<Real> & /* unused */,
- const ElementType & /* unused */, const GhostType & /* unused */) {
+ ElementType /* unused */, GhostType /* unused */) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeRotationMatrices<type>(nodes, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
template <>
inline void ShapeStructural<_ek_structural>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- const ElementType & type, const GhostType & ghost_type) {
+ ElementType type, GhostType ghost_type) {
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
#undef INIT_SHAPE_FUNCTIONS
/* -------------------------------------------------------------------------- */
template <>
template <ElementType type>
void ShapeStructural<_ek_structural>::computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
- Array<Real> & shapes, const GhostType & ghost_type,
+ Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
shapes.resize(nb_element * nb_points);
UInt ndof = ElementClass<type>::getNbDegreeOfFreedom();
#if !defined(AKANTU_NDEBUG)
UInt size_of_shapes = ElementClass<type>::getShapeSize();
AKANTU_DEBUG_ASSERT(shapes.getNbComponent() == size_of_shapes,
"The shapes array does not have the correct "
<< "number of component");
#endif
auto shapes_it = shapes.begin_reinterpret(
ElementClass<type>::getNbNodesPerInterpolationElement(), ndof, nb_points,
nb_element);
auto shapes_begin = shapes_it;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
auto nodes_per_element = getNodesPerElement<type>(mesh, nodes, ghost_type);
auto nodes_it = nodes_per_element->begin(mesh.getSpatialDimension(),
Mesh::getNbNodesPerElement(type));
auto nodes_begin = nodes_it;
for (UInt elem = 0; elem < nb_element; ++elem) {
if (filter_elements != empty_filter) {
shapes_it = shapes_begin + filter_elements(elem);
nodes_it = nodes_begin + filter_elements(elem);
}
Tensor3<Real> & N = *shapes_it;
auto & real_coord = *nodes_it;
ElementClass<type>::computeShapes(integration_points, real_coord, N);
if (filter_elements == empty_filter) {
++shapes_it;
++nodes_it;
}
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::precomputeRotationMatrices(
- const Array<Real> & nodes, const GhostType & ghost_type) {
+ const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
const auto spatial_dimension = mesh.getSpatialDimension();
const auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto nb_element = mesh.getNbElement(type, ghost_type);
const auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
if (not this->rotation_matrices.exists(type, ghost_type)) {
this->rotation_matrices.alloc(0, nb_dof * nb_dof, type, ghost_type);
}
auto & rot_matrices = this->rotation_matrices(type, ghost_type);
rot_matrices.resize(nb_element);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
bool has_extra_normal = mesh.hasData<Real>("extra_normal", type, ghost_type);
Array<Real>::const_vector_iterator extra_normal;
- if (has_extra_normal)
+ if (has_extra_normal) {
extra_normal = mesh.getData<Real>("extra_normal", type, ghost_type)
.begin(spatial_dimension);
+ }
for (auto && tuple :
zip(make_view(x_el, spatial_dimension, nb_nodes_per_element),
make_view(rot_matrices, nb_dof, nb_dof))) {
// compute shape derivatives
auto & X = std::get<0>(tuple);
auto & R = std::get<1>(tuple);
if (has_extra_normal) {
ElementClass<type>::computeRotationMatrix(R, X, *extra_normal);
++extra_normal;
} else {
ElementClass<type>::computeRotationMatrix(
R, X, Vector<Real>(spatial_dimension));
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::precomputeShapesOnIntegrationPoints(
- const Array<Real> & nodes, const GhostType & ghost_type) {
+ const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
const auto & natural_coords = integration_points(type, ghost_type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_points = integration_points(type, ghost_type).cols();
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
const auto dim = ElementClass<type>::getSpatialDimension();
auto itp_type = FEEngine::getInterpolationType(type);
if (not shapes.exists(itp_type, ghost_type)) {
auto size_of_shapes = this->getShapeSize(type);
this->shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
}
auto & shapes_ = this->shapes(itp_type, ghost_type);
shapes_.resize(nb_element * nb_points);
auto nodes_per_element = getNodesPerElement<type>(mesh, nodes, ghost_type);
for (auto && tuple :
zip(make_view(shapes_, nb_dof, nb_dof * nb_nodes_per_element, nb_points),
make_view(*nodes_per_element, dim, nb_nodes_per_element))) {
auto & N = std::get<0>(tuple);
auto & real_coord = std::get<1>(tuple);
ElementClass<type>::computeShapes(natural_coords, real_coord, N);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::precomputeShapeDerivativesOnIntegrationPoints(
- const Array<Real> & nodes, const GhostType & ghost_type) {
+ const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
const auto & natural_coords = integration_points(type, ghost_type);
const auto spatial_dimension = mesh.getSpatialDimension();
const auto natural_spatial_dimension =
ElementClass<type>::getNaturalSpaceDimension();
const auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto nb_points = natural_coords.cols();
const auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
const auto nb_element = mesh.getNbElement(type, ghost_type);
const auto nb_stress_components = ElementClass<type>::getNbStressComponents();
auto itp_type = FEEngine::getInterpolationType(type);
if (not this->shapes_derivatives.exists(itp_type, ghost_type)) {
auto size_of_shapesd = this->getShapeDerivativesSize(type);
this->shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
}
auto & rot_matrices = this->rotation_matrices(type, ghost_type);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
auto & shapesd = this->shapes_derivatives(itp_type, ghost_type);
shapesd.resize(nb_element * nb_points);
for (auto && tuple :
zip(make_view(x_el, spatial_dimension, nb_nodes_per_element),
make_view(shapesd, nb_stress_components,
nb_nodes_per_element * nb_dof, nb_points),
make_view(rot_matrices, nb_dof, nb_dof))) {
// compute shape derivatives
auto & X = std::get<0>(tuple);
auto & B = std::get<1>(tuple);
auto & RDOFs = std::get<2>(tuple);
Tensor3<Real> dnds(natural_spatial_dimension,
ElementClass<type>::interpolation_property::dnds_columns,
B.size(2));
ElementClass<type>::computeDNDS(natural_coords, X, dnds);
Tensor3<Real> J(natural_spatial_dimension, natural_spatial_dimension,
natural_coords.cols());
// Computing the coordinates of the element in the natural space
auto R = RDOFs.block(0, 0, spatial_dimension, spatial_dimension);
Matrix<Real> T(B.size(1), B.size(1), 0);
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
T.block(RDOFs, i * RDOFs.rows(), i * RDOFs.rows());
}
// Rotate to local basis
auto x =
(R * X).block(0, 0, natural_spatial_dimension, nb_nodes_per_element);
ElementClass<type>::computeJMat(natural_coords, x, J);
ElementClass<type>::computeShapeDerivatives(J, dnds, T, B);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_dof,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(out_uq.getNbComponent() == nb_dof,
"The output array shape is not correct");
auto itp_type = FEEngine::getInterpolationType(type);
const auto & shapes_ = shapes(itp_type, ghost_type);
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement();
auto nb_quad_points_per_element = integration_points(type, ghost_type).cols();
Array<Real> u_el(0, nb_nodes_per_element * nb_dof);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
auto nb_quad_points = nb_quad_points_per_element * u_el.size();
out_uq.resize(nb_quad_points);
auto out_it = out_uq.begin_reinterpret(nb_dof, 1, nb_quad_points_per_element,
u_el.size());
auto shapes_it =
shapes_.begin_reinterpret(nb_dof, nb_dof * nb_nodes_per_element,
nb_quad_points_per_element, nb_element);
auto u_it = u_el.begin_reinterpret(nb_dof * nb_nodes_per_element, 1,
nb_quad_points_per_element, u_el.size());
for_each_element(nb_element, filter_elements, [&](auto && el) {
auto & uq = *out_it;
const auto & u = *u_it;
auto N = Tensor3<Real>(shapes_it[el]);
for (auto && q : arange(uq.size(2))) {
auto uq_q = Matrix<Real>(uq(q));
auto u_q = Matrix<Real>(u(q));
auto N_q = Matrix<Real>(N(q));
uq_q.mul<false, false>(N_q, u_q);
}
++out_it;
++u_it;
});
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::gradientOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_nablauq, UInt nb_dof,
- const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
+ GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
auto itp_type = FEEngine::getInterpolationType(type);
const auto & shapesd = shapes_derivatives(itp_type, ghost_type);
auto nb_element = mesh.getNbElement(type, ghost_type);
auto element_dimension = ElementClass<type>::getSpatialDimension();
auto nb_quad_points_per_element = integration_points(type, ghost_type).cols();
auto nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement();
Array<Real> u_el(0, nb_nodes_per_element * nb_dof);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
auto nb_quad_points = nb_quad_points_per_element * u_el.size();
out_nablauq.resize(nb_quad_points);
auto out_it = out_nablauq.begin_reinterpret(
element_dimension, 1, nb_quad_points_per_element, u_el.size());
auto shapesd_it = shapesd.begin_reinterpret(
element_dimension, nb_dof * nb_nodes_per_element,
nb_quad_points_per_element, nb_element);
auto u_it = u_el.begin_reinterpret(nb_dof * nb_nodes_per_element, 1,
nb_quad_points_per_element, u_el.size());
for_each_element(nb_element, filter_elements, [&](auto && el) {
auto & nablau = *out_it;
const auto & u = *u_it;
auto B = Tensor3<Real>(shapesd_it[el]);
for (auto && q : arange(nablau.size(2))) {
auto nablau_q = Matrix<Real>(nablau(q));
auto u_q = Matrix<Real>(u(q));
auto B_q = Matrix<Real>(B(q));
nablau_q.mul<false, false>(B_q, u_q);
}
++out_it;
++u_it;
});
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
template <ElementType type>
void ShapeStructural<_ek_structural>::computeBtD(
const Array<Real> & Ds, Array<Real> & BtDs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
auto nb_stress = ElementClass<type>::getNbStressComponents();
auto nb_dof_per_element = ElementClass<type>::getNbDegreeOfFreedom() *
mesh.getNbNodesPerElement(type);
const auto & shapes_derivatives =
this->shapes_derivatives(itp_type, ghost_type);
Array<Real> shapes_derivatives_filtered(0,
shapes_derivatives.getNbComponent());
auto && view = make_view(shapes_derivatives, nb_stress, nb_dof_per_element);
auto B_it = view.begin();
auto B_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes_derivatives,
shapes_derivatives_filtered, type, ghost_type,
filter_elements);
auto && view =
make_view(shapes_derivatives_filtered, nb_stress, nb_dof_per_element);
B_it = view.begin();
B_end = view.end();
}
for (auto && values : zip(range(B_it, B_end), make_view(Ds, nb_stress),
make_view(BtDs, BtDs.getNbComponent()))) {
const auto & B = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D = std::get<2>(values);
Bt_D.template mul<true>(B, D);
}
}
} // namespace akantu
-#endif /* __AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_HH_ */
diff --git a/src/geometry/aabb_primitives/aabb_primitive.hh b/src/geometry/aabb_primitives/aabb_primitive.hh
index a9d8abe4b..52ddf363b 100644
--- a/src/geometry/aabb_primitives/aabb_primitive.hh
+++ b/src/geometry/aabb_primitives/aabb_primitive.hh
@@ -1,88 +1,88 @@
/**
* @file aabb_primitive.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Macro classe (primitive) for AABB CGAL algos
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_AABB_PRIMITIVE_HH__
-#define __AKANTU_AABB_PRIMITIVE_HH__
+#ifndef AKANTU_AABB_PRIMITIVE_HH_
+#define AKANTU_AABB_PRIMITIVE_HH_
#include "aka_common.hh"
#include "line_arc.hh"
#include "tetrahedron.hh"
#include "triangle.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/**
* This macro defines a class that is used in the CGAL AABB tree algorithm.
* All the `typedef`s and methods are required by the AABB module.
*
* The member variables are
* - the id of the element associated to the primitive
* - the geometric primitive of the element
*
* @param name the name of the primitive type
* @param kernel the name of the kernel used
*/
#define AKANTU_AABB_CLASS(name, kernel) \
class name##_primitive { \
- typedef std::list<name<kernel>>::iterator Iterator; \
+ using Iterator = std::list<name<kernel>>::iterator; /* NOLINT */ \
\
public: \
- typedef UInt Id; \
- typedef kernel::Point_3 Point; \
- typedef kernel::name##_3 Datum; \
+ using Id = UInt; \
+ using Point = kernel::Point_3; \
+ using Datum = kernel::name##_3; \
\
public: \
- name##_primitive() : meshId(0), primitive() {} \
+ name##_primitive() = default; \
name##_primitive(Iterator it) : meshId(it->id()), primitive(*it) {} \
\
public: \
const Datum & datum() const { return primitive; } \
Point reference_point() const; \
const Id & id() const { return meshId; } \
\
protected: \
- Id meshId; \
- name<kernel> primitive; \
+ Id meshId{0}; \
+ name<kernel> primitive; /* NOLINT */ \
}
// If the primitive is supported by CGAL::intersection() then the
// implementation process is really easy with this macro
AKANTU_AABB_CLASS(Triangle, cgal::Cartesian);
AKANTU_AABB_CLASS(Line_arc, cgal::Spherical);
#undef AKANTU_AABB_CLASS
} // namespace akantu
-#endif // __AKANTU_AABB_PRIMITIVE_HH__
+#endif // AKANTU_AABB_PRIMITIVE_HH_
diff --git a/src/geometry/aabb_primitives/line_arc.hh b/src/geometry/aabb_primitives/line_arc.hh
index e11f153aa..a6d1e86ad 100644
--- a/src/geometry/aabb_primitives/line_arc.hh
+++ b/src/geometry/aabb_primitives/line_arc.hh
@@ -1,73 +1,73 @@
/**
* @file line_arc.hh
*
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Mon Jun 19 2017
*
* @brief Segment classe (geometry) for AABB CGAL algos
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_LINE_ARC_HH__
-#define __AKANTU_LINE_ARC_HH__
+#ifndef AKANTU_LINE_ARC_HH_
+#define AKANTU_LINE_ARC_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Triangle_3 primitive
template <typename K> class Line_arc : public CGAL::Line_arc_3<K> {
public:
/// Default constructor
- Line_arc() : CGAL::Line_arc_3<K>(), mesh_id(0), seg_id(0) {}
+ Line_arc() : CGAL::Line_arc_3<K>() {}
/// Copy constructor
Line_arc(const Line_arc & other)
: CGAL::Line_arc_3<K>(other), mesh_id(other.mesh_id),
seg_id(other.seg_id) {}
/// Construct from 3 points
// "CGAL-4.5/doc_html/Circular_kernel_3/classCGAL_1_1Line__arc__3.html"
Line_arc(const CGAL::Line_3<K> & l, const CGAL::Circular_arc_point_3<K> & a,
const CGAL::Circular_arc_point_3<K> & b)
- : CGAL::Line_arc_3<K>(l, a, b), mesh_id(0), seg_id(0) {}
+ : CGAL::Line_arc_3<K>(l, a, b) {}
public:
UInt id() const { return mesh_id; }
UInt segId() const { return seg_id; }
void setId(UInt newId) { mesh_id = newId; }
void setSegId(UInt newId) { seg_id = newId; }
protected:
/// Id of the element represented by the primitive
- UInt mesh_id;
+ UInt mesh_id{0};
/// Id of the segment represented by the primitive
- UInt seg_id;
+ UInt seg_id{0};
};
} // namespace akantu
-#endif // __AKANTU_LINE_ARC_HH__
+#endif // AKANTU_LINE_ARC_HH_
diff --git a/src/geometry/aabb_primitives/tetrahedron.hh b/src/geometry/aabb_primitives/tetrahedron.hh
index 0cfc44f2b..fee6663bb 100644
--- a/src/geometry/aabb_primitives/tetrahedron.hh
+++ b/src/geometry/aabb_primitives/tetrahedron.hh
@@ -1,69 +1,69 @@
/**
* @file tetrahedron.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Feb 27 2015
* @date last modification: Mon Jun 19 2017
*
* @brief Tetrahedron classe (geometry) for AABB CGAL algos
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TETRAHEDRON_HH__
-#define __AKANTU_TETRAHEDRON_HH__
+#ifndef AKANTU_TETRAHEDRON_HH_
+#define AKANTU_TETRAHEDRON_HH_
#include "aka_common.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Tetrahedron_3 primitive
template <typename K> class Tetrahedron : public CGAL::Tetrahedron_3<K> {
public:
/// Default constructor
- Tetrahedron() : CGAL::Tetrahedron_3<K>(), meshId(0) {}
+ Tetrahedron() : CGAL::Tetrahedron_3<K>() {}
/// Copy constructor
Tetrahedron(const Tetrahedron & other)
: CGAL::Tetrahedron_3<K>(other), meshId(other.meshId) {}
/// Construct from 4 points
Tetrahedron(const CGAL::Point_3<K> & a, const CGAL::Point_3<K> & b,
const CGAL::Point_3<K> & c, const CGAL::Point_3<K> & d)
- : CGAL::Tetrahedron_3<K>(a, b, c, d), meshId(0) {}
+ : CGAL::Tetrahedron_3<K>(a, b, c, d) {}
public:
UInt id() const { return meshId; }
void setId(UInt newId) { meshId = newId; }
protected:
/// Id of the element represented by the primitive
- UInt meshId;
+ UInt meshId{0};
};
} // namespace akantu
#endif
diff --git a/src/geometry/aabb_primitives/triangle.hh b/src/geometry/aabb_primitives/triangle.hh
index 4f2c1f7af..11a670902 100644
--- a/src/geometry/aabb_primitives/triangle.hh
+++ b/src/geometry/aabb_primitives/triangle.hh
@@ -1,69 +1,74 @@
/**
* @file triangle.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Mon Jun 19 2017
*
* @brief Triangle classe (geometry) for AABB CGAL algos
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TRIANGLE_HH__
-#define __AKANTU_TRIANGLE_HH__
+#ifndef AKANTU_TRIANGLE_HH_
+#define AKANTU_TRIANGLE_HH_
#include "aka_common.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Triangle_3 primitive
template <typename K> class Triangle : public CGAL::Triangle_3<K> {
+ using parent = CGAL::Triangle_3<K>;
+
public:
/// Default constructor
- Triangle() : CGAL::Triangle_3<K>(), meshId(0) {}
+ Triangle() = default;
/// Copy constructor
- Triangle(const Triangle & other)
- : CGAL::Triangle_3<K>(other), meshId(other.meshId) {}
+ Triangle(const Triangle & other) = default;
+ Triangle(Triangle && other) noexcept = default;
+
+ Triangle & operator=(const Triangle & other) = default;
+ Triangle & operator=(Triangle && other) noexcept = default;
/// Construct from 3 points
Triangle(const CGAL::Point_3<K> & a, const CGAL::Point_3<K> & b,
const CGAL::Point_3<K> & c)
- : CGAL::Triangle_3<K>(a, b, c), meshId(0) {}
+ : parent(a, b, c) {}
public:
UInt id() const { return meshId; }
void setId(UInt newId) { meshId = newId; }
protected:
/// Id of the element represented by the primitive
- UInt meshId;
+ UInt meshId{0};
};
} // namespace akantu
-#endif // __AKANTU_TRIANGLE_HH__
+#endif // AKANTU_TRIANGLE_HH_
diff --git a/src/geometry/geom_helper_functions.hh b/src/geometry/geom_helper_functions.hh
index 06791db0f..747e85b5d 100644
--- a/src/geometry/geom_helper_functions.hh
+++ b/src/geometry/geom_helper_functions.hh
@@ -1,111 +1,113 @@
/**
* @file geom_helper_functions.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Wed Jan 31 2018
*
* @brief Helper functions for the computational geometry algorithms
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef _AKANTU_GEOM_HELPER_FUNCTIONS_HH__
-#define _AKANTU_GEOM_HELPER_FUNCTIONS_HH__
+#ifndef AKANTU_GEOM_HELPER_FUNCTIONS_HH_
+#define AKANTU_GEOM_HELPER_FUNCTIONS_HH_
#include "aka_common.hh"
#include "aka_math.hh"
#include "tree_type_helper.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/// Fuzzy compare of two points
template <class Point>
inline bool comparePoints(const Point & a, const Point & b) {
return Math::are_float_equal(a.x(), b.x()) &&
Math::are_float_equal(a.y(), b.y()) &&
Math::are_float_equal(a.z(), b.z());
}
template <>
inline bool comparePoints(const cgal::Spherical::Circular_arc_point_3 & a,
const cgal::Spherical::Circular_arc_point_3 & b) {
return Math::are_float_equal(CGAL::to_double(a.x()),
CGAL::to_double(b.x())) &&
Math::are_float_equal(CGAL::to_double(a.y()),
CGAL::to_double(b.y())) &&
Math::are_float_equal(CGAL::to_double(a.z()), CGAL::to_double(b.z()));
}
/// Fuzzy compare of two segments
template <class K>
inline bool compareSegments(const CGAL::Segment_3<K> & a,
const CGAL::Segment_3<K> & b) {
return (comparePoints(a.source(), b.source()) &&
comparePoints(a.target(), b.target())) ||
(comparePoints(a.source(), b.target()) &&
comparePoints(a.target(), b.source()));
}
/// Compare segment pairs
inline bool
compareSegmentPairs(const std::pair<cgal::Cartesian::Segment_3, UInt> & a,
const std::pair<cgal::Cartesian::Segment_3, UInt> & b) {
return compareSegments(a.first, b.first);
}
/// Pair ordering operator based on first member
struct segmentPairsLess {
inline bool
operator()(const std::pair<cgal::Cartesian::Segment_3, UInt> & a,
const std::pair<cgal::Cartesian::Segment_3, UInt> & b) {
- return CGAL::compare_lexicographically(a.first.min(), b.first.min()) ||
- CGAL::compare_lexicographically(a.first.max(), b.first.max());
+ return static_cast<bool>(
+ CGAL::compare_lexicographically(a.first.min(), b.first.min())) or
+ static_cast<bool>(
+ CGAL::compare_lexicographically(a.first.max(), b.first.max()));
}
};
/* -------------------------------------------------------------------------- */
/* Predicates */
/* -------------------------------------------------------------------------- */
/// Predicate used to determine if two segments are equal
class IsSameSegment {
public:
IsSameSegment(const cgal::Cartesian::Segment_3 & segment)
: segment(segment) {}
bool
operator()(const std::pair<cgal::Cartesian::Segment_3, UInt> & test_pair) {
return compareSegments(segment, test_pair.first);
}
protected:
const cgal::Cartesian::Segment_3 segment;
};
} // namespace akantu
-#endif // _AKANTU_GEOM_HELPER_FUNCTIONS_HH__
+#endif // AKANTU_GEOM_HELPER_FUNCTIONS_HH_
diff --git a/src/geometry/mesh_abstract_intersector.hh b/src/geometry/mesh_abstract_intersector.hh
index c121f9952..ddde893b9 100644
--- a/src/geometry/mesh_abstract_intersector.hh
+++ b/src/geometry/mesh_abstract_intersector.hh
@@ -1,120 +1,120 @@
/**
* @file mesh_abstract_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Mon Jun 19 2017
*
* @brief Abstract class for intersection computations
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_ABSTRACT_INTERSECTOR_HH__
-#define __AKANTU_MESH_ABSTRACT_INTERSECTOR_HH__
+#ifndef AKANTU_MESH_ABSTRACT_INTERSECTOR_HH_
+#define AKANTU_MESH_ABSTRACT_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_geom_abstract.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Class used to perform intersections on a mesh and construct output
* data
*/
template <class Query> class MeshAbstractIntersector : public MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshAbstractIntersector(Mesh & mesh);
/// Destructor
- virtual ~MeshAbstractIntersector();
+ ~MeshAbstractIntersector() override = default;
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the new_node_per_elem array
AKANTU_GET_MACRO(NewNodePerElem, *new_node_per_elem, const Array<UInt> &);
/// get the intersection_points array
AKANTU_GET_MACRO(IntersectionPoints, intersection_points,
const Array<Real> *);
/// get the nb_seg_by_el UInt
AKANTU_GET_MACRO(NbSegByEl, nb_seg_by_el, UInt);
/**
* @brief Compute the intersection with a query object
*
* This function needs to be implemented for every subclass. It computes the
* intersections
* with the tree of primitives and creates the data for the user.
*
* @param query the CGAL primitive of the query object
*/
virtual void computeIntersectionQuery(const Query & query) = 0;
/// Compute intersection points between the mesh primitives (segments) and a
/// query (surface in 3D or a curve in 2D), double intersection points for the
/// same primitives are not considered. A maximum intersection node per
/// element is set : 2 in 2D and 4 in 3D
virtual void computeMeshQueryIntersectionPoint(const Query & query,
UInt nb_old_nodes) = 0;
/// Compute intersection between the mesh and a list of queries
virtual void
computeIntersectionQueryList(const std::list<Query> & query_list);
/// Compute intersection points between the mesh and a list of queries
virtual void
computeMeshQueryListIntersectionPoint(const std::list<Query> & query_list,
UInt nb_old_nodes);
/// Compute whatever result is needed from the user (should be move to the
/// appropriate specific classe for genericity)
virtual void
buildResultFromQueryList(const std::list<Query> & query_list) = 0;
protected:
/// new node per element (column 0: number of new nodes, then odd is the
/// intersection node number and even the ID of the intersected segment)
- Array<UInt> * new_node_per_elem;
+ Array<UInt> * new_node_per_elem{nullptr};
/// intersection output: new intersection points
/// (computeMeshQueryListIntersectionPoint)
- Array<Real> * intersection_points;
+ Array<Real> * intersection_points{nullptr};
/// number of segment in a considered element of the templated type of element
/// specialized intersector
- const UInt nb_seg_by_el;
+ const UInt nb_seg_by_el{0};
};
} // namespace akantu
#include "mesh_abstract_intersector_tmpl.hh"
-#endif // __AKANTU_MESH_ABSTRACT_INTERSECTOR_HH__
+#endif // AKANTU_MESH_ABSTRACT_INTERSECTOR_HH_
diff --git a/src/geometry/mesh_abstract_intersector_tmpl.hh b/src/geometry/mesh_abstract_intersector_tmpl.hh
index 6f9288893..2ff419809 100644
--- a/src/geometry/mesh_abstract_intersector_tmpl.hh
+++ b/src/geometry/mesh_abstract_intersector_tmpl.hh
@@ -1,82 +1,78 @@
/**
* @file mesh_abstract_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Mon Jun 19 2017
*
* @brief General class for intersection computations
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH__
-#define __AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH__
+#ifndef AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH_
+#define AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH_
#include "aka_common.hh"
#include "mesh_abstract_intersector.hh"
namespace akantu {
template <class Query>
MeshAbstractIntersector<Query>::MeshAbstractIntersector(Mesh & mesh)
- : MeshGeomAbstract(mesh), new_node_per_elem(NULL),
- intersection_points(NULL), nb_seg_by_el(0) {}
-
-template <class Query>
-MeshAbstractIntersector<Query>::~MeshAbstractIntersector() {}
+ : MeshGeomAbstract(mesh) {}
template <class Query>
void MeshAbstractIntersector<Query>::computeIntersectionQueryList(
const std::list<Query> & query_list) {
AKANTU_DEBUG_IN();
- typename std::list<Query>::const_iterator query_it = query_list.begin(),
- query_end = query_list.end();
+ auto query_it = query_list.begin();
+ auto query_end = query_list.end();
for (; query_it != query_end; ++query_it) {
computeIntersectionQuery(*query_it);
}
AKANTU_DEBUG_OUT();
}
template <class Query>
void MeshAbstractIntersector<Query>::computeMeshQueryListIntersectionPoint(
const std::list<Query> & query_list, UInt nb_old_nodes) {
AKANTU_DEBUG_IN();
- typename std::list<Query>::const_iterator query_it = query_list.begin(),
- query_end = query_list.end();
+ auto query_it = query_list.begin();
+ auto query_end = query_list.end();
for (; query_it != query_end; ++query_it) {
computeMeshQueryIntersectionPoint(*query_it, nb_old_nodes);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif // __AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH__
+#endif // AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH_
diff --git a/src/geometry/mesh_geom_abstract.hh b/src/geometry/mesh_geom_abstract.hh
index f8a7ba833..53eb49232 100644
--- a/src/geometry/mesh_geom_abstract.hh
+++ b/src/geometry/mesh_geom_abstract.hh
@@ -1,64 +1,62 @@
/**
* @file mesh_geom_abstract.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Mon Jun 19 2017
*
* @brief Class for constructing the CGAL primitives of a mesh
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_GEOM_ABSTRACT_HH__
-#define __AKANTU_MESH_GEOM_ABSTRACT_HH__
+#ifndef AKANTU_MESH_GEOM_ABSTRACT_HH_
+#define AKANTU_MESH_GEOM_ABSTRACT_HH_
#include "aka_common.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/// Abstract class for mesh geometry operations
class MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshGeomAbstract(Mesh & mesh) : mesh(mesh){};
- /// Destructor
- virtual ~MeshGeomAbstract(){};
-
+ virtual ~MeshGeomAbstract() = default;
public:
/// Construct geometric data for computational geometry algorithms
virtual void constructData(GhostType ghost_type = _not_ghost) = 0;
protected:
/// Mesh used to construct the primitives
Mesh & mesh;
};
} // namespace akantu
-#endif // __AKANTU_MESH_GEOM_ABSTRACT_HH__
+#endif // AKANTU_MESH_GEOM_ABSTRACT_HH_
diff --git a/src/geometry/mesh_geom_common.hh b/src/geometry/mesh_geom_common.hh
index 078080b55..9fb22f1fc 100644
--- a/src/geometry/mesh_geom_common.hh
+++ b/src/geometry/mesh_geom_common.hh
@@ -1,56 +1,56 @@
/**
* @file mesh_geom_common.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Wed Jan 31 2018
*
* @brief Common file for MeshGeom module
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_MESH_GEOM_COMMON_HH__
-#define __AKANTU_MESH_GEOM_COMMON_HH__
+#ifndef AKANTU_MESH_GEOM_COMMON_HH_
+#define AKANTU_MESH_GEOM_COMMON_HH_
#include "aka_common.hh"
#include <CGAL/MP_Float.h>
#include <CGAL/Quotient.h>
#include <CGAL/Algebraic_kernel_for_spheres_2_3.h>
#include <CGAL/Cartesian.h>
#include <CGAL/Simple_cartesian.h>
#include <CGAL/Spherical_kernel_3.h>
namespace akantu {
namespace cgal {
using Cartesian = CGAL::Simple_cartesian<Real>;
using Spherical = CGAL::Spherical_kernel_3<
CGAL::Simple_cartesian<CGAL::Quotient<CGAL::MP_Float>>,
CGAL::Algebraic_kernel_for_spheres_2_3<CGAL::Quotient<CGAL::MP_Float>>>;
} // namespace cgal
} // namespace akantu
-#endif // __AKANTU_MESH_GEOM_COMMON_HH__
+#endif // AKANTU_MESH_GEOM_COMMON_HH_
diff --git a/src/geometry/mesh_geom_factory.hh b/src/geometry/mesh_geom_factory.hh
index 8d1180b62..a8d917f0b 100644
--- a/src/geometry/mesh_geom_factory.hh
+++ b/src/geometry/mesh_geom_factory.hh
@@ -1,106 +1,107 @@
/**
* @file mesh_geom_factory.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 27 2015
* @date last modification: Mon Jun 19 2017
*
* @brief Class for constructing the CGAL primitives of a mesh
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_GEOM_FACTORY_HH__
-#define __AKANTU_MESH_GEOM_FACTORY_HH__
+#ifndef AKANTU_MESH_GEOM_FACTORY_HH_
+#define AKANTU_MESH_GEOM_FACTORY_HH_
-#include "aka_common.hh"
+/* -------------------------------------------------------------------------- */
+#include <algorithm>
+/* -------------------------------------------------------------------------- */
#include "geom_helper_functions.hh"
#include "mesh.hh"
#include "mesh_geom_abstract.hh"
#include "tree_type_helper.hh"
-
-#include <algorithm>
+/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Class used to construct AABB tree for intersection computations
*
* This class constructs a CGAL AABB tree of one type of element in a mesh
* for fast intersection computations.
*/
template <UInt dim, ElementType el_type, class Primitive, class Kernel>
class MeshGeomFactory : public MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshGeomFactory(Mesh & mesh);
/// Desctructor
- virtual ~MeshGeomFactory();
+ ~MeshGeomFactory() override;
+
+ using TreeTypeHelper = TreeTypeHelper<Primitive, Kernel>;
+ using TreeType = typename TreeTypeHelper::tree;
+ using ContainerType = typename TreeTypeHelper::container_type;
public:
/// Construct AABB tree for fast intersection computing
- virtual void constructData(GhostType ghost_type = _not_ghost);
+ void constructData(GhostType ghost_type = _not_ghost) override;
/**
* @brief Construct a primitive and add it to a list of primitives
*
* This function needs to be specialized for every type that is wished to be
* supported.
* @param node_coordinates coordinates of the nodes making up the element
* @param id element number
* @param list the primitive list (not used inside MeshGeomFactory)
*/
- inline void addPrimitive(
- const Matrix<Real> & node_coordinates, UInt id,
- typename TreeTypeHelper<Primitive, Kernel>::container_type & list);
+ inline void addPrimitive(const Matrix<Real> & /*node_coordinates*/,
+ UInt /*id*/, ContainerType & /*list*/);
inline void addPrimitive(const Matrix<Real> & node_coordinates, UInt id);
/// Getter for the AABB tree
- const typename TreeTypeHelper<Primitive, Kernel>::tree & getTree() const {
- return *data_tree;
- }
+ auto getTree() const -> const TreeType & { return *data_tree; }
/// Getter for primitive list
- const typename TreeTypeHelper<Primitive, Kernel>::container_type &
- getPrimitiveList() const {
+ auto getPrimitiveList() const -> const ContainerType & {
return primitive_list;
}
protected:
/// AABB data tree
- typename TreeTypeHelper<Primitive, Kernel>::tree * data_tree;
+ TreeType * data_tree{nullptr};
/// Primitive list
- typename TreeTypeHelper<Primitive, Kernel>::container_type primitive_list;
+ ContainerType primitive_list;
};
} // namespace akantu
#include "mesh_geom_factory_tmpl.hh"
-#endif // __AKANTU_MESH_GEOM_FACTORY_HH__
+#endif // AKANTU_MESH_GEOM_FACTORY_HH_
diff --git a/src/geometry/mesh_geom_factory_tmpl.hh b/src/geometry/mesh_geom_factory_tmpl.hh
index b1f1f1c78..1db91632a 100644
--- a/src/geometry/mesh_geom_factory_tmpl.hh
+++ b/src/geometry/mesh_geom_factory_tmpl.hh
@@ -1,270 +1,242 @@
/**
* @file mesh_geom_factory_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 27 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Class for constructing the CGAL primitives of a mesh
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-
-#ifndef __AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
-#define __AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
-
/* -------------------------------------------------------------------------- */
-
-#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "mesh_geom_factory.hh"
-
/* -------------------------------------------------------------------------- */
+#ifndef AKANTU_MESH_GEOM_FACTORY_TMPL_HH_
+#define AKANTU_MESH_GEOM_FACTORY_TMPL_HH_
+
namespace akantu {
+/* -------------------------------------------------------------------------- */
template <UInt dim, ElementType type, class Primitive, class Kernel>
MeshGeomFactory<dim, type, Primitive, Kernel>::MeshGeomFactory(Mesh & mesh)
- : MeshGeomAbstract(mesh), data_tree(NULL), primitive_list() {}
+ : MeshGeomAbstract(mesh) {}
+/* -------------------------------------------------------------------------- */
template <UInt dim, ElementType type, class Primitive, class Kernel>
MeshGeomFactory<dim, type, Primitive, Kernel>::~MeshGeomFactory() {
delete data_tree;
}
+/* -------------------------------------------------------------------------- */
/**
* This function loops over the elements of `type` in the mesh and creates the
* AABB tree of geometrical primitves (`data_tree`).
*/
template <UInt dim, ElementType type, class Primitive, class Kernel>
void MeshGeomFactory<dim, type, Primitive, Kernel>::constructData(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
primitive_list.clear();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
const Array<Real> & nodes = mesh.getNodes();
UInt el_index = 0;
- Array<UInt>::const_vector_iterator it =
- connectivity.begin(nb_nodes_per_element);
- Array<UInt>::const_vector_iterator end =
- connectivity.end(nb_nodes_per_element);
+ auto it = connectivity.begin(nb_nodes_per_element);
+ auto end = connectivity.end(nb_nodes_per_element);
Matrix<Real> node_coordinates(dim, nb_nodes_per_element);
// This loop builds the list of primitives
for (; it != end; ++it, ++el_index) {
const Vector<UInt> & el_connectivity = *it;
- for (UInt i = 0; i < nb_nodes_per_element; i++)
- for (UInt j = 0; j < dim; j++)
+ for (UInt i = 0; i < nb_nodes_per_element; i++) {
+ for (UInt j = 0; j < dim; j++) {
node_coordinates(j, i) = nodes(el_connectivity(i), j);
+ }
+ }
// the unique elemental id assigned to the primitive is the
// linearized element index over ghost type
addPrimitive(node_coordinates, el_index);
}
delete data_tree;
// This condition allows the use of the mesh geom module
// even if types are not compatible with AABB tree algorithm
- if (TreeTypeHelper<Primitive, Kernel>::is_valid)
- data_tree = new typename TreeTypeHelper<Primitive, Kernel>::tree(
- primitive_list.begin(), primitive_list.end());
+ if (TreeTypeHelper::is_valid) {
+ data_tree = new TreeType(primitive_list.begin(), primitive_list.end());
+ }
AKANTU_DEBUG_OUT();
}
-template <UInt dim, ElementType type, class Primitive, class Kernel>
-void MeshGeomFactory<dim, type, Primitive, Kernel>::addPrimitive(
- const Matrix<Real> & node_coordinates, UInt id) {
- this->addPrimitive(node_coordinates, id, this->primitive_list);
-}
-
-// (2D, _triangle_3) decomposed into Triangle<cgal::Cartesian>
-template <>
-inline void
-MeshGeomFactory<2, _triangle_3, Triangle<cgal::Cartesian>, cgal::Cartesian>::
- addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
- TreeTypeHelper<Triangle<cgal::Cartesian>,
- cgal::Cartesian>::container_type & list) {
-
- TreeTypeHelper<Triangle<cgal::Cartesian>, cgal::Cartesian>::point_type a(
- node_coordinates(0, 0), node_coordinates(1, 0), 0.),
- b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
- c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
-
- Triangle<cgal::Cartesian> t(a, b, c);
- t.setId(id);
- list.push_back(t);
-}
-
-// (2D, _triangle_6) decomposed into Triangle<cgal::Cartesian>
-template <>
-inline void
-MeshGeomFactory<2, _triangle_6, Triangle<cgal::Cartesian>, cgal::Cartesian>::
- addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
- TreeTypeHelper<Triangle<cgal::Cartesian>,
- cgal::Cartesian>::container_type & list) {
-
- TreeTypeHelper<Triangle<cgal::Cartesian>, cgal::Cartesian>::point_type a(
- node_coordinates(0, 0), node_coordinates(1, 0), 0.),
- b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
- c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
-
- Triangle<cgal::Cartesian> t(a, b, c);
- t.setId(id);
- list.push_back(t);
-}
+/* -------------------------------------------------------------------------- */
-// (2D, _triangle_3) decomposed into Line_arc<cgal::Spherical>
-template <>
-inline void
-MeshGeomFactory<2, _triangle_3, Line_arc<cgal::Spherical>, cgal::Spherical>::
- addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
- TreeTypeHelper<Line_arc<cgal::Spherical>,
- cgal::Spherical>::container_type & list) {
-
- TreeTypeHelper<Line_arc<cgal::Spherical>, cgal::Spherical>::point_type a(
- node_coordinates(0, 0), node_coordinates(1, 0), 0.),
- b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
- c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
-
- /*std::cout << "elem " << id << " node 1 : x_node=" << node_coordinates(0, 0)
- << ", x_arc_node=" << a.x() << ", y_node=" << node_coordinates(1, 0)
- << ", y_arc_node=" << a.y() << std::endl ;
- std::cout << "elem " << id << " node 2 : x_node=" << node_coordinates(0, 1)
- << ", x_arc_node=" << b.x() << ", y_node=" << node_coordinates(1, 1)
- << ", y_arc_node=" << b.y() << std::endl ;
- std::cout << "elem " << id << " node 2 : x_node=" << node_coordinates(0, 2)
- << ", x_arc_node=" << c.x() << ", y_node=" << node_coordinates(1, 2)
- << ", y_arc_node=" << c.y() << std::endl ;*/
-
- CGAL::Line_3<cgal::Spherical> l1(a, b), l2(b, c), l3(c, a);
- Line_arc<cgal::Spherical> s1(l1, a, b), s2(l2, b, c), s3(l3, c, a);
-
- s1.setId(id);
- s1.setSegId(0);
- s2.setId(id);
- s2.setSegId(1);
- s3.setId(id);
- s3.setSegId(2);
-
- list.push_back(s1);
- list.push_back(s2);
- list.push_back(s3);
-}
+/* -------------------------------------------------------------------------- */
+namespace {
+ namespace details {
+ enum class GeometricalType {
+ _triangle,
+ _tetrahedron,
+ };
+ template <ElementType element_type> struct GeometricalTypeHelper {};
+
+ template <> struct GeometricalTypeHelper<_triangle_3> {
+ static const GeometricalType type{GeometricalType::_triangle};
+ };
+
+ template <> struct GeometricalTypeHelper<_triangle_6> {
+ static const GeometricalType type{GeometricalType::_triangle};
+ };
+
+ template <> struct GeometricalTypeHelper<_tetrahedron_4> {
+ static const GeometricalType type{GeometricalType::_triangle};
+ };
#if defined(AKANTU_IGFEM)
+ template <> struct GeometricalTypeHelper<_igfem_triangle_4> {
+ static const GeometricalType type{GeometricalType::_triangle};
+ };
+ template <> struct GeometricalTypeHelper<_igfem_triangle_5> {
+ static const GeometricalType type{GeometricalType::_triangle};
+ };
+#endif
-// (2D, _igfem_triangle_4) decomposed into Line_arc<cgal::Spherical>
-template <>
-inline void MeshGeomFactory<2, _igfem_triangle_4, Line_arc<cgal::Spherical>,
- cgal::Spherical>::
- addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
- TreeTypeHelper<Line_arc<cgal::Spherical>,
- cgal::Spherical>::container_type & list) {
-
- TreeTypeHelper<Line_arc<cgal::Spherical>, cgal::Spherical>::point_type a(
- node_coordinates(0, 0), node_coordinates(1, 0), 0.),
- b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
- c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
-
- CGAL::Line_3<cgal::Spherical> l1(a, b), l2(b, c), l3(c, a);
- Line_arc<cgal::Spherical> s1(l1, a, b), s2(l2, b, c), s3(l3, c, a);
-
- s1.setId(id);
- s1.setSegId(0);
- s2.setId(id);
- s2.setSegId(1);
- s3.setId(id);
- s3.setSegId(2);
-
- list.push_back(s1);
- list.push_back(s2);
- list.push_back(s3);
-}
+ template <details::GeometricalType geom_type, class Primitive, class Kernel>
+ struct AddPrimitiveHelper {};
+
+ template <class Primitive>
+ struct AddPrimitiveHelper<GeometricalType::_triangle, Primitive,
+ cgal::Cartesian> {
+ using TreeTypeHelper = TreeTypeHelper<Primitive, cgal::Cartesian>;
+ using ContainerType = typename TreeTypeHelper::container_type;
+ static void addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
+ ContainerType & list) {
+ using Point = typename TreeTypeHelper::point_type;
+ Point a(node_coordinates(0, 0), node_coordinates(1, 0), 0.);
+ Point b(node_coordinates(0, 1), node_coordinates(1, 1), 0.);
+ Point c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
+
+ Triangle<cgal::Cartesian> t(a, b, c);
+ t.setId(id);
+ list.push_back(t);
+ }
+ };
+
+ template <class Primitive>
+ struct AddPrimitiveHelper<GeometricalType::_triangle, Primitive,
+ cgal::Spherical> {
+ using TreeTypeHelper = TreeTypeHelper<Primitive, cgal::Spherical>;
+ using ContainerType = typename TreeTypeHelper::container_type;
+ static void addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
+ ContainerType & list) {
+ using Point = typename TreeTypeHelper::point_type;
+ Point a(node_coordinates(0, 0), node_coordinates(1, 0), 0.);
+ Point b(node_coordinates(0, 1), node_coordinates(1, 1), 0.);
+ Point c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
+
+ using Line = CGAL::Line_3<cgal::Spherical>;
+ Line l1(a, b);
+ Line l2(b, c);
+ Line l3(c, a);
+
+ using Arc = Line_arc<cgal::Spherical>;
+ Arc s1(l1, a, b);
+ Arc s2(l2, b, c);
+ Arc s3(l3, c, a);
+
+ s1.setId(id);
+ s1.setSegId(0);
+ s2.setId(id);
+ s2.setSegId(1);
+ s3.setId(id);
+ s3.setSegId(2);
+
+ list.push_back(s1);
+ list.push_back(s2);
+ list.push_back(s3);
+ }
+ };
+
+ template <class Primitive>
+ struct AddPrimitiveHelper<GeometricalType::_tetrahedron, Primitive,
+ cgal::Cartesian> {
+ using TreeTypeHelper = TreeTypeHelper<Primitive, cgal::Cartesian>;
+ using ContainerType = typename TreeTypeHelper::container_type;
+ static void addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
+ ContainerType & list) {
+ using Point = typename TreeTypeHelper::point_type;
+ Point a(node_coordinates(0, 0), node_coordinates(1, 0),
+ node_coordinates(2, 0));
+ Point b(node_coordinates(0, 1), node_coordinates(1, 1),
+ node_coordinates(2, 1));
+ Point c(node_coordinates(0, 2), node_coordinates(1, 2),
+ node_coordinates(2, 2));
+ Point d(node_coordinates(0, 3), node_coordinates(1, 3),
+ node_coordinates(2, 3));
+
+ Triangle<cgal::Cartesian> t1(a, b, c);
+ Triangle<cgal::Cartesian> t2(b, c, d);
+ Triangle<cgal::Cartesian> t3(c, d, a);
+ Triangle<cgal::Cartesian> t4(d, a, b);
+
+ t1.setId(id);
+ t2.setId(id);
+ t3.setId(id);
+ t4.setId(id);
+
+ list.push_back(t1);
+ list.push_back(t2);
+ list.push_back(t3);
+ list.push_back(t4);
+ }
+ };
+ } // namespace details
+} // namespace
-// (2D, _igfem_triangle_4) decomposed into Line_arc<cgal::Spherical>
-template <>
-inline void MeshGeomFactory<2, _igfem_triangle_5, Line_arc<cgal::Spherical>,
- cgal::Spherical>::
- addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
- TreeTypeHelper<Line_arc<cgal::Spherical>,
- cgal::Spherical>::container_type & list) {
-
- TreeTypeHelper<Line_arc<cgal::Spherical>, cgal::Spherical>::point_type a(
- node_coordinates(0, 0), node_coordinates(1, 0), 0.),
- b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
- c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
-
- CGAL::Line_3<cgal::Spherical> l1(a, b), l2(b, c), l3(c, a);
- Line_arc<cgal::Spherical> s1(l1, a, b), s2(l2, b, c), s3(l3, c, a);
-
- s1.setId(id);
- s1.setSegId(0);
- s2.setId(id);
- s2.setSegId(1);
- s3.setId(id);
- s3.setSegId(2);
-
- list.push_back(s1);
- list.push_back(s2);
- list.push_back(s3);
+/* -------------------------------------------------------------------------- */
+template <UInt dim, ElementType type, class Primitive, class Kernel>
+void MeshGeomFactory<dim, type, Primitive, Kernel>::addPrimitive(
+ const Matrix<Real> & node_coordinates, UInt id, ContainerType & list) {
+ details::AddPrimitiveHelper<details::GeometricalTypeHelper<type>::type,
+ Primitive, Kernel>::addPrimitive(node_coordinates,
+ id, list);
}
-#endif
-
-// (3D, _tetrahedron_4) decomposed into Triangle<cgal::Cartesian>
-template <>
-inline void
-MeshGeomFactory<3, _tetrahedron_4, Triangle<cgal::Cartesian>, cgal::Cartesian>::
- addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
- TreeTypeHelper<Triangle<cgal::Cartesian>,
- cgal::Cartesian>::container_type & list) {
-
- TreeTypeHelper<Triangle<cgal::Cartesian>, cgal::Cartesian>::point_type a(
- node_coordinates(0, 0), node_coordinates(1, 0), node_coordinates(2, 0)),
- b(node_coordinates(0, 1), node_coordinates(1, 1), node_coordinates(2, 1)),
- c(node_coordinates(0, 2), node_coordinates(1, 2), node_coordinates(2, 2)),
- d(node_coordinates(0, 3), node_coordinates(1, 3), node_coordinates(2, 3));
-
- Triangle<cgal::Cartesian> t1(a, b, c), t2(b, c, d), t3(c, d, a), t4(d, a, b);
-
- t1.setId(id);
- t2.setId(id);
- t3.setId(id);
- t4.setId(id);
-
- list.push_back(t1);
- list.push_back(t2);
- list.push_back(t3);
- list.push_back(t4);
+/* -------------------------------------------------------------------------- */
+template <UInt dim, ElementType type, class Primitive, class Kernel>
+void MeshGeomFactory<dim, type, Primitive, Kernel>::addPrimitive(
+ const Matrix<Real> & node_coordinates, UInt id) {
+ this->addPrimitive(node_coordinates, id, this->primitive_list);
}
} // namespace akantu
-#endif // __AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
+#endif // AKANTU_MESH_GEOM_FACTORY_TMPL_HH_
diff --git a/src/geometry/mesh_geom_intersector.hh b/src/geometry/mesh_geom_intersector.hh
index 25591f912..a39f65b87 100644
--- a/src/geometry/mesh_geom_intersector.hh
+++ b/src/geometry/mesh_geom_intersector.hh
@@ -1,73 +1,73 @@
/**
* @file mesh_geom_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Mon Jun 19 2017
*
* @brief General class for intersection computations
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_GEOM_INTERSECTOR_HH__
-#define __AKANTU_MESH_GEOM_INTERSECTOR_HH__
+#ifndef AKANTU_MESH_GEOM_INTERSECTOR_HH_
+#define AKANTU_MESH_GEOM_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_abstract_intersector.hh"
#include "mesh_geom_factory.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Class used to perform intersections on a mesh and construct output
* data
*/
template <UInt dim, ElementType type, class Primitive, class Query,
class Kernel>
class MeshGeomIntersector : public MeshAbstractIntersector<Query> {
public:
/// Construct from mesh
explicit MeshGeomIntersector(Mesh & mesh);
/// Destructor
- virtual ~MeshGeomIntersector();
+ ~MeshGeomIntersector() override = default;
public:
/// Construct the primitive tree object
- virtual void constructData(GhostType ghost_type = _not_ghost);
+ void constructData(GhostType ghost_type = _not_ghost) override;
protected:
/// Factory object containing the primitive tree
MeshGeomFactory<dim, type, Primitive, Kernel> factory;
};
} // namespace akantu
#include "mesh_geom_intersector_tmpl.hh"
-#endif // __AKANTU_MESH_GEOM_INTERSECTOR_HH__
+#endif // AKANTU_MESH_GEOM_INTERSECTOR_HH_
diff --git a/src/geometry/mesh_geom_intersector_tmpl.hh b/src/geometry/mesh_geom_intersector_tmpl.hh
index 132852326..88b0ed78b 100644
--- a/src/geometry/mesh_geom_intersector_tmpl.hh
+++ b/src/geometry/mesh_geom_intersector_tmpl.hh
@@ -1,63 +1,58 @@
/**
* @file mesh_geom_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Mon Jun 19 2017
*
* @brief General class for intersection computations
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
-#define __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
+#ifndef AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH_
+#define AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH_
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type, class Primitive, class Query,
class Kernel>
MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::MeshGeomIntersector(
Mesh & mesh)
: MeshAbstractIntersector<Query>(mesh), factory(mesh) {}
-template <UInt dim, ElementType type, class Primitive, class Query,
- class Kernel>
-MeshGeomIntersector<dim, type, Primitive, Query,
- Kernel>::~MeshGeomIntersector() {}
-
template <UInt dim, ElementType type, class Primitive, class Query,
class Kernel>
void MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::constructData(
GhostType ghost_type) {
this->intersection_points->resize(0);
factory.constructData(ghost_type);
}
} // namespace akantu
-#endif // __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
+#endif // AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH_
diff --git a/src/geometry/mesh_segment_intersector.hh b/src/geometry/mesh_segment_intersector.hh
index 67a5473e0..4d3cc5110 100644
--- a/src/geometry/mesh_segment_intersector.hh
+++ b/src/geometry/mesh_segment_intersector.hh
@@ -1,108 +1,108 @@
/**
* @file mesh_segment_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Computation of mesh intersection with segments
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
-#define __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
+#ifndef AKANTU_MESH_SEGMENT_INTERSECTOR_HH_
+#define AKANTU_MESH_SEGMENT_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type>
class MeshSegmentIntersector
: public MeshGeomIntersector<dim, type, Triangle<cgal::Cartesian>,
cgal::Cartesian::Segment_3, cgal::Cartesian> {
using K = cgal::Cartesian;
/// Parent class type
- typedef MeshGeomIntersector<dim, type, Triangle<K>, K::Segment_3, K>
- parent_type;
+ using parent_type =
+ MeshGeomIntersector<dim, type, Triangle<K>, K::Segment_3, K>;
/// Result of intersection function type
- typedef typename IntersectionTypeHelper<TreeTypeHelper<Triangle<K>, K>,
- K::Segment_3>::intersection_type
- result_type;
+ using result_type =
+ typename IntersectionTypeHelper<TreeTypeHelper<Triangle<K>, K>,
+ K::Segment_3>::intersection_type;
/// Pair of segments and element id
- typedef std::pair<K::Segment_3, UInt> pair_type;
+ using pair_type = std::pair<K::Segment_3, UInt>;
public:
/// Construct from mesh
explicit MeshSegmentIntersector(Mesh & mesh, Mesh & result_mesh);
/// Destructor
- virtual ~MeshSegmentIntersector();
+ ~MeshSegmentIntersector() override = default;
public:
/**
* @brief Computes the intersection of the mesh with a segment
*
* @param query the segment to compute the intersections with the mesh
*/
- virtual void computeIntersectionQuery(const K::Segment_3 & query);
+ void computeIntersectionQuery(const K::Segment_3 & query) override;
/// Compute intersection points between the mesh and a query
- virtual void computeMeshQueryIntersectionPoint(const K::Segment_3 & query,
- UInt nb_old_nodes);
+ void computeMeshQueryIntersectionPoint(const K::Segment_3 & query,
+ UInt nb_old_nodes) override;
/// Compute the embedded mesh
- virtual void
- buildResultFromQueryList(const std::list<K::Segment_3> & query_list);
+ void
+ buildResultFromQueryList(const std::list<K::Segment_3> & query_list) override;
void setPhysicalName(const std::string & other) {
current_physical_name = other;
}
protected:
/// Compute segments from intersection list
void computeSegments(const std::list<result_type> & intersections,
std::set<pair_type, segmentPairsLess> & segments,
const K::Segment_3 & query);
protected:
/// Result mesh
Mesh & result_mesh;
/// Physical name of the current batch of queries
std::string current_physical_name;
};
} // namespace akantu
#include "mesh_segment_intersector_tmpl.hh"
-#endif // __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
+#endif // AKANTU_MESH_SEGMENT_INTERSECTOR_HH_
diff --git a/src/geometry/mesh_segment_intersector_tmpl.hh b/src/geometry/mesh_segment_intersector_tmpl.hh
index 0c730c164..31e1de1b8 100644
--- a/src/geometry/mesh_segment_intersector_tmpl.hh
+++ b/src/geometry/mesh_segment_intersector_tmpl.hh
@@ -1,282 +1,283 @@
/**
* @file mesh_segment_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Computation of mesh intersection with segments
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
-#define __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
+#ifndef AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH_
+#define AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH_
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "tree_type_helper.hh"
namespace akantu {
template <UInt dim, ElementType type>
MeshSegmentIntersector<dim, type>::MeshSegmentIntersector(Mesh & mesh,
Mesh & result_mesh)
- : parent_type(mesh), result_mesh(result_mesh), current_physical_name() {
+ : parent_type(mesh), result_mesh(result_mesh) {
this->intersection_points = new Array<Real>(0, dim);
this->constructData();
}
-template <UInt dim, ElementType type>
-MeshSegmentIntersector<dim, type>::~MeshSegmentIntersector() {}
-
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeIntersectionQuery(
const K::Segment_3 & query) {
AKANTU_DEBUG_IN();
result_mesh.addConnectivityType(_segment_2, _not_ghost);
result_mesh.addConnectivityType(_segment_2, _ghost);
std::list<result_type> result_list;
std::set<std::pair<K::Segment_3, UInt>, segmentPairsLess> segment_set;
this->factory.getTree().all_intersections(query,
std::back_inserter(result_list));
this->computeSegments(result_list, segment_set, query);
// Arrays for storing nodes and connectivity
Array<Real> & nodes = result_mesh.getNodes();
Array<UInt> & connectivity = result_mesh.getConnectivity(_segment_2);
// Arrays for storing associated element and physical name
bool valid_elemental_data = true;
- Array<Element> * associated_element = NULL;
- Array<std::string> * associated_physical_name = NULL;
+ Array<Element> * associated_element = nullptr;
+ Array<std::string> * associated_physical_name = nullptr;
try {
associated_element =
&result_mesh.getData<Element>("associated_element", _segment_2);
associated_physical_name =
&result_mesh.getData<std::string>("physical_names", _segment_2);
} catch (debug::Exception & e) {
valid_elemental_data = false;
}
- std::set<pair_type, segmentPairsLess>::iterator it = segment_set.begin(),
- end = segment_set.end();
+ auto it = segment_set.begin();
+ auto end = segment_set.end();
// Loop over the segment pairs
for (; it != end; ++it) {
if (!it->first.is_degenerate()) {
Vector<UInt> segment_connectivity(2);
segment_connectivity(0) = result_mesh.getNbNodes();
segment_connectivity(1) = result_mesh.getNbNodes() + 1;
connectivity.push_back(segment_connectivity);
// Copy nodes
- Vector<Real> source(dim), target(dim);
+ Vector<Real> source(dim);
+ Vector<Real> target(dim);
for (UInt j = 0; j < dim; j++) {
source(j) = it->first.source()[j];
target(j) = it->first.target()[j];
}
nodes.push_back(source);
nodes.push_back(target);
// Copy associated element info
if (valid_elemental_data) {
associated_element->push_back(Element{type, it->second, _not_ghost});
associated_physical_name->push_back(current_physical_name);
}
}
}
AKANTU_DEBUG_OUT();
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeMeshQueryIntersectionPoint(
const K::Segment_3 & /*query*/, UInt /*nb_old_nodes*/) {
AKANTU_ERROR("The method: computeMeshQueryIntersectionPoint has not "
"been implemented in class MeshSegmentIntersector!");
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::buildResultFromQueryList(
const std::list<K::Segment_3> & query_list) {
AKANTU_DEBUG_IN();
this->computeIntersectionQueryList(query_list);
AKANTU_DEBUG_OUT();
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeSegments(
const std::list<result_type> & intersections,
std::set<pair_type, segmentPairsLess> & segments,
const K::Segment_3 & query) {
AKANTU_DEBUG_IN();
/*
* Number of intersections = 0 means
*
* - query is completely outside mesh
* - query is completely inside primitive
*
* We try to determine the case and still construct the segment list
*/
- if (intersections.size() == 0) {
+ if (intersections.empty()) {
// We look at all the primitives intersected by two rays
// If there is one primitive in common, then query is inside
// that primitive
K::Ray_3 ray1(query.source(), query.target());
K::Ray_3 ray2(query.target(), query.source());
- std::set<UInt> ray1_results, ray2_results;
+ std::set<UInt> ray1_results;
+ std::set<UInt> ray2_results;
this->factory.getTree().all_intersected_primitives(
ray1, std::inserter(ray1_results, ray1_results.begin()));
this->factory.getTree().all_intersected_primitives(
ray2, std::inserter(ray2_results, ray2_results.begin()));
bool inside_primitive = false;
UInt primitive_id = 0;
- std::set<UInt>::iterator ray2_it = ray2_results.begin(),
- ray2_end = ray2_results.end();
+ auto ray2_it = ray2_results.begin();
+ auto ray2_end = ray2_results.end();
// Test if first list contains an element of second list
for (; ray2_it != ray2_end && !inside_primitive; ++ray2_it) {
if (ray1_results.find(*ray2_it) != ray1_results.end()) {
inside_primitive = true;
primitive_id = *ray2_it;
}
}
if (inside_primitive) {
segments.insert(std::make_pair(query, primitive_id));
}
}
else {
- typename std::list<result_type>::const_iterator it = intersections.begin(),
- end = intersections.end();
+ auto it = intersections.begin();
+ auto end = intersections.end();
for (; it != end; ++it) {
UInt el = (*it)->second;
// Result of intersection is a segment
if (const K::Segment_3 * segment =
boost::get<K::Segment_3>(&((*it)->first))) {
// Check if the segment was alread created
segments.insert(std::make_pair(*segment, el));
}
// Result of intersection is a point
else if (const K::Point_3 * point =
boost::get<K::Point_3>(&((*it)->first))) {
// We only want to treat points differently if we're in 3D with Tetra4
// elements This should be optimized by compilator
if (dim == 3 && type == _tetrahedron_4) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
TreeTypeHelper<Triangle<K>, K>::container_type facets;
const Array<Real> & nodes = this->mesh.getNodes();
Array<UInt>::const_vector_iterator connectivity_vec =
this->mesh.getConnectivity(type).begin(nb_nodes_per_element);
const Vector<UInt> & el_connectivity = connectivity_vec[el];
Matrix<Real> node_coordinates(dim, nb_nodes_per_element);
- for (UInt i = 0; i < nb_nodes_per_element; i++)
- for (UInt j = 0; j < dim; j++)
+ for (UInt i = 0; i < nb_nodes_per_element; i++) {
+ for (UInt j = 0; j < dim; j++) {
node_coordinates(j, i) = nodes(el_connectivity(i), j);
+ }
+ }
this->factory.addPrimitive(node_coordinates, el, facets);
// Local tree
- TreeTypeHelper<Triangle<K>, K>::tree * local_tree =
+ auto * local_tree =
new TreeTypeHelper<Triangle<K>, K>::tree(facets.begin(),
facets.end());
// Compute local intersections (with current element)
std::list<result_type> local_intersections;
local_tree->all_intersections(
query, std::back_inserter(local_intersections));
bool out_point_found = false;
- typename std::list<result_type>::const_iterator
- local_it = local_intersections.begin(),
- local_end = local_intersections.end();
+ auto local_it = local_intersections.begin();
+ auto local_end = local_intersections.end();
for (; local_it != local_end; ++local_it) {
- if (const K::Point_3 * local_point =
+ if (const auto * local_point =
boost::get<K::Point_3>(&((*local_it)->first))) {
if (!comparePoints(*point, *local_point)) {
K::Segment_3 seg(*point, *local_point);
segments.insert(std::make_pair(seg, el));
out_point_found = true;
}
}
}
if (!out_point_found) {
- TreeTypeHelper<Triangle<K>, K>::point_type a(
- node_coordinates(0, 0), node_coordinates(1, 0),
- node_coordinates(2, 0)),
- b(node_coordinates(0, 1), node_coordinates(1, 1),
- node_coordinates(2, 1)),
- c(node_coordinates(0, 2), node_coordinates(1, 2),
- node_coordinates(2, 2)),
- d(node_coordinates(0, 3), node_coordinates(1, 3),
- node_coordinates(2, 3));
+ using Point = TreeTypeHelper<Triangle<K>, K>::point_type;
+ Point a(node_coordinates(0, 0), node_coordinates(1, 0),
+ node_coordinates(2, 0));
+ Point b(node_coordinates(0, 1), node_coordinates(1, 1),
+ node_coordinates(2, 1));
+ Point c(node_coordinates(0, 2), node_coordinates(1, 2),
+ node_coordinates(2, 2));
+ Point d(node_coordinates(0, 3), node_coordinates(1, 3),
+ node_coordinates(2, 3));
K::Tetrahedron_3 tetra(a, b, c, d);
- const K::Point_3 * inside_point = NULL;
+ const K::Point_3 * inside_point = nullptr;
if (tetra.has_on_bounded_side(query.source()) &&
- !tetra.has_on_boundary(query.source()))
+ !tetra.has_on_boundary(query.source())) {
inside_point = &query.source();
- else if (tetra.has_on_bounded_side(query.target()) &&
- !tetra.has_on_boundary(query.target()))
+ } else if (tetra.has_on_bounded_side(query.target()) &&
+ !tetra.has_on_boundary(query.target())) {
inside_point = &query.target();
+ }
- if (inside_point) {
+ if (inside_point != nullptr) {
K::Segment_3 seg(*inside_point, *point);
segments.insert(std::make_pair(seg, el));
}
}
delete local_tree;
}
}
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif // __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
+#endif // AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH_
diff --git a/src/geometry/mesh_sphere_intersector.hh b/src/geometry/mesh_sphere_intersector.hh
index 107d87f5a..dbd19cd46 100644
--- a/src/geometry/mesh_sphere_intersector.hh
+++ b/src/geometry/mesh_sphere_intersector.hh
@@ -1,118 +1,118 @@
/**
* @file mesh_sphere_intersector.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jun 23 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Computation of mesh intersection with sphere(s)
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_SPHERE_INTERSECTOR_HH__
-#define __AKANTU_MESH_SPHERE_INTERSECTOR_HH__
+#ifndef AKANTU_MESH_SPHERE_INTERSECTOR_HH_
+#define AKANTU_MESH_SPHERE_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type>
class MeshSphereIntersector
: public MeshGeomIntersector<dim, type, Line_arc<cgal::Spherical>,
cgal::Spherical::Sphere_3, cgal::Spherical> {
using SK = cgal::Spherical;
using K = cgal::Cartesian;
/// Parent class type
typedef MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK>
parent_type;
/// Result of intersection function type
typedef typename IntersectionTypeHelper<TreeTypeHelper<Triangle<K>, K>,
K::Segment_3>::intersection_type
result_type;
/// Pair of intersection points and element id
typedef std::pair<SK::Circular_arc_point_3, UInt> pair_type;
public:
/// Construct from mesh
explicit MeshSphereIntersector(Mesh & mesh);
/// Destructor
virtual ~MeshSphereIntersector();
public:
/// Construct the primitive tree object
virtual void constructData(GhostType ghost_type = _not_ghost);
/**
* @brief Computes the intersection of the mesh with a sphere
*/
virtual void computeIntersectionQuery(const SK::Sphere_3 & /* query */) {
AKANTU_ERROR("This function is not implemented for spheres (It was "
"to generic and has been replaced by "
"computeMeshQueryIntersectionPoint");
}
/**
* Compute intersection points between the mesh primitives (segments) and a
* query (surface in 3D or a curve in 2D), double intersection points for the
* same primitives are not considered. A maximum is set to the number of
* intersection nodes per element: 2 in 2D and 4 in 3D
*/
virtual void computeMeshQueryIntersectionPoint(const SK::Sphere_3 & query,
UInt nb_old_nodes);
/// Build the IGFEM mesh
virtual void
buildResultFromQueryList(const std::list<SK::Sphere_3> & /*query*/) {
AKANTU_ERROR("This function is no longer implemented to split "
"geometrical operations and dedicated result "
"construction");
}
/// Set the tolerance
void setToleranceIntersectionOnNode(UInt tol) {
this->tol_intersection_on_node = tol;
}
protected:
/// tolerance for which the intersection is considered on the mesh node
/// (relative to the segment lenght)
Real tol_intersection_on_node;
};
} // namespace akantu
#include "mesh_sphere_intersector_tmpl.hh"
-#endif // __AKANTU_MESH_SPHERE_INTERSECTOR_HH__
+#endif // AKANTU_MESH_SPHERE_INTERSECTOR_HH_
diff --git a/src/geometry/mesh_sphere_intersector_tmpl.hh b/src/geometry/mesh_sphere_intersector_tmpl.hh
index 00eb284d8..e11373440 100644
--- a/src/geometry/mesh_sphere_intersector_tmpl.hh
+++ b/src/geometry/mesh_sphere_intersector_tmpl.hh
@@ -1,214 +1,214 @@
/**
* @file mesh_sphere_intersector_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jun 23 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Computation of mesh intersection with spheres
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__
-#define __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__
+#ifndef AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH_
+#define AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH_
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "mesh_sphere_intersector.hh"
#include "tree_type_helper.hh"
namespace akantu {
template <UInt dim, ElementType type>
MeshSphereIntersector<dim, type>::MeshSphereIntersector(Mesh & mesh)
: parent_type(mesh), tol_intersection_on_node(1e-10) {
#if defined(AKANTU_IGFEM)
if ((type == _triangle_3) || (type == _igfem_triangle_4) ||
(type == _igfem_triangle_5)) {
const_cast<UInt &>(this->nb_seg_by_el) = 3;
} else {
AKANTU_ERROR("Not ready for mesh type " << type);
}
#else
if ((type != _triangle_3))
AKANTU_ERROR("Not ready for mesh type " << type);
#endif
// initialize the intersection pointsss array with the spatial dimension
this->intersection_points = new Array<Real>(0, dim);
// A maximum is set to the number of intersection nodes per element to limit
// the size of new_node_per_elem: 2 in 2D and 4 in 3D
this->new_node_per_elem = new Array<UInt>(0, 1 + 4 * (dim - 1));
}
template <UInt dim, ElementType type>
MeshSphereIntersector<dim, type>::~MeshSphereIntersector() {
delete this->new_node_per_elem;
delete this->intersection_points;
}
template <UInt dim, ElementType type>
void MeshSphereIntersector<dim, type>::constructData(GhostType ghost_type) {
this->new_node_per_elem->resize(this->mesh.getNbElement(type, ghost_type));
this->new_node_per_elem->clear();
MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK>::constructData(
ghost_type);
}
template <UInt dim, ElementType type>
void MeshSphereIntersector<dim, type>::computeMeshQueryIntersectionPoint(
const SK::Sphere_3 & query, UInt nb_old_nodes) {
/// function to replace computeIntersectionQuery in a more generic geometry
/// module version
// The newNodeEvent is not send from this method who only compute the
// intersection points
AKANTU_DEBUG_IN();
Array<Real> & nodes = this->mesh.getNodes();
UInt nb_node = nodes.size() + this->intersection_points->size();
// Tolerance for proximity checks should be defined by user
Real global_tolerance = Math::getTolerance();
Math::setTolerance(tol_intersection_on_node);
typedef boost::variant<pair_type> sk_inter_res;
TreeTypeHelper<Line_arc<cgal::Spherical>, cgal::Spherical>::const_iterator
it = this->factory.getPrimitiveList().begin(),
end = this->factory.getPrimitiveList().end();
for (; it != end; ++it) { // loop on the primitives (segments)
std::list<sk_inter_res> s_results;
CGAL::intersection(*it, query, std::back_inserter(s_results));
if (s_results.size() == 1) { // just one point
if (pair_type * pair = boost::get<pair_type>(&s_results.front())) {
if (pair->second == 1) { // not a point tangent to the sphere
// the intersection point written as a vector
Vector<Real> new_node(dim, 0.0);
cgal::Cartesian::Point_3 point(CGAL::to_double(pair->first.x()),
CGAL::to_double(pair->first.y()),
CGAL::to_double(pair->first.z()));
for (UInt i = 0; i < dim; i++) {
new_node(i) = point[i];
}
/// boolean to decide wheter intersection point is on a standard node
/// of the mesh or not
bool is_on_mesh = false;
/// boolean to decide if this intersection point has been already
/// computed for a neighbor element
bool is_new = true;
/// check if intersection point has already been computed
UInt n = nb_old_nodes;
// check if we already compute this intersection and add it as a node
// for a neighboor element of another type
auto existing_node = nodes.begin(dim);
for (; n < nodes.size(); ++n) { // loop on the nodes from nb_old_nodes
if (Math::are_vector_equal(dim, new_node.storage(),
existing_node[n].storage())) {
is_new = false;
break;
}
}
if (is_new) {
auto intersection_points_it = this->intersection_points->begin(dim);
auto intersection_points_end = this->intersection_points->end(dim);
for (; intersection_points_it != intersection_points_end;
++intersection_points_it, ++n) {
if (Math::are_vector_equal(dim, new_node.storage(),
intersection_points_it->storage())) {
is_new = false;
break;
}
}
}
// get the initial and final points of the primitive (segment) and
// write them as vectors
cgal::Cartesian::Point_3 source_cgal(
CGAL::to_double(it->source().x()),
CGAL::to_double(it->source().y()),
CGAL::to_double(it->source().z()));
cgal::Cartesian::Point_3 target_cgal(
CGAL::to_double(it->target().x()),
CGAL::to_double(it->target().y()),
CGAL::to_double(it->target().z()));
Vector<Real> source(dim), target(dim);
for (UInt i = 0; i < dim; i++) {
source(i) = source_cgal[i];
target(i) = target_cgal[i];
}
// Check if we are close from a node of the primitive (segment)
if (Math::are_vector_equal(dim, source.storage(),
new_node.storage()) ||
Math::are_vector_equal(dim, target.storage(),
new_node.storage())) {
is_on_mesh = true;
is_new = false;
}
if (is_new) { // if the intersection point is a new one add it to the
// list
this->intersection_points->push_back(new_node);
nb_node++;
}
// deduce the element id
UInt element_id = it->id();
// fill the new_node_per_elem array
if (!is_on_mesh) { // if the node is not on a mesh node
UInt & nb_new_nodes_per_el =
(*this->new_node_per_elem)(element_id, 0);
nb_new_nodes_per_el += 1;
AKANTU_DEBUG_ASSERT(
2 * nb_new_nodes_per_el <
this->new_node_per_elem->getNbComponent(),
"You might have to interface crossing the same material");
(*this->new_node_per_elem)(element_id,
(2 * nb_new_nodes_per_el) - 1) = n;
(*this->new_node_per_elem)(element_id, 2 * nb_new_nodes_per_el) =
it->segId();
}
}
}
}
}
Math::setTolerance(global_tolerance);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif // __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__
+#endif // AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH_
diff --git a/src/geometry/tree_type_helper.hh b/src/geometry/tree_type_helper.hh
index 2d50a41a5..c7d846983 100644
--- a/src/geometry/tree_type_helper.hh
+++ b/src/geometry/tree_type_helper.hh
@@ -1,108 +1,109 @@
/**
* @file tree_type_helper.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Thu Feb 01 2018
*
* @brief Converts element types of a mesh to CGAL primitive types
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TREE_TYPE_HELPER_HH__
-#define __AKANTU_TREE_TYPE_HELPER_HH__
+#ifndef AKANTU_TREE_TYPE_HELPER_HH_
+#define AKANTU_TREE_TYPE_HELPER_HH_
#include "aka_common.hh"
#include "line_arc.hh"
#include "tetrahedron.hh"
#include "triangle.hh"
#include "aabb_primitive.hh"
#include "mesh_geom_common.hh"
#include <CGAL/AABB_traits.h>
#include <CGAL/AABB_tree.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Replacement class for algorithm that can't use the AABB tree types
template <typename iterator> struct VoidTree {
VoidTree(const iterator & /*begin*/, const iterator & /*end*/) {}
};
/// Helper class used to ease the use of CGAL AABB tree algorithm
template <class Primitive, class Kernel> struct TreeTypeHelper {
static const bool is_valid = false;
- typedef Primitive primitive_type;
- typedef typename std::list<primitive_type> container_type;
- typedef typename container_type::iterator iterator;
- typedef typename container_type::const_iterator const_iterator;
- typedef typename CGAL::Point_3<Kernel> point_type;
- typedef VoidTree<iterator> tree;
+ using primitive_type = Primitive;
+ using container_type = typename std::list<primitive_type>;
+ using iterator = typename container_type::iterator;
+ using const_iterator = typename container_type::const_iterator;
+ using point_type = typename CGAL::Point_3<Kernel>;
+ using tree = VoidTree<iterator>;
};
/// Helper class used to ease the use of intersections
template <class TTHelper, class Query> struct IntersectionTypeHelper;
/**
* Macro used to specialize TreeTypeHelper
* @param my_primitive associated primitive type
* @param my_query query_type
* @param my_kernel kernel type
*/
#define TREE_TYPE_HELPER_MACRO(my_primitive, my_query, my_kernel) \
- template <> struct TreeTypeHelper<my_primitive<my_kernel>, my_kernel> { \
+ template <> \
+ struct TreeTypeHelper<my_primitive<my_kernel> /*NOLINT*/, my_kernel> { \
static const bool is_valid = true; \
- typedef my_primitive<my_kernel> primitive_type; \
- typedef my_primitive##_primitive aabb_primitive_type; \
- typedef CGAL::Point_3<my_kernel> point_type; \
- \
- typedef std::list<primitive_type> container_type; \
- typedef container_type::iterator iterator; \
- typedef CGAL::AABB_traits<my_kernel, aabb_primitive_type> \
- aabb_traits_type; \
- typedef CGAL::AABB_tree<aabb_traits_type> tree; \
- typedef tree::Primitive_id id_type; \
+ using primitive_type = my_primitive<my_kernel>; /*NOLINT*/ \
+ using aabb_primitive_type = my_primitive##_primitive; \
+ using point_type = CGAL::Point_3<my_kernel>; \
+ using container_type = std::list<primitive_type>; \
+ using iterator = container_type::iterator; \
+ using aabb_traits_type = \
+ CGAL::AABB_traits<my_kernel, aabb_primitive_type>; \
+ using tree = CGAL::AABB_tree<aabb_traits_type>; \
+ using id_type = tree::Primitive_id; \
}; \
\
template <> \
struct IntersectionTypeHelper< \
- TreeTypeHelper<my_primitive<my_kernel>, my_kernel>, my_query> { \
+ TreeTypeHelper<my_primitive<my_kernel>, /*NOLINT*/ my_kernel>, \
+ my_query> { \
typedef boost::optional<TreeTypeHelper< \
- my_primitive<my_kernel>, \
+ my_primitive<my_kernel>, /*NOLINT*/ \
my_kernel>::tree::Intersection_and_primitive_id<my_query>::Type> \
intersection_type; \
}
TREE_TYPE_HELPER_MACRO(Triangle, cgal::Cartesian::Segment_3, cgal::Cartesian);
// TREE_TYPE_HELPER_MACRO(Line_arc, cgal::Spherical::Sphere_3, cgal::Spherical);
#undef TREE_TYPE_HELPER_MACRO
} // namespace akantu
-#endif // __AKANTU_TREE_TYPE_HELPER_HH__
+#endif // AKANTU_TREE_TYPE_HELPER_HH_
diff --git a/src/io/dumper/dumpable.cc b/src/io/dumper/dumpable.cc
index 2f0e53548..0a3df6a52 100644
--- a/src/io/dumper/dumpable.cc
+++ b/src/io/dumper/dumpable.cc
@@ -1,276 +1,277 @@
/**
* @file dumpable.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the dumpable interface
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumpable.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include <io_helper.hh>
+#include <utility>
namespace akantu {
/* -------------------------------------------------------------------------- */
-Dumpable::Dumpable() : default_dumper("") {}
+Dumpable::Dumpable() = default;
/* -------------------------------------------------------------------------- */
Dumpable::~Dumpable() = default;
/* -------------------------------------------------------------------------- */
void Dumpable::registerExternalDumper(std::shared_ptr<DumperIOHelper> dumper,
const std::string & dumper_name,
const bool is_default) {
- this->dumpers[dumper_name] = dumper;
- if (is_default)
+ this->dumpers[dumper_name] = std::move(dumper);
+ if (is_default) {
this->default_dumper = dumper_name;
+ }
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpMesh(const Mesh & mesh, UInt spatial_dimension,
- const GhostType & ghost_type,
- const ElementKind & element_kind) {
+ GhostType ghost_type, ElementKind element_kind) {
this->addDumpMeshToDumper(this->default_dumper, mesh, spatial_dimension,
ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpMeshToDumper(const std::string & dumper_name,
const Mesh & mesh, UInt spatial_dimension,
- const GhostType & ghost_type,
- const ElementKind & element_kind) {
+ GhostType ghost_type,
+ ElementKind element_kind) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerMesh(mesh, spatial_dimension, ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
- const GhostType & ghost_type, const ElementKind & element_kind) {
+ GhostType ghost_type, ElementKind element_kind) {
this->addDumpFilteredMeshToDumper(this->default_dumper, mesh, elements_filter,
nodes_filter, spatial_dimension, ghost_type,
element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
- const GhostType & ghost_type, const ElementKind & element_kind) {
+ GhostType ghost_type, ElementKind element_kind) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerFilteredMesh(mesh, elements_filter, nodes_filter,
spatial_dimension, ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpField(const std::string & field_id) {
this->addDumpFieldToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldExternal(const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
- this->addDumpFieldExternalToDumper(this->default_dumper, field_id, field);
+ this->addDumpFieldExternalToDumper(this->default_dumper, field_id,
+ std::move(field));
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
- dumper.registerField(field_id, field);
+ dumper.registerField(field_id, std::move(field));
}
/* -------------------------------------------------------------------------- */
void Dumpable::removeDumpField(const std::string & field_id) {
this->removeDumpFieldFromDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.unRegisterField(field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldVector(const std::string & field_id) {
this->addDumpFieldVectorToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
-void Dumpable::addDumpFieldVectorToDumper(__attribute__((unused))
- const std::string & dumper_name,
- __attribute__((unused))
- const std::string & field_id) {
+void Dumpable::addDumpFieldVectorToDumper(const std::string & /*dumper_name*/,
+ const std::string & /*field_id*/) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldTensor(const std::string & field_id) {
this->addDumpFieldTensorToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldTensorToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::setDirectory(const std::string & directory) {
this->setDirectoryToDumper(this->default_dumper, directory);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setBaseName(const std::string & basename) {
this->setBaseNameToDumper(this->default_dumper, basename);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setBaseName(basename);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTimeStepToDumper(Real time_step) {
this->setTimeStepToDumper(this->default_dumper, time_step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTimeStepToDumper(const std::string & dumper_name,
Real time_step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTextModeToDumper(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.getDumper().setMode(iohelper::TEXT);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTextModeToDumper() {
DumperIOHelper & dumper = this->getDumper(this->default_dumper);
dumper.getDumper().setMode(iohelper::TEXT);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump();
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump() { this->dump(this->default_dumper); }
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name, UInt step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump(step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(UInt step) { this->dump(this->default_dumper, step); }
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name, Real time, UInt step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump(time, step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(Real time, UInt step) {
this->dump(this->default_dumper, time, step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::internalAddDumpFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
- dumper.registerField(field_id, field);
+ dumper.registerField(field_id, std::move(field));
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Dumpable::getDumper() {
return this->getDumper(this->default_dumper);
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Dumpable::getDumper(const std::string & dumper_name) {
auto it = this->dumpers.find(dumper_name);
auto end = this->dumpers.end();
- if (it == end)
+ if (it == end) {
AKANTU_EXCEPTION("Dumper " << dumper_name
<< "has not been registered, yet.");
+ }
return *(it->second);
}
/* -------------------------------------------------------------------------- */
std::string Dumpable::getDefaultDumperName() const {
return this->default_dumper;
}
} // namespace akantu
#endif
diff --git a/src/io/dumper/dumpable.hh b/src/io/dumper/dumpable.hh
index 5b9abae1d..913c184bf 100644
--- a/src/io/dumper/dumpable.hh
+++ b/src/io/dumper/dumpable.hh
@@ -1,46 +1,46 @@
/**
* @file dumpable.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
* @date last modification: Wed Feb 03 2016
*
* @brief Interface for object who wants to dump themselves
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DUMPABLE_HH__
-#define __AKANTU_DUMPABLE_HH__
+#ifndef AKANTU_DUMPABLE_HH_
+#define AKANTU_DUMPABLE_HH_
#ifdef AKANTU_USE_IOHELPER
#include "dumpable_iohelper.hh"
#else
#include "dumpable_dummy.hh"
#endif // AKANTU_USE_IOHELPER
-#endif /* __AKANTU_DUMPABLE_HH__ */
+#endif /* AKANTU_DUMPABLE_HH_ */
diff --git a/src/io/dumper/dumpable_dummy.hh b/src/io/dumper/dumpable_dummy.hh
index b50dc14f2..15e0f05a9 100644
--- a/src/io/dumper/dumpable_dummy.hh
+++ b/src/io/dumper/dumpable_dummy.hh
@@ -1,267 +1,267 @@
/**
* @file dumpable_dummy.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
* @date last modification: Tue Feb 20 2018
*
* @brief Interface for object who wants to dump themselves
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#if !defined(DOXYGEN)
-#ifndef __AKANTU_DUMPABLE_DUMMY_HH__
-#define __AKANTU_DUMPABLE_DUMMY_HH__
+#ifndef AKANTU_DUMPABLE_DUMMY_HH_
+#define AKANTU_DUMPABLE_DUMMY_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wunused"
namespace dumpers {
class Field;
}
class DumperIOHelper;
class Mesh;
/* -------------------------------------------------------------------------- */
class Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Dumpable(){};
virtual ~Dumpable(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <class T>
inline void registerDumper(const std::string & dumper_name,
const std::string & file_name = "",
const bool is_default = false) {}
void registerExternalDumper(std::shared_ptr<DumperIOHelper> dumper,
const std::string & dumper_name,
const bool is_default = false) {}
void addDumpMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined) {}
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined) {}
void addDumpMeshToDumper(const std::string & dumper_name, const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined) {
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined) {
}
void addDumpFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined) {
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined) {
}
void addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined) {}
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined) {}
virtual void addDumpField(const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
virtual void addDumpFieldExternal(const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
virtual void
addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void addDumpFieldExternal(const std::string & field_id,
const Array<T> & field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void
addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined) {
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined) {
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void removeDumpField(const std::string & field_id) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setDirecory(const std::string & directory) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setBaseName(const std::string & basename) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setTextModeToDumper(const std::string & dumper_name) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setTextModeToDumper() {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump() {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name, UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(Real current_time, UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name, Real current_time, UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
protected:
void internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
protected:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper & getDumper() {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
DumperIOHelper & getDumper(const std::string & dumper_name) {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <class T> T & getDumper(const std::string & dumper_name) {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
std::string getDefaultDumperName() {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
#pragma GCC diagnostic pop
} // namespace akantu
-#endif /* __AKANTU_DUMPABLE_DUMMY_HH__ */
+#endif /* AKANTU_DUMPABLE_DUMMY_HH_ */
#endif // DOXYGEN
diff --git a/src/io/dumper/dumpable_inline_impl.hh b/src/io/dumper/dumpable_inline_impl.hh
index 158cf1908..ddf4d2c8b 100644
--- a/src/io/dumper/dumpable_inline_impl.hh
+++ b/src/io/dumper/dumpable_inline_impl.hh
@@ -1,133 +1,135 @@
/**
* @file dumpable_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the Dumpable class
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPABLE_INLINE_IMPL_HH__
-#define __AKANTU_DUMPABLE_INLINE_IMPL_HH__
+#ifndef AKANTU_DUMPABLE_INLINE_IMPL_HH_
+#define AKANTU_DUMPABLE_INLINE_IMPL_HH_
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_elemental_field.hh"
#include "dumper_nodal_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class T>
inline void Dumpable::registerDumper(const std::string & dumper_name,
const std::string & file_name,
const bool is_default) {
if (this->dumpers.find(dumper_name) != this->dumpers.end()) {
AKANTU_DEBUG_INFO("Dumper " + dumper_name + "is already registered.");
}
std::string name = file_name;
- if (name == "")
+ if (name.empty()) {
name = dumper_name;
+ }
this->dumpers[dumper_name] = std::make_shared<T>(name);
- if (is_default)
+ if (is_default) {
this->default_dumper = dumper_name;
+ }
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternal(const std::string & field_id,
const Array<T> & field) {
this->addDumpFieldExternalToDumper<T>(this->default_dumper, field_id, field);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void
Dumpable::addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field) {
auto field_cont = std::make_shared<dumpers::NodalField<T>>(field);
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field_cont);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension,
- const GhostType & ghost_type,
- const ElementKind & element_kind) {
+ GhostType ghost_type,
+ ElementKind element_kind) {
this->addDumpFieldExternalToDumper(this->default_dumper, field_id, field,
spatial_dimension, ghost_type,
element_kind);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field, UInt spatial_dimension,
- const GhostType & ghost_type, const ElementKind & element_kind) {
+ GhostType ghost_type, ElementKind element_kind) {
std::shared_ptr<dumpers::Field> field_cont;
#if defined(AKANTU_IGFEM)
if (element_kind == _ek_igfem) {
field_cont = std::make_shared<dumpers::IGFEMElementalField<T>>(
field, spatial_dimension, ghost_type, element_kind);
} else
#endif
field_cont = std::make_shared<dumpers::ElementalField<T>>(
field, spatial_dimension, ghost_type, element_kind);
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field_cont);
}
/* -------------------------------------------------------------------------- */
template <class T>
inline T & Dumpable::getDumper(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
try {
auto & templated_dumper = aka::as_type<T>(dumper);
return templated_dumper;
} catch (std::bad_cast &) {
AKANTU_EXCEPTION("Dumper " << dumper_name << " is not of type: "
<< debug::demangle(typeid(T).name()));
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif
-#endif /* __AKANTU_DUMPABLE_INLINE_IMPL_HH__ */
+#endif /* AKANTU_DUMPABLE_INLINE_IMPL_HH_ */
diff --git a/src/io/dumper/dumpable_iohelper.hh b/src/io/dumper/dumpable_iohelper.hh
index 30a63360f..02597fa7a 100644
--- a/src/io/dumper/dumpable_iohelper.hh
+++ b/src/io/dumper/dumpable_iohelper.hh
@@ -1,192 +1,192 @@
/**
* @file dumpable_iohelper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 06 2015
* @date last modification: Sun Dec 03 2017
*
* @brief Interface for object who wants to dump themselves
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DUMPABLE_IOHELPER_HH__
-#define __AKANTU_DUMPABLE_IOHELPER_HH__
+#ifndef AKANTU_DUMPABLE_IOHELPER_HH_
+#define AKANTU_DUMPABLE_IOHELPER_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Dumpable();
virtual ~Dumpable();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create a new dumper (of templated type T) and register it under
/// dumper_name. file_name is used for construction of T. is default states if
/// this dumper is the default dumper.
template <class T>
inline void registerDumper(const std::string & dumper_name,
const std::string & file_name = "",
- const bool is_default = false);
+ bool is_default = false);
/// register an externally created dumper
void registerExternalDumper(std::shared_ptr<DumperIOHelper> dumper,
const std::string & dumper_name,
- const bool is_default = false);
+ bool is_default = false);
/// register a mesh to the default dumper
void addDumpMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
/// register a mesh to the default identified by its name
void addDumpMeshToDumper(const std::string & dumper_name, const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
/// register a filtered mesh as the default dumper
void addDumpFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
/// register a filtered mesh and provides a name
void addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
/// to implement
virtual void addDumpField(const std::string & field_id);
/// to implement
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/// add a field
virtual void addDumpFieldExternal(const std::string & field_id,
std::shared_ptr<dumpers::Field> field);
virtual void
addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
std::shared_ptr<dumpers::Field> field);
template <typename T>
inline void addDumpFieldExternal(const std::string & field_id,
const Array<T> & field);
template <typename T>
inline void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field);
template <typename T>
inline void
addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
template <typename T>
inline void addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
void removeDumpField(const std::string & field_id);
void removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldVector(const std::string & field_id);
virtual void addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensor(const std::string & field_id);
virtual void addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id);
void setDirectory(const std::string & directory);
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory);
void setBaseName(const std::string & basename);
void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename);
void setTimeStepToDumper(Real time_step);
void setTimeStepToDumper(const std::string & dumper_name, Real time_step);
void setTextModeToDumper(const std::string & dumper_name);
void setTextModeToDumper();
virtual void dump();
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
virtual void dump(const std::string & dumper_name);
virtual void dump(const std::string & dumper_name, UInt step);
virtual void dump(const std::string & dumper_name, Real time, UInt step);
public:
void internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
std::shared_ptr<dumpers::Field> field);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper & getDumper();
DumperIOHelper & getDumper(const std::string & dumper_name);
template <class T> T & getDumper(const std::string & dumper_name);
std::string getDefaultDumperName() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using DumperMap = std::map<std::string, std::shared_ptr<DumperIOHelper>>;
using DumperSet = std::set<std::string>;
DumperMap dumpers;
std::string default_dumper;
};
} // namespace akantu
-#endif /* __AKANTU_DUMPABLE_IOHELPER_HH__ */
+#endif /* AKANTU_DUMPABLE_IOHELPER_HH_ */
diff --git a/src/io/dumper/dumper_compute.hh b/src/io/dumper/dumper_compute.hh
index 3913fff1f..e84b97bb5 100644
--- a/src/io/dumper/dumper_compute.hh
+++ b/src/io/dumper/dumper_compute.hh
@@ -1,261 +1,287 @@
/**
* @file dumper_compute.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Sun Dec 03 2017
*
* @brief Field that map a function to another field
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_COMPUTE_HH__
-#define __AKANTU_DUMPER_COMPUTE_HH__
+#ifndef AKANTU_DUMPER_COMPUTE_HH_
+#define AKANTU_DUMPER_COMPUTE_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dumper_field.hh"
#include "dumper_iohelper.hh"
#include "dumper_type_traits.hh"
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
-class ComputeFunctorInterface {
-public:
- virtual ~ComputeFunctorInterface() = default;
+ class ComputeFunctorInterface {
+ public:
+ virtual ~ComputeFunctorInterface() = default;
- virtual UInt getDim() = 0;
- virtual UInt getNbComponent(UInt old_nb_comp) = 0;
-};
+ virtual UInt getDim() = 0;
+ virtual UInt getNbComponent(UInt old_nb_comp) = 0;
+ };
-/* -------------------------------------------------------------------------- */
+ /* --------------------------------------------------------------------------
+ */
-template <typename return_type>
-class ComputeFunctorOutput : public ComputeFunctorInterface {
-public:
- ComputeFunctorOutput() = default;
- ~ComputeFunctorOutput() override = default;
-};
+ template <typename return_type>
+ class ComputeFunctorOutput : public ComputeFunctorInterface {
+ public:
+ ComputeFunctorOutput() = default;
+ ~ComputeFunctorOutput() override = default;
+ };
-/* -------------------------------------------------------------------------- */
-template <typename input_type, typename return_type>
-class ComputeFunctor : public ComputeFunctorOutput<return_type> {
-public:
- ComputeFunctor() = default;
- ~ComputeFunctor() override = default;
+ /* --------------------------------------------------------------------------
+ */
+ template <typename input_type, typename return_type>
+ class ComputeFunctor : public ComputeFunctorOutput<return_type> {
+ public:
+ ComputeFunctor() = default;
+ ~ComputeFunctor() override = default;
- virtual return_type func(const input_type & d, Element global_index) = 0;
-};
+ virtual return_type func(const input_type & d, Element global_index) = 0;
+ };
-/* -------------------------------------------------------------------------- */
-template <typename SubFieldCompute, typename _return_type>
-class FieldCompute : public Field {
- /* ------------------------------------------------------------------------ */
- /* Typedefs */
- /* ------------------------------------------------------------------------ */
-public:
- using sub_iterator = typename SubFieldCompute::iterator;
- using sub_types = typename SubFieldCompute::types;
- using sub_return_type = typename sub_types::return_type;
- using return_type = _return_type;
- using data_type = typename sub_types::data_type;
-
- using types =
- TypeTraits<data_type, return_type, ElementTypeMapArray<data_type>>;
-
- class iterator {
+ /* --------------------------------------------------------------------------
+ */
+ template <typename SubFieldCompute, typename _return_type>
+ class FieldCompute : public Field {
+ /* ------------------------------------------------------------------------
+ */
+ /* Typedefs */
+ /* ------------------------------------------------------------------------
+ */
public:
- iterator(const sub_iterator & it,
- ComputeFunctor<sub_return_type, return_type> & func)
- : it(it), func(func) {}
-
- bool operator!=(const iterator & it) const { return it.it != this->it; }
- iterator operator++() {
- ++this->it;
- return *this;
- }
+ using sub_iterator = typename SubFieldCompute::iterator;
+ using sub_types = typename SubFieldCompute::types;
+ using sub_return_type = typename sub_types::return_type;
+ using return_type = _return_type;
+ using data_type = typename sub_types::data_type;
- UInt currentGlobalIndex() { return this->it.currentGlobalIndex(); }
+ using types =
+ TypeTraits<data_type, return_type, ElementTypeMapArray<data_type>>;
- return_type operator*() { return func.func(*it, it.getCurrentElement()); }
+ class iterator {
+ public:
+ iterator(const sub_iterator & it,
+ ComputeFunctor<sub_return_type, return_type> & func)
+ : it(it), func(func) {}
- Element getCurrentElement() { return this->it.getCurrentElement(); }
+ bool operator!=(const iterator & it) const { return it.it != this->it; }
+ iterator operator++() {
+ ++this->it;
+ return *this;
+ }
- UInt element_type() { return this->it.element_type(); }
+ UInt currentGlobalIndex() { return this->it.currentGlobalIndex(); }
- protected:
- sub_iterator it;
- ComputeFunctor<sub_return_type, return_type> & func;
- };
+ return_type operator*() { return func.func(*it, it.getCurrentElement()); }
- /* ------------------------------------------------------------------------ */
- /* Constructors/Destructors */
- /* ------------------------------------------------------------------------ */
-public:
- FieldCompute(SubFieldCompute & cont,
- std::unique_ptr<ComputeFunctorInterface> func)
- : sub_field(aka::as_type<SubFieldCompute>(cont.shared_from_this())),
- func(aka::as_type<ComputeFunctor<sub_return_type, return_type>>(
- func.release())) {
- this->checkHomogeneity();
- };
+ Element getCurrentElement() { return this->it.getCurrentElement(); }
- ~FieldCompute() override = default;
+ UInt element_type() { return this->it.element_type(); }
- void registerToDumper(const std::string & id,
- iohelper::Dumper & dumper) override {
- dumper.addElemDataField(id, *this);
- }
+ protected:
+ sub_iterator it;
+ ComputeFunctor<sub_return_type, return_type> & func;
+ };
- /* ------------------------------------------------------------------------ */
- /* Class Members */
- /* ------------------------------------------------------------------------ */
-public:
- iterator begin() { return iterator(sub_field->begin(), *func); }
- iterator end() { return iterator(sub_field->end(), *func); }
+ /* ------------------------------------------------------------------------
+ */
+ /* Constructors/Destructors */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ FieldCompute(SubFieldCompute & cont,
+ std::unique_ptr<ComputeFunctorInterface> func)
+ : sub_field(aka::as_type<SubFieldCompute>(cont.shared_from_this())),
+ func(aka::as_type<ComputeFunctor<sub_return_type, return_type>>(
+ func.release())) {
+ this->checkHomogeneity();
+ };
+
+ ~FieldCompute() override = default;
+
+ void registerToDumper(const std::string & id,
+ iohelper::Dumper & dumper) override {
+ dumper.addElemDataField(id, *this);
+ }
- UInt getDim() { return func->getDim(); }
+ /* ------------------------------------------------------------------------
+ */
+ /* Class Members */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ iterator begin() { return iterator(sub_field->begin(), *func); }
+ iterator end() { return iterator(sub_field->end(), *func); }
- UInt size() {
- throw;
- // return Functor::size();
- return 0;
- }
+ UInt getDim() { return func->getDim(); }
- void checkHomogeneity() override { this->homogeneous = true; };
+ UInt size() {
+ throw;
+ // return Functor::size();
+ return 0;
+ }
- iohelper::DataType getDataType() {
- return iohelper::getDataType<data_type>();
- }
+ void checkHomogeneity() override { this->homogeneous = true; };
- /// get the number of components of the hosted field
- ElementTypeMap<UInt>
- getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
- ElementKind kind = _ek_not_defined) override {
- ElementTypeMap<UInt> nb_components;
- const auto & old_nb_components =
- this->sub_field->getNbComponents(dim, ghost_type, kind);
-
- for (auto type : old_nb_components.elementTypes(dim, ghost_type, kind)) {
- UInt nb_comp = old_nb_components(type, ghost_type);
- nb_components(type, ghost_type) = func->getNbComponent(nb_comp);
+ iohelper::DataType getDataType() {
+ return iohelper::getDataType<data_type>();
}
- return nb_components;
+
+ /// get the number of components of the hosted field
+ ElementTypeMap<UInt>
+ getNbComponents(UInt dim = _all_dimensions,
+ GhostType ghost_type = _not_ghost,
+ ElementKind kind = _ek_not_defined) override {
+ ElementTypeMap<UInt> nb_components;
+ const auto & old_nb_components =
+ this->sub_field->getNbComponents(dim, ghost_type, kind);
+
+ for (auto type : old_nb_components.elementTypes(dim, ghost_type, kind)) {
+ UInt nb_comp = old_nb_components(type, ghost_type);
+ nb_components(type, ghost_type) = func->getNbComponent(nb_comp);
+ }
+ return nb_components;
+ };
+
+ /// for connection to a FieldCompute
+ inline std::shared_ptr<Field> connect(FieldComputeProxy & proxy) override;
+
+ /// for connection to a FieldCompute
+ std::unique_ptr<ComputeFunctorInterface>
+ connect(HomogenizerProxy & proxy) override;
+
+ /* ------------------------------------------------------------------------
+ */
+ /* Class Members */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ std::shared_ptr<SubFieldCompute> sub_field;
+ std::unique_ptr<ComputeFunctor<sub_return_type, return_type>> func;
};
- /// for connection to a FieldCompute
- inline std::shared_ptr<Field> connect(FieldComputeProxy & proxy) override;
+ /* --------------------------------------------------------------------------
+ */
- /// for connection to a FieldCompute
- std::unique_ptr<ComputeFunctorInterface>
- connect(HomogenizerProxy & proxy) override;
+ /* --------------------------------------------------------------------------
+ */
- /* ------------------------------------------------------------------------ */
- /* Class Members */
- /* ------------------------------------------------------------------------ */
-public:
- std::shared_ptr<SubFieldCompute> sub_field;
- std::unique_ptr<ComputeFunctor<sub_return_type, return_type>> func;
-};
+ class FieldComputeProxy {
+ /* ------------------------------------------------------------------------
+ */
+ /* Constructors/Destructors */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ FieldComputeProxy(std::unique_ptr<ComputeFunctorInterface> func)
+ : func(std::move(func)){};
+
+ inline static std::shared_ptr<Field>
+ createFieldCompute(std::shared_ptr<Field> & field,
+ std::unique_ptr<ComputeFunctorInterface> func) {
+ FieldComputeProxy compute_proxy(std::move(func));
+ return field->connect(compute_proxy);
+ }
-/* -------------------------------------------------------------------------- */
+ template <typename T> std::shared_ptr<Field> connectToField(T * ptr) {
+ if (aka::is_of_type<ComputeFunctorOutput<Vector<Real>>>(func)) {
+ return this->connectToFunctor<Vector<Real>>(ptr);
+ }
-/* -------------------------------------------------------------------------- */
+ if (aka::is_of_type<ComputeFunctorOutput<Vector<UInt>>>(func)) {
+ return this->connectToFunctor<Vector<UInt>>(ptr);
+ }
-class FieldComputeProxy {
- /* ------------------------------------------------------------------------ */
- /* Constructors/Destructors */
- /* ------------------------------------------------------------------------ */
-public:
- FieldComputeProxy(std::unique_ptr<ComputeFunctorInterface> func)
- : func(std::move(func)){};
-
- inline static std::shared_ptr<Field>
- createFieldCompute(std::shared_ptr<Field> field,
- std::unique_ptr<ComputeFunctorInterface> func) {
- FieldComputeProxy compute_proxy(std::move(func));
- return field->connect(compute_proxy);
- }
+ if (aka::is_of_type<ComputeFunctorOutput<Matrix<UInt>>>(func)) {
+ return this->connectToFunctor<Matrix<UInt>>(ptr);
+ }
- template <typename T> std::shared_ptr<Field> connectToField(T * ptr) {
- if (aka::is_of_type<ComputeFunctorOutput<Vector<Real>>>(func)) {
- return this->connectToFunctor<Vector<Real>>(ptr);
- } else if (aka::is_of_type<ComputeFunctorOutput<Vector<UInt>>>(func)) {
- return this->connectToFunctor<Vector<UInt>>(ptr);
- } else if (aka::is_of_type<ComputeFunctorOutput<Matrix<UInt>>>(func)) {
- return this->connectToFunctor<Matrix<UInt>>(ptr);
- } else if (aka::is_of_type<ComputeFunctorOutput<Matrix<Real>>>(func)) {
- return this->connectToFunctor<Matrix<Real>>(ptr);
- } else {
+ if (aka::is_of_type<ComputeFunctorOutput<Matrix<Real>>>(func)) {
+ return this->connectToFunctor<Matrix<Real>>(ptr);
+ }
throw;
}
- }
- template <typename output, typename T>
- std::shared_ptr<Field> connectToFunctor(T * ptr) {
- return std::make_shared<FieldCompute<T, output>>(*ptr, std::move(func));
- }
+ template <typename output, typename T>
+ std::shared_ptr<Field> connectToFunctor(T * ptr) {
+ return std::make_shared<FieldCompute<T, output>>(*ptr, std::move(func));
+ }
- template <typename output, typename SubFieldCompute, typename return_type1,
- typename return_type2>
- std::shared_ptr<Field>
- connectToFunctor(__attribute__((unused))
- FieldCompute<FieldCompute<SubFieldCompute, return_type1>,
- return_type2> * ptr) {
- throw; // return new FieldCompute<T,output>(*ptr,func);
- return nullptr;
- }
+ template <typename output, typename SubFieldCompute, typename return_type1,
+ typename return_type2>
+ std::shared_ptr<Field>
+ connectToFunctor(FieldCompute<FieldCompute<SubFieldCompute, return_type1>,
+ return_type2> * /*ptr*/) {
+ throw; // return new FieldCompute<T,output>(*ptr,func);
+ return nullptr;
+ }
- template <typename output, typename SubFieldCompute, typename return_type1,
- typename return_type2, typename return_type3, typename return_type4>
- std::shared_ptr<Field> connectToFunctor(
- __attribute__((unused)) FieldCompute<
- FieldCompute<FieldCompute<FieldCompute<SubFieldCompute, return_type1>,
- return_type2>,
- return_type3>,
- return_type4> * ptr) {
- throw; // return new FieldCompute<T,output>(*ptr,func);
- return nullptr;
- }
+ template <typename output, typename SubFieldCompute, typename return_type1,
+ typename return_type2, typename return_type3,
+ typename return_type4>
+ std::shared_ptr<Field> connectToFunctor(
+ FieldCompute<FieldCompute<FieldCompute<FieldCompute<SubFieldCompute,
+ return_type1>,
+ return_type2>,
+ return_type3>,
+ return_type4> * /*ptr*/) {
+ throw; // return new FieldCompute<T,output>(*ptr,func);
+ return nullptr;
+ }
- /* ------------------------------------------------------------------------ */
- /* Class Members */
- /* ------------------------------------------------------------------------ */
-public:
- std::unique_ptr<ComputeFunctorInterface> func;
-};
+ /* ------------------------------------------------------------------------
+ */
+ /* Class Members */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ std::unique_ptr<ComputeFunctorInterface> func;
+ };
-/* -------------------------------------------------------------------------- */
-/// for connection to a FieldCompute
-template <typename SubFieldCompute, typename return_type>
-inline std::shared_ptr<Field>
-FieldCompute<SubFieldCompute, return_type>::connect(FieldComputeProxy & proxy) {
- return proxy.connectToField(this);
-}
+ /* --------------------------------------------------------------------------
+ */
+ /// for connection to a FieldCompute
+ template <typename SubFieldCompute, typename return_type>
+ inline std::shared_ptr<Field>
+ FieldCompute<SubFieldCompute, return_type>::connect(
+ FieldComputeProxy & proxy) {
+ return proxy.connectToField(this);
+ }
-/* -------------------------------------------------------------------------- */
+ /* --------------------------------------------------------------------------
+ */
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_COMPUTE_HH__ */
+#endif /* AKANTU_DUMPER_COMPUTE_HH_ */
diff --git a/src/io/dumper/dumper_element_iterator.hh b/src/io/dumper/dumper_element_iterator.hh
index e9179338a..97db57d48 100644
--- a/src/io/dumper/dumper_element_iterator.hh
+++ b/src/io/dumper/dumper_element_iterator.hh
@@ -1,177 +1,178 @@
/**
* @file dumper_element_iterator.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Sun Dec 03 2017
*
* @brief Iterators for elemental fields
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_ELEMENT_ITERATOR_HH__
-#define __AKANTU_DUMPER_ELEMENT_ITERATOR_HH__
+#ifndef AKANTU_DUMPER_ELEMENT_ITERATOR_HH_
+#define AKANTU_DUMPER_ELEMENT_ITERATOR_HH_
/* -------------------------------------------------------------------------- */
#include "element.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <class types, template <class> class final_iterator>
class element_iterator {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using it_type = typename types::it_type;
using field_type = typename types::field_type;
using array_type = typename types::array_type;
using array_iterator = typename types::array_iterator;
using iterator = final_iterator<types>;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
element_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: field(field), tit(t_it), tit_end(t_it_end), array_it(array_it),
array_it_end(array_it_end), ghost_type(ghost_type) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
bool operator!=(const iterator & it) const {
return (ghost_type != it.ghost_type) ||
(tit != it.tit || (array_it != it.array_it));
}
iterator & operator++() {
++array_it;
while (array_it == array_it_end && tit != tit_end) {
++tit;
if (tit != tit_end) {
const array_type & vect = field(*tit, ghost_type);
UInt _nb_data_per_elem = getNbDataPerElem(*tit);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.size() * nb_component) / _nb_data_per_elem;
array_it = vect.begin_reinterpret(_nb_data_per_elem, size);
array_it_end = vect.end_reinterpret(_nb_data_per_elem, size);
}
}
return *(static_cast<iterator *>(this));
};
ElementType getType() { return *tit; }
UInt element_type() { return getIOHelperType(*tit); }
Element getCurrentElement() {
return Element{*tit, array_it.getCurrentIndex(), _not_ghost};
}
- UInt getNbDataPerElem(const ElementType & type) const {
- if (!nb_data_per_elem.exists(type, ghost_type))
+ UInt getNbDataPerElem(ElementType type) const {
+ if (!nb_data_per_elem.exists(type, ghost_type)) {
return field(type, ghost_type).getNbComponent();
+ }
return nb_data_per_elem(type, ghost_type);
}
void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data) {
this->nb_data_per_elem = nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the field to iterate on
const field_type & field;
/// field iterator
typename field_type::type_iterator tit;
/// field iterator end
typename field_type::type_iterator tit_end;
/// array iterator
array_iterator array_it;
/// internal iterator end
array_iterator array_it_end;
/// ghost type identification
const GhostType ghost_type;
/// number of data per element
ElementTypeMap<UInt> nb_data_per_elem;
};
/* -------------------------------------------------------------------------- */
template <typename types>
class elemental_field_iterator
: public element_iterator<types, elemental_field_iterator> {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
using parent =
element_iterator<types, ::akantu::dumpers::elemental_field_iterator>;
using it_type = typename types::it_type;
using return_type = typename types::return_type;
using field_type = typename types::field_type;
using array_iterator = typename types::array_iterator;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
elemental_field_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
return_type operator*() { return *this->array_it; }
private:
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_DUMPER_ELEMENT_ITERATOR_HH__ */
+#endif /* AKANTU_DUMPER_ELEMENT_ITERATOR_HH_ */
diff --git a/src/io/dumper/dumper_elemental_field.hh b/src/io/dumper/dumper_elemental_field.hh
index ecbf4e82f..409bad555 100644
--- a/src/io/dumper/dumper_elemental_field.hh
+++ b/src/io/dumper/dumper_elemental_field.hh
@@ -1,75 +1,75 @@
/**
* @file dumper_elemental_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief description of elemental fields
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_ELEMENTAL_FIELD_HH__
-#define __AKANTU_DUMPER_ELEMENTAL_FIELD_HH__
+#ifndef AKANTU_DUMPER_ELEMENTAL_FIELD_HH_
+#define AKANTU_DUMPER_ELEMENTAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "dumper_field.hh"
#include "dumper_generic_elemental_field.hh"
#ifdef AKANTU_IGFEM
#include "dumper_igfem_elemental_field.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename T, template <class> class ret = Vector,
bool filtered = false>
class ElementalField
: public GenericElementalField<SingleType<T, ret, filtered>,
elemental_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using types = SingleType<T, ret, filtered>;
using field_type = typename types::field_type;
using iterator = elemental_field_iterator<types>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: GenericElementalField<types, elemental_field_iterator>(
field, spatial_dimension, ghost_type, element_kind) {}
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_ELEMENTAL_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_ELEMENTAL_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_field.hh b/src/io/dumper/dumper_field.hh
index 8b911f36c..87106bc9b 100644
--- a/src/io/dumper/dumper_field.hh
+++ b/src/io/dumper/dumper_field.hh
@@ -1,136 +1,136 @@
/**
* @file dumper_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Tue Feb 20 2018
*
* @brief Common interface for fields
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_FIELD_HH__
-#define __AKANTU_DUMPER_FIELD_HH__
+#ifndef AKANTU_DUMPER_FIELD_HH_
+#define AKANTU_DUMPER_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
class FieldComputeProxy;
class FieldComputeBaseInterface;
class ComputeFunctorInterface;
class HomogenizerProxy;
/* -------------------------------------------------------------------------- */
/// Field interface
class Field : public std::enable_shared_from_this<Field> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Field() = default;
virtual ~Field() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
#ifdef AKANTU_USE_IOHELPER
/// register this to the provided dumper
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) = 0;
#endif
/// set the number of data per item (used for elements fields at the moment)
virtual void setNbData([[gnu::unused]] UInt nb_data) {
AKANTU_TO_IMPLEMENT();
};
/// set the number of data per elem (used for elements fields at the moment)
virtual void setNbDataPerElem([
[gnu::unused]] const ElementTypeMap<UInt> & nb_data) {
AKANTU_TO_IMPLEMENT();
};
/// set the number of data per elem (used for elements fields at the moment)
virtual void setNbDataPerElem([[gnu::unused]] UInt nb_data) {
AKANTU_TO_IMPLEMENT();
};
/// get the number of components of the hosted field
virtual ElementTypeMap<UInt>
getNbComponents([[gnu::unused]] UInt dim = _all_dimensions,
[[gnu::unused]] GhostType ghost_type = _not_ghost,
[[gnu::unused]] ElementKind kind = _ek_not_defined) {
throw;
};
/// for connection to a FieldCompute
inline virtual std::shared_ptr<Field> connect([
[gnu::unused]] FieldComputeProxy & proxy) {
throw;
};
/// for connection to a FieldCompute
inline virtual std::unique_ptr<ComputeFunctorInterface>
connect(HomogenizerProxy & /*proxy*/) {
throw;
};
/// check if the same quantity of data for all element types
virtual void checkHomogeneity() = 0;
/// return the dumper name
std::string getGroupName() { return group_name; };
/// return the id of the field
std::string getID() { return field_id; };
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the flag to know if the field is homogeneous/contiguous
virtual bool isHomogeneous() { return homogeneous; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the flag to know if it is homogeneous
bool homogeneous{false};
/// the name of the group it was associated to
std::string group_name;
/// the name of the dumper it was associated to
std::string field_id;
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_filtered_connectivity.hh b/src/io/dumper/dumper_filtered_connectivity.hh
index afff4153b..ad5b1313d 100644
--- a/src/io/dumper/dumper_filtered_connectivity.hh
+++ b/src/io/dumper/dumper_filtered_connectivity.hh
@@ -1,151 +1,172 @@
/**
* @file dumper_filtered_connectivity.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Wed Nov 08 2017
*
* @brief FilteredConnectivities field
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "dumper_generic_elemental_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
-/* -------------------------------------------------------------------------- */
-
-template <class types>
-class filtered_connectivity_field_iterator
- : public element_iterator<types, filtered_connectivity_field_iterator> {
- /* ------------------------------------------------------------------------ */
- /* Typedefs */
- /* ------------------------------------------------------------------------ */
-public:
- typedef element_iterator<types, dumpers::filtered_connectivity_field_iterator>
- parent;
- using return_type = typename types::return_type;
- using field_type = typename types::field_type;
- using array_iterator = typename types::array_iterator;
-
- /* ------------------------------------------------------------------------ */
- /* Constructors/Destructors */
- /* ------------------------------------------------------------------------ */
-public:
- filtered_connectivity_field_iterator(
- const field_type & field, const typename field_type::type_iterator & t_it,
- const typename field_type::type_iterator & t_it_end,
- const array_iterator & array_it, const array_iterator & array_it_end,
- const GhostType ghost_type = _not_ghost)
- : parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
-
- /* ------------------------------------------------------------------------ */
- /* Methods */
- /* ------------------------------------------------------------------------ */
-public:
- return_type operator*() {
- const Vector<UInt> & old_connect = *this->array_it;
- Vector<UInt> new_connect(old_connect.size());
- Array<UInt>::const_iterator<UInt> nodes_begin = nodal_filter->begin();
- Array<UInt>::const_iterator<UInt> nodes_end = nodal_filter->end();
- for (UInt i(0); i < old_connect.size(); ++i) {
- Array<UInt>::const_iterator<UInt> new_id =
- std::find(nodes_begin, nodes_end, old_connect(i));
- if (new_id == nodes_end)
- AKANTU_EXCEPTION("Node not found in the filter!");
- new_connect(i) = new_id - nodes_begin;
+ /* --------------------------------------------------------------------------
+ */
+
+ template <class types>
+ class filtered_connectivity_field_iterator
+ : public element_iterator<types, filtered_connectivity_field_iterator> {
+ /* ------------------------------------------------------------------------
+ */
+ /* Typedefs */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ using parent =
+ element_iterator<types, dumpers::filtered_connectivity_field_iterator>;
+ using return_type = typename types::return_type;
+ using field_type = typename types::field_type;
+ using array_iterator = typename types::array_iterator;
+
+ /* ------------------------------------------------------------------------
+ */
+ /* Constructors/Destructors */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ filtered_connectivity_field_iterator(
+ const field_type & field,
+ const typename field_type::type_iterator & t_it,
+ const typename field_type::type_iterator & t_it_end,
+ const array_iterator & array_it, const array_iterator & array_it_end,
+ const GhostType ghost_type = _not_ghost)
+ : parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
+
+ /* ------------------------------------------------------------------------
+ */
+ /* Methods */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ return_type operator*() {
+ const Vector<UInt> & old_connect = *this->array_it;
+ Vector<UInt> new_connect(old_connect.size());
+ Array<UInt>::const_iterator<UInt> nodes_begin = nodal_filter->begin();
+ Array<UInt>::const_iterator<UInt> nodes_end = nodal_filter->end();
+ for (UInt i(0); i < old_connect.size(); ++i) {
+ Array<UInt>::const_iterator<UInt> new_id =
+ std::find(nodes_begin, nodes_end, old_connect(i));
+ if (new_id == nodes_end) {
+ AKANTU_EXCEPTION("Node not found in the filter!");
+ }
+ new_connect(i) = new_id - nodes_begin;
+ }
+ return new_connect;
}
- return new_connect;
- }
- void setNodalFilter(const Array<UInt> & new_nodal_filter) {
- nodal_filter = &new_nodal_filter;
- }
+ void setNodalFilter(const Array<UInt> & new_nodal_filter) {
+ nodal_filter = &new_nodal_filter;
+ }
- /* ------------------------------------------------------------------------ */
- /* Class Members */
- /* ------------------------------------------------------------------------ */
-private:
- const Array<UInt> * nodal_filter;
-};
+ /* ------------------------------------------------------------------------
+ */
+ /* Class Members */
+ /* ------------------------------------------------------------------------
+ */
+ private:
+ const Array<UInt> * nodal_filter;
+ };
+
+ /* --------------------------------------------------------------------------
+ */
+
+ class FilteredConnectivityField
+ : public GenericElementalField<SingleType<UInt, Vector, true>,
+ filtered_connectivity_field_iterator> {
+ /* ------------------------------------------------------------------------
+ */
+ /* Typedefs */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ using types = SingleType<UInt, Vector, true>;
+ using iterator = filtered_connectivity_field_iterator<types>;
+ using field_type = types::field_type;
+ using parent =
+ GenericElementalField<types, filtered_connectivity_field_iterator>;
+
+ /* ------------------------------------------------------------------------
+ */
+ /* Constructors/Destructors */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ FilteredConnectivityField(const field_type & field,
+ const Array<UInt> & nodal_filter,
+ UInt spatial_dimension = _all_dimensions,
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined)
+ : parent(field, spatial_dimension, ghost_type, element_kind),
+ nodal_filter(nodal_filter) {}
+
+ ~FilteredConnectivityField() override {
+ // since the field is created in registerFilteredMesh it is destroyed here
+ delete const_cast<field_type *>(&this->field);
+ }
-/* -------------------------------------------------------------------------- */
+ /* ------------------------------------------------------------------------
+ */
+ /* Methods */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ iterator begin() override {
+ iterator it = parent::begin();
+ it.setNodalFilter(nodal_filter);
+ return it;
+ }
-class FilteredConnectivityField
- : public GenericElementalField<SingleType<UInt, Vector, true>,
- filtered_connectivity_field_iterator> {
- /* ------------------------------------------------------------------------ */
- /* Typedefs */
- /* ------------------------------------------------------------------------ */
-public:
- typedef SingleType<UInt, Vector, true> types;
- using iterator = filtered_connectivity_field_iterator<types>;
- using field_type = types::field_type;
- typedef GenericElementalField<types, filtered_connectivity_field_iterator>
- parent;
-
- /* ------------------------------------------------------------------------ */
- /* Constructors/Destructors */
- /* ------------------------------------------------------------------------ */
-public:
- FilteredConnectivityField(const field_type & field,
- const Array<UInt> & nodal_filter,
- UInt spatial_dimension = _all_dimensions,
- GhostType ghost_type = _not_ghost,
- ElementKind element_kind = _ek_not_defined)
- : parent(field, spatial_dimension, ghost_type, element_kind),
- nodal_filter(nodal_filter) {}
-
- ~FilteredConnectivityField() override {
- // since the field is created in registerFilteredMesh it is destroyed here
- delete const_cast<field_type *>(&this->field);
- }
-
- /* ------------------------------------------------------------------------ */
- /* Methods */
- /* ------------------------------------------------------------------------ */
-public:
- iterator begin() override {
- iterator it = parent::begin();
- it.setNodalFilter(nodal_filter);
- return it;
- }
-
- iterator end() override {
- iterator it = parent::end();
- it.setNodalFilter(nodal_filter);
- return it;
- }
-
- /* ------------------------------------------------------------------------ */
- /* Class Members */
- /* ------------------------------------------------------------------------ */
-private:
- const Array<UInt> & nodal_filter;
-};
+ iterator end() override {
+ iterator it = parent::end();
+ it.setNodalFilter(nodal_filter);
+ return it;
+ }
-/* -------------------------------------------------------------------------- */
+ /* ------------------------------------------------------------------------
+ */
+ /* Class Members */
+ /* ------------------------------------------------------------------------
+ */
+ private:
+ const Array<UInt> & nodal_filter;
+ };
+
+ /* --------------------------------------------------------------------------
+ */
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
diff --git a/src/io/dumper/dumper_generic_elemental_field.hh b/src/io/dumper/dumper_generic_elemental_field.hh
index 496868dfa..26fbf377e 100644
--- a/src/io/dumper/dumper_generic_elemental_field.hh
+++ b/src/io/dumper/dumper_generic_elemental_field.hh
@@ -1,217 +1,220 @@
/**
* @file dumper_generic_elemental_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Wed Nov 08 2017
*
* @brief Generic interface for elemental fields
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH__
-#define __AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH__
+#ifndef AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH_
+#define AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_element_iterator.hh"
#include "dumper_field.hh"
#include "dumper_homogenizing_field.hh"
#include "element_type_map_filter.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <class _types, template <class> class iterator_type>
class GenericElementalField : public Field {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
// check dumper_type_traits.hh for additional information over these types
using types = _types;
using data_type = typename types::data_type;
using it_type = typename types::it_type;
using field_type = typename types::field_type;
using array_type = typename types::array_type;
using array_iterator = typename types::array_iterator;
using field_type_iterator = typename field_type::type_iterator;
using iterator = iterator_type<types>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GenericElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: field(field), spatial_dimension(spatial_dimension),
ghost_type(ghost_type), element_kind(element_kind) {
this->checkHomogeneity();
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the number of components of the hosted field
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) override {
return this->field.getNbComponents(dim, ghost_type, kind);
};
/// return the size of the contained data: i.e. the number of elements ?
virtual UInt size() {
checkHomogeneity();
return this->nb_total_element;
}
/// return the iohelper datatype to be dumped
iohelper::DataType getDataType() {
return iohelper::getDataType<data_type>();
}
protected:
/// return the number of entries per element
- UInt getNbDataPerElem(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const {
- if (!nb_data_per_elem.exists(type, ghost_type))
+ UInt getNbDataPerElem(ElementType type,
+ GhostType ghost_type = _not_ghost) const {
+ if (!nb_data_per_elem.exists(type, ghost_type)) {
return field(type, ghost_type).getNbComponent();
+ }
return nb_data_per_elem(type, this->ghost_type);
}
/// check if the same quantity of data for all element types
void checkHomogeneity() override;
public:
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addElemDataField(id, *this);
};
/// for connection to a FieldCompute
inline std::shared_ptr<Field> connect(FieldComputeProxy & proxy) override {
return proxy.connectToField(this);
}
/// for connection to a Homogenizer
inline std::unique_ptr<ComputeFunctorInterface>
connect(HomogenizerProxy & proxy) override {
return proxy.connectToField(this);
};
virtual iterator begin() {
/// type iterators on the elemental field
auto types = this->field.elementTypes(this->spatial_dimension,
this->ghost_type, this->element_kind);
auto tit = types.begin();
auto end = types.end();
/// skip all types without data
- for (; tit != end && this->field(*tit, this->ghost_type).size() == 0;
+ for (; tit != end and this->field(*tit, this->ghost_type).empty();
++tit) {
}
auto type = *tit;
- if (tit == end)
+ if (tit == end) {
return this->end();
+ }
/// getting information for the field of the given type
const auto & vect = this->field(type, this->ghost_type);
UInt nb_data_per_elem = this->getNbDataPerElem(type);
/// define element-wise iterator
auto view = make_view(vect, nb_data_per_elem);
auto it = view.begin();
auto it_end = view.end();
/// define data iterator
iterator rit =
iterator(this->field, tit, end, it, it_end, this->ghost_type);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
virtual iterator end() {
auto types = this->field.elementTypes(this->spatial_dimension,
this->ghost_type, this->element_kind);
auto tit = types.begin();
auto end = types.end();
auto type = *tit;
- for (; tit != end; ++tit)
+ for (; tit != end; ++tit) {
type = *tit;
+ }
const array_type & vect = this->field(type, this->ghost_type);
UInt nb_data = this->getNbDataPerElem(type);
auto it = make_view(vect, nb_data).end();
auto rit = iterator(this->field, end, end, it, it, this->ghost_type);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
virtual UInt getDim() {
if (this->homogeneous) {
auto tit = this->field
.elementTypes(this->spatial_dimension, this->ghost_type,
this->element_kind)
.begin();
return this->getNbDataPerElem(*tit);
}
throw;
return 0;
}
void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data) override {
nb_data_per_elem = nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the ElementTypeMapArray embedded in the field
const field_type & field;
/// total number of elements
UInt nb_total_element;
/// the spatial dimension of the problem
UInt spatial_dimension;
/// whether this is a ghost field or not (for type selection)
GhostType ghost_type;
/// The element kind to operate on
ElementKind element_kind;
/// The number of data per element type
ElementTypeMap<UInt> nb_data_per_elem;
};
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "dumper_generic_elemental_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_generic_elemental_field_tmpl.hh b/src/io/dumper/dumper_generic_elemental_field_tmpl.hh
index a8d7660f1..3ac648b7b 100644
--- a/src/io/dumper/dumper_generic_elemental_field_tmpl.hh
+++ b/src/io/dumper/dumper_generic_elemental_field_tmpl.hh
@@ -1,71 +1,73 @@
/**
* @file dumper_generic_elemental_field_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the template functions of the ElementalField
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_generic_elemental_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* ------------------------------------------------------------------------ */
template <class types, template <class> class iterator>
void GenericElementalField<types, iterator>::checkHomogeneity() {
auto types =
field.elementTypes(spatial_dimension, ghost_type, element_kind);
auto tit = types.begin();
auto end = types.end();
this->nb_total_element = 0;
UInt nb_comp = 0;
bool homogen = true;
if (tit != end) {
nb_comp = this->field(*tit, ghost_type).getNbComponent();
for (; tit != end; ++tit) {
const auto & vect = this->field(*tit, ghost_type);
auto nb_element = vect.size();
auto nb_comp_cur = vect.getNbComponent();
- if (homogen && nb_comp != nb_comp_cur)
+ if (homogen && nb_comp != nb_comp_cur) {
homogen = false;
+ }
this->nb_total_element += nb_element;
// this->nb_data_per_elem(*tit,this->ghost_type) = nb_comp_cur;
}
- if (!homogen)
+ if (!homogen) {
nb_comp = 0;
+ }
}
this->homogeneous = homogen;
}
/* --------------------------------------------------------------------------
*/
} // namespace dumpers
} // namespace akantu
diff --git a/src/io/dumper/dumper_homogenizing_field.hh b/src/io/dumper/dumper_homogenizing_field.hh
index ce062acdb..96395e2b1 100644
--- a/src/io/dumper/dumper_homogenizing_field.hh
+++ b/src/io/dumper/dumper_homogenizing_field.hh
@@ -1,201 +1,204 @@
/**
* @file dumper_homogenizing_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Wed Nov 08 2017
*
* @brief description of field homogenizing field
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__
-#define __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__
+#ifndef AKANTU_DUMPER_HOMOGENIZING_FIELD_HH_
+#define AKANTU_DUMPER_HOMOGENIZING_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_compute.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename type>
inline type
typeConverter(const type & input,
[[gnu::unused]] Vector<typename type::value_type> & res,
[[gnu::unused]] UInt nb_data) {
throw;
return input;
}
/* -------------------------------------------------------------------------- */
template <typename type>
inline Matrix<type> typeConverter(const Matrix<type> & input,
Vector<type> & res, UInt nb_data) {
Matrix<type> tmp(res.storage(), input.rows(), nb_data / input.rows());
Matrix<type> tmp2(tmp, true);
return tmp2;
}
/* -------------------------------------------------------------------------- */
template <typename type>
-inline Vector<type> typeConverter(const Vector<type> &, Vector<type> & res,
- UInt) {
+inline Vector<type> typeConverter(const Vector<type> & /*unused*/,
+ Vector<type> & res, UInt /*unused*/) {
return res;
}
/* -------------------------------------------------------------------------- */
template <typename type>
class AvgHomogenizingFunctor : public ComputeFunctor<type, type> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
using value_type = typename type::value_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
AvgHomogenizingFunctor(ElementTypeMap<UInt> & nb_datas) {
auto types = nb_datas.elementTypes();
auto tit = types.begin();
auto end = types.end();
nb_data = nb_datas(*tit);
- for (; tit != end; ++tit)
- if (nb_data != nb_datas(*tit))
+ for (; tit != end; ++tit) {
+ if (nb_data != nb_datas(*tit)) {
throw;
+ }
+ }
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
type func(const type & d, Element /*global_index*/) override {
Vector<value_type> res(this->nb_data);
- if (d.size() % this->nb_data)
+ if (d.size() % this->nb_data) {
throw;
+ }
UInt nb_to_average = d.size() / this->nb_data;
value_type * ptr = d.storage();
for (UInt i = 0; i < nb_to_average; ++i) {
Vector<value_type> tmp(ptr, this->nb_data);
res += tmp;
ptr += this->nb_data;
}
res /= nb_to_average;
return typeConverter(d, res, this->nb_data);
};
UInt getDim() override { return nb_data; };
UInt getNbComponent(UInt /*old_nb_comp*/) override { throw; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// The size of data: i.e. the size of the vector to be returned
UInt nb_data;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class HomogenizerProxy {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
HomogenizerProxy() = default;
public:
inline static std::unique_ptr<ComputeFunctorInterface>
createHomogenizer(Field & field);
template <typename T>
inline std::unique_ptr<ComputeFunctorInterface> connectToField(T * field) {
ElementTypeMap<UInt> nb_components = field->getNbComponents();
using ret_type = typename T::types::return_type;
return this->instantiateHomogenizer<ret_type>(nb_components);
}
template <typename ret_type>
inline std::unique_ptr<ComputeFunctorInterface>
instantiateHomogenizer(ElementTypeMap<UInt> & nb_components);
};
/* -------------------------------------------------------------------------- */
template <typename ret_type>
inline std::unique_ptr<ComputeFunctorInterface>
HomogenizerProxy::instantiateHomogenizer(ElementTypeMap<UInt> & nb_components) {
using Homogenizer = dumpers::AvgHomogenizingFunctor<ret_type>;
return std::make_unique<Homogenizer>(nb_components);
}
template <>
inline std::unique_ptr<ComputeFunctorInterface>
HomogenizerProxy::instantiateHomogenizer<Vector<iohelper::ElemType>>([
[gnu::unused]] ElementTypeMap<UInt> & nb_components) {
throw;
return nullptr;
}
/* -------------------------------------------------------------------------- */
/// for connection to a FieldCompute
template <typename SubFieldCompute, typename return_type>
inline std::unique_ptr<ComputeFunctorInterface>
FieldCompute<SubFieldCompute, return_type>::connect(HomogenizerProxy & proxy) {
return proxy.connectToField(this);
}
/* -------------------------------------------------------------------------- */
inline std::unique_ptr<ComputeFunctorInterface>
HomogenizerProxy::createHomogenizer(Field & field) {
HomogenizerProxy homogenizer_proxy;
return field.connect(homogenizer_proxy);
}
/* -------------------------------------------------------------------------- */
// inline ComputeFunctorInterface & createHomogenizer(Field & field){
// HomogenizerProxy::createHomogenizer(field);
// throw;
// ComputeFunctorInterface * ptr = NULL;
// return *ptr;
// }
// /* --------------------------------------------------------------------------
// */
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_HOMOGENIZING_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_internal_material_field.hh b/src/io/dumper/dumper_internal_material_field.hh
index 4b2b1fab4..8bad2ffef 100644
--- a/src/io/dumper/dumper_internal_material_field.hh
+++ b/src/io/dumper/dumper_internal_material_field.hh
@@ -1,71 +1,71 @@
/**
* @file dumper_internal_material_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief description of material internal field
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH__
-#define __AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH__
+#ifndef AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH_
+#define AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_quadrature_point_iterator.hh"
#ifdef AKANTU_IGFEM
#include "dumper_igfem_material_internal_field.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename T, bool filtered = false>
class InternalMaterialField
: public GenericElementalField<SingleType<T, Vector, filtered>,
quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using types = SingleType<T, Vector, filtered>;
using parent = GenericElementalField<types, quadrature_point_iterator>;
using field_type = typename types::field_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
InternalMaterialField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: parent(field, spatial_dimension, ghost_type, element_kind) {}
};
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_iohelper.cc b/src/io/dumper/dumper_iohelper.cc
index 692b32ea7..7aedfd549 100644
--- a/src/io/dumper/dumper_iohelper.cc
+++ b/src/io/dumper/dumper_iohelper.cc
@@ -1,313 +1,320 @@
/**
* @file dumper_iohelper.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
* @date last modification: Tue Feb 20 2018
*
* @brief implementation of DumperIOHelper
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <io_helper.hh>
#include "dumper_elemental_field.hh"
#include "dumper_filtered_connectivity.hh"
#include "dumper_iohelper.hh"
#include "dumper_nodal_field.hh"
#include "dumper_variable.hh"
#include "mesh.hh"
#if defined(AKANTU_IGFEM)
#include "dumper_igfem_connectivity.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DumperIOHelper::DumperIOHelper() = default;
/* -------------------------------------------------------------------------- */
-DumperIOHelper::~DumperIOHelper() {}
+DumperIOHelper::~DumperIOHelper() = default;
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setParallelContext(bool is_parallel) {
UInt whoami = Communicator::getStaticCommunicator().whoAmI();
UInt nb_proc = Communicator::getStaticCommunicator().getNbProc();
- if (is_parallel)
+ if (is_parallel) {
dumper->setParallelContext(whoami, nb_proc);
- else
+ } else {
dumper->setParallelContext(0, 1);
+ }
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setDirectory(const std::string & directory) {
this->directory = directory;
dumper->setPrefix(directory);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setBaseName(const std::string & basename) {
filename = basename;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setTimeStep(Real time_step) {
- if (!time_activated)
+ if (!time_activated) {
this->dumper->activateTimeDescFiles(time_step);
- else
+ } else {
this->dumper->setTimeStep(time_step);
+ }
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump() {
try {
dumper->dump(filename, count);
} catch (iohelper::IOHelperException & e) {
AKANTU_ERROR(
"I was not able to dump your data with a Dumper: " << e.what());
}
++count;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump(UInt step) {
this->count = step;
this->dump();
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump(Real current_time, UInt step) {
this->dumper->setCurrentTime(current_time);
this->dump(step);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerMesh(const Mesh & mesh, UInt spatial_dimension,
- const GhostType & ghost_type,
- const ElementKind & element_kind) {
+ GhostType ghost_type,
+ ElementKind element_kind) {
#if defined(AKANTU_IGFEM)
if (element_kind == _ek_igfem) {
registerField("connectivities",
new dumpers::IGFEMConnectivityField(
mesh.getConnectivities(), spatial_dimension, ghost_type));
} else
#endif
registerField("connectivities",
std::make_shared<dumpers::ElementalField<UInt>>(
mesh.getConnectivities(), spatial_dimension, ghost_type,
element_kind));
registerField("positions",
std::make_shared<dumpers::NodalField<Real>>(mesh.getNodes()));
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
- const GhostType & ghost_type, const ElementKind & element_kind) {
+ GhostType ghost_type, ElementKind element_kind) {
auto * f_connectivities = new ElementTypeMapArrayFilter<UInt>(
mesh.getConnectivities(), elements_filter);
this->registerField("connectivities",
std::make_shared<dumpers::FilteredConnectivityField>(
*f_connectivities, nodes_filter, spatial_dimension,
ghost_type, element_kind));
this->registerField("positions",
std::make_shared<dumpers::NodalField<Real, true>>(
mesh.getNodes(), 0, 0, &nodes_filter));
}
/* -------------------------------------------------------------------------- */
-void DumperIOHelper::registerField(const std::string & field_id,
- std::shared_ptr<dumpers::Field> field) {
+void DumperIOHelper::registerField(
+ const std::string & field_id,
+ std::shared_ptr<dumpers::Field>
+ field) // NOLINT(performance-unnecessary-value-param)
+{
auto it = fields.find(field_id);
if (it != fields.end()) {
AKANTU_DEBUG_WARNING(
"The field "
<< field_id << " is already registered in this Dumper. Field ignored.");
return;
}
fields[field_id] = field;
field->registerToDumper(field_id, *dumper);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::unRegisterField(const std::string & field_id) {
auto it = fields.find(field_id);
if (it == fields.end()) {
AKANTU_DEBUG_WARNING(
"The field " << field_id
<< " is not registered in this Dumper. Nothing to do.");
return;
}
fields.erase(it);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerVariable(
const std::string & variable_id,
- std::shared_ptr<dumpers::VariableBase> variable) {
+ std::shared_ptr<dumpers::VariableBase>
+ variable) // NOLINT(performance-unnecessary-value-param)
+{
auto it = variables.find(variable_id);
if (it != variables.end()) {
AKANTU_DEBUG_WARNING(
"The Variable "
<< variable_id
<< " is already registered in this Dumper. Variable ignored.");
return;
}
variables[variable_id] = variable;
variable->registerToDumper(variable_id, *dumper);
-}
+} // namespace akantu
/* -------------------------------------------------------------------------- */
void DumperIOHelper::unRegisterVariable(const std::string & variable_id) {
auto it = variables.find(variable_id);
if (it == variables.end()) {
AKANTU_DEBUG_WARNING(
"The variable " << variable_id
<< " is not registered in this Dumper. Nothing to do.");
return;
}
variables.erase(it);
}
/* -------------------------------------------------------------------------- */
template <ElementType type> iohelper::ElemType getIOHelperType() {
AKANTU_TO_IMPLEMENT();
return iohelper::MAX_ELEM_TYPE;
}
template <> iohelper::ElemType getIOHelperType<_point_1>() {
return iohelper::POINT_SET;
}
template <> iohelper::ElemType getIOHelperType<_segment_2>() {
return iohelper::LINE1;
}
template <> iohelper::ElemType getIOHelperType<_segment_3>() {
return iohelper::LINE2;
}
template <> iohelper::ElemType getIOHelperType<_triangle_3>() {
return iohelper::TRIANGLE1;
}
template <> iohelper::ElemType getIOHelperType<_triangle_6>() {
return iohelper::TRIANGLE2;
}
template <> iohelper::ElemType getIOHelperType<_quadrangle_4>() {
return iohelper::QUAD1;
}
template <> iohelper::ElemType getIOHelperType<_quadrangle_8>() {
return iohelper::QUAD2;
}
template <> iohelper::ElemType getIOHelperType<_tetrahedron_4>() {
return iohelper::TETRA1;
}
template <> iohelper::ElemType getIOHelperType<_tetrahedron_10>() {
return iohelper::TETRA2;
}
template <> iohelper::ElemType getIOHelperType<_hexahedron_8>() {
return iohelper::HEX1;
}
template <> iohelper::ElemType getIOHelperType<_hexahedron_20>() {
return iohelper::HEX2;
}
template <> iohelper::ElemType getIOHelperType<_pentahedron_6>() {
return iohelper::PRISM1;
}
template <> iohelper::ElemType getIOHelperType<_pentahedron_15>() {
return iohelper::PRISM2;
}
#if defined(AKANTU_COHESIVE_ELEMENT)
template <> iohelper::ElemType getIOHelperType<_cohesive_1d_2>() {
return iohelper::COH1D2;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_2d_4>() {
return iohelper::COH2D4;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_2d_6>() {
return iohelper::COH2D6;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_3d_6>() {
return iohelper::COH3D6;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_3d_12>() {
return iohelper::COH3D12;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_3d_8>() {
return iohelper::COH3D8;
}
// template <>
// iohelper::ElemType getIOHelperType<_cohesive_3d_16>() { return
// iohelper::COH3D16; }
#endif
#if defined(AKANTU_STRUCTURAL_MECHANICS)
template <> iohelper::ElemType getIOHelperType<_bernoulli_beam_2>() {
return iohelper::BEAM2;
}
template <> iohelper::ElemType getIOHelperType<_bernoulli_beam_3>() {
return iohelper::BEAM3;
}
#endif
/* -------------------------------------------------------------------------- */
UInt getIOHelperType(ElementType type) {
UInt ioh_type = iohelper::MAX_ELEM_TYPE;
#define GET_IOHELPER_TYPE(type) ioh_type = getIOHelperType<type>();
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_IOHELPER_TYPE);
#undef GET_IOHELPER_TYPE
return ioh_type;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
namespace iohelper {
template <> DataType getDataType<akantu::NodeFlag>() {
return getDataType<std::underlying_type_t<akantu::NodeFlag>>();
}
} // namespace iohelper
diff --git a/src/io/dumper/dumper_iohelper.hh b/src/io/dumper/dumper_iohelper.hh
index 3a3c4a75f..8404ff193 100644
--- a/src/io/dumper/dumper_iohelper.hh
+++ b/src/io/dumper/dumper_iohelper.hh
@@ -1,160 +1,160 @@
/**
* @file dumper_iohelper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
* @date last modification: Sun Dec 03 2017
*
* @brief Define the akantu dumper interface for IOhelper dumpers
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_types.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DUMPER_IOHELPER_HH__
-#define __AKANTU_DUMPER_IOHELPER_HH__
+#ifndef AKANTU_DUMPER_IOHELPER_HH_
+#define AKANTU_DUMPER_IOHELPER_HH_
/* -------------------------------------------------------------------------- */
namespace iohelper {
class Dumper;
}
namespace akantu {
UInt getIOHelperType(ElementType type);
namespace dumpers {
class Field;
class VariableBase;
} // namespace dumper
class Mesh;
class DumperIOHelper : public std::enable_shared_from_this<DumperIOHelper> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper();
virtual ~DumperIOHelper();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register a given Mesh for the current dumper
virtual void registerMesh(const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
/// register a filtered Mesh (provided filter lists) for the current dumper
virtual void
registerFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
/// register a Field object identified by name and provided by pointer
void registerField(const std::string & field_id,
std::shared_ptr<dumpers::Field> field);
/// remove the Field identified by name from managed fields
void unRegisterField(const std::string & field_id);
/// register a VariableBase object identified by name and provided by pointer
void registerVariable(const std::string & variable_id,
std::shared_ptr<dumpers::VariableBase> variable);
/// remove a VariableBase identified by name from managed fields
void unRegisterVariable(const std::string & variable_id);
/// request dump: this calls IOHelper dump routine
virtual void dump();
/// request dump: this first set the current step and then calls IOHelper dump
/// routine
virtual void dump(UInt step);
/// request dump: this first set the current step and current time and then
/// calls IOHelper dump routine
virtual void dump(Real current_time, UInt step);
/// set the parallel context for IOHeper
virtual void setParallelContext(bool is_parallel);
/// set the directory where to generate the dumped files
virtual void setDirectory(const std::string & directory);
/// set the base name (needed by most IOHelper dumpers)
virtual void setBaseName(const std::string & basename);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// direct access to the iohelper::Dumper object
AKANTU_GET_MACRO(Dumper, *dumper, iohelper::Dumper &)
/// set the timestep of the iohelper::Dumper
void setTimeStep(Real time_step);
public:
/* ------------------------------------------------------------------------ */
/* Variable wrapper */
template <typename T, bool is_scal = std::is_arithmetic<T>::value>
class Variable;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// internal iohelper::Dumper
std::unique_ptr<iohelper::Dumper> dumper;
using Fields = std::map<std::string, std::shared_ptr<dumpers::Field>>;
using Variables =
std::map<std::string, std::shared_ptr<dumpers::VariableBase>>;
/// list of registered fields to dump
Fields fields;
Variables variables;
/// dump counter
UInt count{0};
/// directory name
std::string directory;
/// filename prefix
std::string filename;
/// is time tracking activated in the dumper
bool time_activated{false};
};
} // namespace akantu
-#endif /* __AKANTU_DUMPER_IOHELPER_HH__ */
+#endif /* AKANTU_DUMPER_IOHELPER_HH_ */
diff --git a/src/io/dumper/dumper_iohelper_paraview.cc b/src/io/dumper/dumper_iohelper_paraview.cc
index b70ab6186..7cdcc76f0 100644
--- a/src/io/dumper/dumper_iohelper_paraview.cc
+++ b/src/io/dumper/dumper_iohelper_paraview.cc
@@ -1,64 +1,64 @@
/**
* @file dumper_iohelper_paraview.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
* @date last modification: Mon Jan 22 2018
*
* @brief implementations of DumperParaview
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper_paraview.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
DumperParaview::DumperParaview(const std::string & filename,
const std::string & directory, bool parallel)
- : DumperIOHelper() {
+ {
dumper = std::make_unique<iohelper::DumperParaview>();
setBaseName(filename);
this->setParallelContext(parallel);
dumper->setMode(iohelper::BASE64);
dumper->setPrefix(directory);
dumper->init();
}
/* -------------------------------------------------------------------------- */
DumperParaview::~DumperParaview() = default;
/* -------------------------------------------------------------------------- */
void DumperParaview::setBaseName(const std::string & basename) {
DumperIOHelper::setBaseName(basename);
static_cast<iohelper::DumperParaview *>(dumper.get())
->setVTUSubDirectory(filename + "-VTU");
}
} // namespace akantu
diff --git a/src/io/dumper/dumper_iohelper_paraview.hh b/src/io/dumper/dumper_iohelper_paraview.hh
index cf1075e52..67f9b9ee2 100644
--- a/src/io/dumper/dumper_iohelper_paraview.hh
+++ b/src/io/dumper/dumper_iohelper_paraview.hh
@@ -1,70 +1,70 @@
/**
* @file dumper_iohelper_paraview.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jan 22 2018
*
* @brief Dumper Paraview using IOHelper
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DUMPER_PARAVIEW_HH__
-#define __AKANTU_DUMPER_PARAVIEW_HH__
+#ifndef AKANTU_DUMPER_PARAVIEW_HH_
+#define AKANTU_DUMPER_PARAVIEW_HH_
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class DumperParaview : public DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperParaview(const std::string & filename,
const std::string & directory = "./paraview",
bool parallel = true);
~DumperParaview() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
// void dump();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
void setBaseName(const std::string & basename) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
-#endif /* __AKANTU_DUMPER_PARAVIEW_HH__ */
+#endif /* AKANTU_DUMPER_PARAVIEW_HH_ */
diff --git a/src/io/dumper/dumper_material_padders.hh b/src/io/dumper/dumper_material_padders.hh
index e33ca1af0..b40d2df1b 100644
--- a/src/io/dumper/dumper_material_padders.hh
+++ b/src/io/dumper/dumper_material_padders.hh
@@ -1,288 +1,320 @@
/**
* @file dumper_material_padders.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Wed Nov 29 2017
*
* @brief Material padders for plane stress/ plane strain
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_MATERIAL_PADDERS_HH__
-#define __AKANTU_DUMPER_MATERIAL_PADDERS_HH__
+#ifndef AKANTU_DUMPER_MATERIAL_PADDERS_HH_
+#define AKANTU_DUMPER_MATERIAL_PADDERS_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_padding_helper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
-/* -------------------------------------------------------------------------- */
-class MaterialFunctor {
- /* ------------------------------------------------------------------------ */
- /* Constructors/Destructors */
- /* ------------------------------------------------------------------------ */
-public:
- MaterialFunctor(const SolidMechanicsModel & model)
- : model(model), material_index(model.getMaterialByElement()),
- nb_data_per_element("nb_data_per_element", model.getID(),
- model.getMemoryID()),
- spatial_dimension(model.getSpatialDimension()) {}
-
- /* ------------------------------------------------------------------------ */
- /* Methods */
- /* ------------------------------------------------------------------------ */
- /// return the material from the global element index
- const Material & getMaterialFromGlobalIndex(Element global_index) {
- UInt index = global_index.element;
- UInt material_id = material_index(global_index.type)(index);
- const Material & material = model.getMaterial(material_id);
- return material;
- }
-
- /// return the type of the element from global index
- ElementType getElementTypeFromGlobalIndex(Element global_index) {
- return global_index.type;
- }
-
-protected:
- /* ------------------------------------------------------------------------ */
- /* Class Members */
- /* ------------------------------------------------------------------------ */
-
- /// all material padders probably need access to solid mechanics model
- const SolidMechanicsModel & model;
-
- /// they also need an access to the map from global ids to material id and
- /// local ids
- const ElementTypeMapArray<UInt> & material_index;
-
- /// the number of data per element
- const ElementTypeMapArray<UInt> nb_data_per_element;
-
- UInt spatial_dimension;
-};
+ /* --------------------------------------------------------------------------
+ */
+ class MaterialFunctor {
+ /* ------------------------------------------------------------------------
+ */
+ /* Constructors/Destructors */
+ /* ------------------------------------------------------------------------
+ */
+ public:
+ MaterialFunctor(const SolidMechanicsModel & model)
+ : model(model), material_index(model.getMaterialByElement()),
+ nb_data_per_element("nb_data_per_element", model.getID(),
+ model.getMemoryID()),
+ spatial_dimension(model.getSpatialDimension()) {}
+
+ /* ------------------------------------------------------------------------
+ */
+ /* Methods */
+ /* ------------------------------------------------------------------------
+ */
+ /// return the material from the global element index
+ const Material & getMaterialFromGlobalIndex(Element global_index) {
+ UInt index = global_index.element;
+ UInt material_id = material_index(global_index.type)(index);
+ const Material & material = model.getMaterial(material_id);
+ return material;
+ }
-/* -------------------------------------------------------------------------- */
-template <class T, class R>
-class MaterialPadder : public MaterialFunctor,
- public PadderGeneric<Vector<T>, R> {
-public:
- MaterialPadder(const SolidMechanicsModel & model) : MaterialFunctor(model) {}
-};
+ /// return the type of the element from global index
+ ElementType
+ getElementTypeFromGlobalIndex( // NOLINT(readability-convert-member-functions-to-static)
+ Element global_index) {
+ return global_index.type;
+ }
-/* -------------------------------------------------------------------------- */
+ protected:
+ /* ------------------------------------------------------------------------
+ */
+ /* Class Members */
+ /* ------------------------------------------------------------------------
+ */
+
+ /// all material padders probably need access to solid mechanics model
+ const SolidMechanicsModel & model;
+
+ /// they also need an access to the map from global ids to material id and
+ /// local ids
+ const ElementTypeMapArray<UInt> & material_index;
+
+ /// the number of data per element
+ const ElementTypeMapArray<UInt> nb_data_per_element;
+
+ UInt spatial_dimension;
+ };
+
+ /* --------------------------------------------------------------------------
+ */
+ template <class T, class R>
+ class MaterialPadder : public MaterialFunctor,
+ public PadderGeneric<Vector<T>, R> {
+ public:
+ MaterialPadder(const SolidMechanicsModel & model)
+ : MaterialFunctor(model) {}
+ };
+
+ /* --------------------------------------------------------------------------
+ */
+
+ template <UInt spatial_dimension>
+ class StressPadder : public MaterialPadder<Real, Matrix<Real>> {
+
+ public:
+ StressPadder(const SolidMechanicsModel & model)
+ : MaterialPadder<Real, Matrix<Real>>(model) {
+ this->setPadding(3, 3);
+ }
-template <UInt spatial_dimension>
-class StressPadder : public MaterialPadder<Real, Matrix<Real>> {
-
-public:
- StressPadder(const SolidMechanicsModel & model)
- : MaterialPadder<Real, Matrix<Real>>(model) {
- this->setPadding(3, 3);
- }
-
- inline Matrix<Real> func(const Vector<Real> & in,
- Element global_element_id) override {
- UInt nrows = spatial_dimension;
- UInt ncols = in.size() / nrows;
- UInt nb_data = in.size() / (nrows * nrows);
-
- Matrix<Real> stress = this->pad(in, nrows, ncols, nb_data);
- const Material & material =
- this->getMaterialFromGlobalIndex(global_element_id);
- bool plane_strain = true;
- if (spatial_dimension == 2)
- plane_strain = !((bool)material.getParam("Plane_Stress"));
-
- if (plane_strain) {
- Real nu = material.getParam("nu");
- for (UInt d = 0; d < nb_data; ++d) {
- stress(2, 2 + 3 * d) =
- nu * (stress(0, 0 + 3 * d) + stress(1, 1 + 3 * d));
+ inline Matrix<Real> func(const Vector<Real> & in,
+ Element global_element_id) override {
+ UInt nrows = spatial_dimension;
+ UInt ncols = in.size() / nrows;
+ UInt nb_data = in.size() / (nrows * nrows);
+
+ Matrix<Real> stress = this->pad(in, nrows, ncols, nb_data);
+ const Material & material =
+ this->getMaterialFromGlobalIndex(global_element_id);
+ bool plane_strain = true;
+ if (spatial_dimension == 2) {
+ plane_strain = !((bool)material.getParam("Plane_Stress"));
}
- }
- return stress;
- }
- UInt getDim() override { return 9; };
+ if (plane_strain) {
+ Real nu = material.getParam("nu");
+ for (UInt d = 0; d < nb_data; ++d) {
+ stress(2, 2 + 3 * d) =
+ nu * (stress(0, 0 + 3 * d) + stress(1, 1 + 3 * d));
+ }
+ }
+ return stress;
+ }
- UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
-};
+ UInt getDim() override { return 9; };
+
+ UInt getNbComponent(UInt /*old_nb_comp*/) override {
+ return this->getDim();
+ };
+ };
+
+ /* --------------------------------------------------------------------------
+ */
+ template <UInt spatial_dimension>
+ class StrainPadder : public MaterialFunctor,
+ public PadderGeneric<Matrix<Real>, Matrix<Real>> {
+ public:
+ StrainPadder(const SolidMechanicsModel & model) : MaterialFunctor(model) {
+ this->setPadding(3, 3);
+ }
-/* -------------------------------------------------------------------------- */
-template <UInt spatial_dimension>
-class StrainPadder : public MaterialFunctor,
- public PadderGeneric<Matrix<Real>, Matrix<Real>> {
-public:
- StrainPadder(const SolidMechanicsModel & model) : MaterialFunctor(model) {
- this->setPadding(3, 3);
- }
-
- inline Matrix<Real> func(const Matrix<Real> & in,
- Element global_element_id) override {
- UInt nrows = spatial_dimension;
- UInt nb_data = in.size() / (nrows * nrows);
-
- Matrix<Real> strain = this->pad(in, nb_data);
- const Material & material =
- this->getMaterialFromGlobalIndex(global_element_id);
- bool plane_stress = material.getParam("Plane_Stress");
-
- if (plane_stress) {
- Real nu = material.getParam("nu");
- for (UInt d = 0; d < nb_data; ++d) {
- strain(2, 2 + 3 * d) =
- nu / (nu - 1) * (strain(0, 0 + 3 * d) + strain(1, 1 + 3 * d));
+ inline Matrix<Real> func(const Matrix<Real> & in,
+ Element global_element_id) override {
+ UInt nrows = spatial_dimension;
+ UInt nb_data = in.size() / (nrows * nrows);
+
+ Matrix<Real> strain = this->pad(in, nb_data);
+ const Material & material =
+ this->getMaterialFromGlobalIndex(global_element_id);
+ bool plane_stress = material.getParam("Plane_Stress");
+
+ if (plane_stress) {
+ Real nu = material.getParam("nu");
+ for (UInt d = 0; d < nb_data; ++d) {
+ strain(2, 2 + 3 * d) =
+ nu / (nu - 1) * (strain(0, 0 + 3 * d) + strain(1, 1 + 3 * d));
+ }
}
+
+ return strain;
}
- return strain;
- }
+ UInt getDim() override { return 9; };
- UInt getDim() override { return 9; };
+ UInt getNbComponent(UInt /*old_nb_comp*/) override {
+ return this->getDim();
+ };
+ };
- UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
-};
+ /* --------------------------------------------------------------------------
+ */
+ template <bool green_strain>
+ class ComputeStrain : public MaterialFunctor,
+ public ComputeFunctor<Vector<Real>, Matrix<Real>> {
+ public:
+ ComputeStrain(const SolidMechanicsModel & model) : MaterialFunctor(model) {}
-/* -------------------------------------------------------------------------- */
-template <bool green_strain>
-class ComputeStrain : public MaterialFunctor,
- public ComputeFunctor<Vector<Real>, Matrix<Real>> {
-public:
- ComputeStrain(const SolidMechanicsModel & model) : MaterialFunctor(model) {}
-
- inline Matrix<Real> func(const Vector<Real> & in,
- Element /*global_element_id*/) override {
- UInt nrows = spatial_dimension;
- UInt ncols = in.size() / nrows;
- UInt nb_data = in.size() / (nrows * nrows);
-
- Matrix<Real> ret_all_strain(nrows, ncols);
- Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
- Tensor3<Real> all_strain(ret_all_strain.storage(), nrows, nrows, nb_data);
-
- for (UInt d = 0; d < nb_data; ++d) {
- Matrix<Real> grad_u = all_grad_u(d);
- Matrix<Real> strain = all_strain(d);
+ inline Matrix<Real> func(const Vector<Real> & in,
+ Element /*global_element_id*/) override {
+ UInt nrows = spatial_dimension;
+ UInt ncols = in.size() / nrows;
+ UInt nb_data = in.size() / (nrows * nrows);
- if (spatial_dimension == 2) {
- if (green_strain)
- Material::gradUToE<2>(grad_u, strain);
- else
- Material::gradUToEpsilon<2>(grad_u, strain);
- } else if (spatial_dimension == 3) {
- if (green_strain)
- Material::gradUToE<3>(grad_u, strain);
- else
- Material::gradUToEpsilon<3>(grad_u, strain);
+ Matrix<Real> ret_all_strain(nrows, ncols);
+ Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
+ Tensor3<Real> all_strain(ret_all_strain.storage(), nrows, nrows, nb_data);
+
+ for (UInt d = 0; d < nb_data; ++d) {
+ Matrix<Real> grad_u = all_grad_u(d);
+ Matrix<Real> strain = all_strain(d);
+
+ if (spatial_dimension == 2) {
+ if (green_strain) {
+ Material::gradUToE<2>(grad_u, strain);
+ } else {
+ Material::gradUToEpsilon<2>(grad_u, strain);
+ }
+ } else if (spatial_dimension == 3) {
+ if (green_strain) {
+ Material::gradUToE<3>(grad_u, strain);
+ } else {
+ Material::gradUToEpsilon<3>(grad_u, strain);
+ }
+ }
}
+
+ return ret_all_strain;
}
- return ret_all_strain;
- }
+ UInt getDim() override { return spatial_dimension * spatial_dimension; };
- UInt getDim() override { return spatial_dimension * spatial_dimension; };
+ UInt getNbComponent(UInt /*old_nb_comp*/) override {
+ return this->getDim();
+ };
+ };
- UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
-};
+ /* --------------------------------------------------------------------------
+ */
+ template <bool green_strain>
+ class ComputePrincipalStrain
+ : public MaterialFunctor,
+ public ComputeFunctor<Vector<Real>, Matrix<Real>> {
+ public:
+ ComputePrincipalStrain(const SolidMechanicsModel & model)
+ : MaterialFunctor(model) {}
-/* -------------------------------------------------------------------------- */
-template <bool green_strain>
-class ComputePrincipalStrain
- : public MaterialFunctor,
- public ComputeFunctor<Vector<Real>, Matrix<Real>> {
-public:
- ComputePrincipalStrain(const SolidMechanicsModel & model)
- : MaterialFunctor(model) {}
-
- inline Matrix<Real> func(const Vector<Real> & in,
- Element /*global_element_id*/) override {
- UInt nrows = spatial_dimension;
- UInt nb_data = in.size() / (nrows * nrows);
-
- Matrix<Real> ret_all_strain(nrows, nb_data);
- Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
- Matrix<Real> strain(nrows, nrows);
-
- for (UInt d = 0; d < nb_data; ++d) {
- Matrix<Real> grad_u = all_grad_u(d);
+ inline Matrix<Real> func(const Vector<Real> & in,
+ Element /*global_element_id*/) override {
+ UInt nrows = spatial_dimension;
+ UInt nb_data = in.size() / (nrows * nrows);
- if (spatial_dimension == 2) {
- if (green_strain)
- Material::gradUToE<2>(grad_u, strain);
- else
- Material::gradUToEpsilon<2>(grad_u, strain);
- } else if (spatial_dimension == 3) {
- if (green_strain)
- Material::gradUToE<3>(grad_u, strain);
- else
- Material::gradUToEpsilon<3>(grad_u, strain);
+ Matrix<Real> ret_all_strain(nrows, nb_data);
+ Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
+ Matrix<Real> strain(nrows, nrows);
+
+ for (UInt d = 0; d < nb_data; ++d) {
+ Matrix<Real> grad_u = all_grad_u(d);
+
+ if (spatial_dimension == 2) {
+ if (green_strain) {
+ Material::gradUToE<2>(grad_u, strain);
+ } else {
+ Material::gradUToEpsilon<2>(grad_u, strain);
+ }
+ } else if (spatial_dimension == 3) {
+ if (green_strain) {
+ Material::gradUToE<3>(grad_u, strain);
+ } else {
+ Material::gradUToEpsilon<3>(grad_u, strain);
+ }
+ }
+
+ Vector<Real> principal_strain(ret_all_strain(d));
+ strain.eig(principal_strain);
}
- Vector<Real> principal_strain(ret_all_strain(d));
- strain.eig(principal_strain);
+ return ret_all_strain;
}
- return ret_all_strain;
- }
+ UInt getDim() override { return spatial_dimension; };
- UInt getDim() override { return spatial_dimension; };
+ UInt getNbComponent(UInt /*old_nb_comp*/) override {
+ return this->getDim();
+ };
+ };
- UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
-};
+ /* --------------------------------------------------------------------------
+ */
+ class ComputeVonMisesStress
+ : public MaterialFunctor,
+ public ComputeFunctor<Vector<Real>, Vector<Real>> {
+ public:
+ ComputeVonMisesStress(const SolidMechanicsModel & model)
+ : MaterialFunctor(model) {}
-/* -------------------------------------------------------------------------- */
-class ComputeVonMisesStress
- : public MaterialFunctor,
- public ComputeFunctor<Vector<Real>, Vector<Real>> {
-public:
- ComputeVonMisesStress(const SolidMechanicsModel & model)
- : MaterialFunctor(model) {}
-
- inline Vector<Real> func(const Vector<Real> & in,
- Element /*global_element_id*/) override {
- UInt nrows = spatial_dimension;
- UInt nb_data = in.size() / (nrows * nrows);
-
- Vector<Real> von_mises_stress(nb_data);
- Matrix<Real> deviatoric_stress(3, 3);
-
- for (UInt d = 0; d < nb_data; ++d) {
- Matrix<Real> cauchy_stress(in.storage() + d * nrows * nrows, nrows,
- nrows);
- von_mises_stress(d) = Material::stressToVonMises(cauchy_stress);
- }
+ inline Vector<Real> func(const Vector<Real> & in,
+ Element /*global_element_id*/) override {
+ UInt nrows = spatial_dimension;
+ UInt nb_data = in.size() / (nrows * nrows);
+
+ Vector<Real> von_mises_stress(nb_data);
+ Matrix<Real> deviatoric_stress(3, 3);
+
+ for (UInt d = 0; d < nb_data; ++d) {
+ Matrix<Real> cauchy_stress(in.storage() + d * nrows * nrows, nrows,
+ nrows);
+ von_mises_stress(d) = Material::stressToVonMises(cauchy_stress);
+ }
- return von_mises_stress;
- }
+ return von_mises_stress;
+ }
- UInt getDim() override { return 1; };
+ UInt getDim() override { return 1; };
- UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
-};
+ UInt getNbComponent(UInt /*old_nb_comp*/) override {
+ return this->getDim();
+ };
+ };
-/* -------------------------------------------------------------------------- */
+ /* --------------------------------------------------------------------------
+ */
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_MATERIAL_PADDERS_HH__ */
+#endif /* AKANTU_DUMPER_MATERIAL_PADDERS_HH_ */
diff --git a/src/io/dumper/dumper_nodal_field.hh b/src/io/dumper/dumper_nodal_field.hh
index 0049e2631..2749754a9 100644
--- a/src/io/dumper/dumper_nodal_field.hh
+++ b/src/io/dumper/dumper_nodal_field.hh
@@ -1,241 +1,243 @@
/**
* @file dumper_nodal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
* @date last modification: Wed Nov 08 2017
*
* @brief Description of nodal fields
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_NODAL_FIELD_HH__
-#define __AKANTU_DUMPER_NODAL_FIELD_HH__
+#ifndef AKANTU_DUMPER_NODAL_FIELD_HH_
+#define AKANTU_DUMPER_NODAL_FIELD_HH_
#include "dumper_field.hh"
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
// This represents a iohelper compatible field
template <typename T, bool filtered = false, class Container = Array<T>,
class Filter = Array<UInt>>
class NodalField;
/* -------------------------------------------------------------------------- */
template <typename T, class Container, class Filter>
class NodalField<T, false, Container, Filter> : public dumpers::Field {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
/// associated iterator with any nodal field (non filetered)
class iterator : public iohelper::iterator<T, iterator, Vector<T>> {
public:
iterator(T * vect, UInt offset, UInt n, UInt stride,
__attribute__((unused)) const UInt * filter = nullptr)
:
internal_it(vect), offset(offset), n(n), stride(stride) {}
bool operator!=(const iterator & it) const override {
return internal_it != it.internal_it;
}
iterator & operator++() override {
internal_it += offset;
return *this;
};
Vector<T> operator*() override {
return Vector<T>(internal_it + stride, n);
};
private:
T * internal_it;
UInt offset, n, stride;
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
NodalField(const Container & field, UInt n = 0, UInt stride = 0,
[[gnu::unused]] const Filter * filter = nullptr)
: field(field), n(n), stride(stride), padding(0) {
AKANTU_DEBUG_ASSERT(filter == nullptr,
"Filter passed to unfiltered NodalField!");
if (n == 0) {
this->n = field.getNbComponent() - stride;
}
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addNodeDataField(id, *this);
}
inline iterator begin() {
return iterator(field.storage(), field.getNbComponent(), n, stride);
}
inline iterator end() {
return iterator(field.storage() + field.getNbComponent() * field.size(),
field.getNbComponent(), n, stride);
}
bool isHomogeneous() override { return true; }
void checkHomogeneity() override { this->homogeneous = true; }
virtual UInt getDim() {
- if (this->padding)
+ if (this->padding) {
return this->padding;
- else
+ }
return n;
+
}
void setPadding(UInt padding) { this->padding = padding; }
UInt size() { return field.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Container & field;
UInt n, stride;
UInt padding;
};
/* -------------------------------------------------------------------------- */
template <typename T, class Container, class Filter>
class NodalField<T, true, Container, Filter> : public dumpers::Field {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
class iterator : public iohelper::iterator<T, iterator, Vector<T>> {
public:
iterator(T * const vect, UInt _offset, UInt _n, UInt _stride,
const UInt * filter)
:
internal_it(vect), offset(_offset), n(_n), stride(_stride),
filter(filter) {}
bool operator!=(const iterator & it) const override {
return filter != it.filter;
}
iterator & operator++() override {
++filter;
return *this;
}
Vector<T> operator*() override {
return Vector<T>(internal_it + *(filter)*offset + stride, n);
}
private:
T * const internal_it;
UInt offset, n, stride;
const UInt * filter;
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
NodalField(const Container & _field, UInt _n = 0, UInt _stride = 0,
const Filter * filter = NULL)
: field(_field), n(_n), stride(_stride), filter(filter), padding(0) {
AKANTU_DEBUG_ASSERT(this->filter != nullptr,
"No filter passed to filtered NodalField!");
AKANTU_DEBUG_ASSERT(this->filter->getNbComponent() == 1,
"Multi-component filter given to NodalField ("
<< this->filter->getNbComponent()
<< " components detected, sould be 1");
if (n == 0) {
this->n = field.getNbComponent() - stride;
}
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addNodeDataField(id, *this);
}
inline iterator begin() {
return iterator(field.storage(), field.getNbComponent(), n, stride,
filter->storage());
}
inline iterator end() {
return iterator(field.storage(), field.getNbComponent(), n, stride,
filter->storage() + filter->size());
}
bool isHomogeneous() override { return true; }
void checkHomogeneity() override { this->homogeneous = true; }
virtual UInt getDim() {
- if (this->padding)
+ if (this->padding) {
return this->padding;
- else
+ }
return n;
+
}
void setPadding(UInt padding) { this->padding = padding; }
UInt size() { return filter->size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Container & field;
UInt n, stride;
const Filter * filter;
UInt padding;
};
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_DUMPER_NODAL_FIELD_HH__ */
+#endif /* AKANTU_DUMPER_NODAL_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_padding_helper.hh b/src/io/dumper/dumper_padding_helper.hh
index 6cd22990a..396e20d3e 100644
--- a/src/io/dumper/dumper_padding_helper.hh
+++ b/src/io/dumper/dumper_padding_helper.hh
@@ -1,131 +1,150 @@
/**
* @file dumper_padding_helper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Mon Jun 19 2017
*
* @brief Padding helper for field iterators
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_PADDING_HELPER_HH__
-#define __AKANTU_DUMPER_PADDING_HELPER_HH__
+#ifndef AKANTU_DUMPER_PADDING_HELPER_HH_
+#define AKANTU_DUMPER_PADDING_HELPER_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_compute.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
-/* -------------------------------------------------------------------------- */
-
-class PadderInterface {
-
- /* ------------------------------------------------------------------------ */
- /* Constructors/Destructors */
- /* ------------------------------------------------------------------------ */
-
-public:
- PadderInterface() {
- padding_m = 0;
- padding_n = 0;
- }
-
- /* ------------------------------------------------------------------------ */
- /* Methods */
- /* ------------------------------------------------------------------------ */
-
-public:
- void setPadding(UInt m, UInt n = 0) {
- padding_m = m;
- padding_n = n;
- }
-
- virtual UInt getPaddedDim(UInt nb_data) { return nb_data; }
-
- /* ------------------------------------------------------------------------ */
- /* Class Members */
- /* ------------------------------------------------------------------------ */
+ /* --------------------------------------------------------------------------
+ */
-public:
- /// padding informations
- UInt padding_n, padding_m;
-};
+ class PadderInterface {
-/* -------------------------------------------------------------------------- */
+ /* ------------------------------------------------------------------------
+ */
+ /* Constructors/Destructors */
+ /* ------------------------------------------------------------------------
+ */
-template <class input_type, class output_type>
-class PadderGeneric : public ComputeFunctor<input_type, output_type>,
- public PadderInterface {
+ public:
+ PadderInterface() {
+ padding_m = 0;
+ padding_n = 0;
+ }
- /* ------------------------------------------------------------------------ */
- /* Constructors/Destructors */
- /* ------------------------------------------------------------------------ */
+ /* ------------------------------------------------------------------------
+ */
+ /* Methods */
+ /* ------------------------------------------------------------------------
+ */
-public:
- PadderGeneric() : PadderInterface() {}
+ public:
+ void setPadding(UInt m, UInt n = 0) {
+ padding_m = m;
+ padding_n = n;
+ }
- /* ------------------------------------------------------------------------ */
- /* Methods */
- /* ------------------------------------------------------------------------ */
+ virtual UInt getPaddedDim(UInt nb_data) { return nb_data; }
+
+ /* ------------------------------------------------------------------------
+ */
+ /* Class Members */
+ /* ------------------------------------------------------------------------
+ */
+
+ public:
+ /// padding informations
+ UInt padding_n, padding_m;
+ };
+
+ /* --------------------------------------------------------------------------
+ */
+
+ template <class input_type, class output_type>
+ class PadderGeneric : public ComputeFunctor<input_type, output_type>,
+ public PadderInterface {
+
+ /* ------------------------------------------------------------------------
+ */
+ /* Constructors/Destructors */
+ /* ------------------------------------------------------------------------
+ */
+
+ public:
+ PadderGeneric() : PadderInterface() {}
+
+ /* ------------------------------------------------------------------------
+ */
+ /* Methods */
+ /* ------------------------------------------------------------------------
+ */
+
+ public:
+ inline output_type pad(const input_type & in,
+ __attribute__((unused)) UInt nb_data) {
+ return in; // trick due to the fact that IOHelper padds the vectors (avoid
+ // a copy of data)
+ }
+ };
+ /* --------------------------------------------------------------------------
+ */
-public:
- inline output_type pad(const input_type & in,
- __attribute__((unused)) UInt nb_data) {
- return in; // trick due to the fact that IOHelper padds the vectors (avoid a
- // copy of data)
- }
-};
-/* -------------------------------------------------------------------------- */
+ template <class T>
+ class PadderGeneric<Vector<T>, Matrix<T>>
+ : public ComputeFunctor<Vector<T>, Matrix<T>>, public PadderInterface {
-template <class T>
-class PadderGeneric<Vector<T>, Matrix<T>>
- : public ComputeFunctor<Vector<T>, Matrix<T>>, public PadderInterface {
+ /* ------------------------------------------------------------------------
+ */
+ /* Constructors/Destructors */
+ /* ------------------------------------------------------------------------
+ */
- /* ------------------------------------------------------------------------ */
- /* Constructors/Destructors */
- /* ------------------------------------------------------------------------ */
+ public:
+ inline Matrix<T> pad(const Vector<T> & _in, UInt nrows, UInt ncols,
+ UInt nb_data) {
+ Matrix<T> in(_in.storage(), nrows, ncols);
-public:
- inline Matrix<T> pad(const Vector<T> & _in, UInt nrows, UInt ncols,
- UInt nb_data) {
- Matrix<T> in(_in.storage(), nrows, ncols);
+ if (padding_m <= nrows && padding_n * nb_data <= ncols) {
+ return in;
+ }
- if (padding_m <= nrows && padding_n * nb_data <= ncols)
- return in;
- else {
Matrix<T> ret(padding_m, padding_n * nb_data);
UInt nb_cols_per_data = in.cols() / nb_data;
- for (UInt d = 0; d < nb_data; ++d)
- for (UInt i = 0; i < in.rows(); ++i)
- for (UInt j = 0; j < nb_cols_per_data; ++j)
+ for (UInt d = 0; d < nb_data; ++d) {
+ for (UInt i = 0; i < in.rows(); ++i) {
+ for (UInt j = 0; j < nb_cols_per_data; ++j) {
ret(i, j + d * padding_n) = in(i, j + d * nb_cols_per_data);
+ }
+ }
+ }
return ret;
}
- }
-};
+ };
-/* -------------------------------------------------------------------------- */
+ /* --------------------------------------------------------------------------
+ */
-} // namespace akantu
} // namespace dumpers
+} // namespace akantu
-#endif /* __AKANTU_DUMPER_PADDING_HELPER_HH__ */
+#endif /* AKANTU_DUMPER_PADDING_HELPER_HH_ */
diff --git a/src/io/dumper/dumper_quadrature_point_iterator.hh b/src/io/dumper/dumper_quadrature_point_iterator.hh
index e00824c91..2356d5c2a 100644
--- a/src/io/dumper/dumper_quadrature_point_iterator.hh
+++ b/src/io/dumper/dumper_quadrature_point_iterator.hh
@@ -1,73 +1,73 @@
/**
* @file dumper_quadrature_point_iterator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Description of quadrature point iterator
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH__
-#define __AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH__
+#ifndef AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH_
+#define AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_elemental_field.hh"
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename types>
class quadrature_point_iterator
: public element_iterator<types, quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using parent = element_iterator<types, dumpers::quadrature_point_iterator>;
using data_type = typename types::data_type;
using return_type = typename types::return_type;
using field_type = typename types::field_type;
using array_iterator = typename types::array_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
quadrature_point_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
return_type operator*() { return *this->array_it; }
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
-#endif /* __AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH__ */
+#endif /* AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH_ */
diff --git a/src/io/dumper/dumper_text.cc b/src/io/dumper/dumper_text.cc
index 8b542bfc5..7c6022b39 100644
--- a/src/io/dumper/dumper_text.cc
+++ b/src/io/dumper/dumper_text.cc
@@ -1,112 +1,110 @@
/**
* @file dumper_text.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Nov 07 2017
*
* @brief implementation of text dumper
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_text.hh"
#include "communicator.hh"
#include "dumper_nodal_field.hh"
#include "mesh.hh"
#include <io_helper.hh>
namespace akantu {
/* -------------------------------------------------------------------------- */
DumperText::DumperText(const std::string & basename,
- iohelper::TextDumpMode mode, bool parallel)
- : DumperIOHelper() {
+ iohelper::TextDumpMode mode, bool parallel) {
AKANTU_DEBUG_IN();
this->dumper = std::make_unique<iohelper::DumperText>(mode);
this->setBaseName(basename);
this->setParallelContext(parallel);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DumperText::registerMesh(const Mesh & mesh,
__attribute__((unused)) UInt spatial_dimension,
+ __attribute__((unused)) GhostType ghost_type,
__attribute__((unused))
- const GhostType & ghost_type,
- __attribute__((unused))
- const ElementKind & element_kind) {
+ ElementKind element_kind) {
registerField("position",
std::make_shared<dumpers::NodalField<Real>>(mesh.getNodes()));
// in parallel we need node type
UInt nb_proc = mesh.getCommunicator().getNbProc();
if (nb_proc > 1) {
registerField("nodes_type", std::make_shared<dumpers::NodalField<NodeFlag>>(
mesh.getNodesFlags()));
}
}
/* -------------------------------------------------------------------------- */
void DumperText::registerFilteredMesh(
const Mesh & mesh,
__attribute__((unused)) const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
__attribute__((unused)) UInt spatial_dimension,
- __attribute__((unused)) const GhostType & ghost_type,
- __attribute__((unused)) const ElementKind & element_kind) {
+ __attribute__((unused)) GhostType ghost_type,
+ __attribute__((unused)) ElementKind element_kind) {
registerField("position", std::make_shared<dumpers::NodalField<Real, true>>(
mesh.getNodes(), 0, 0, &nodes_filter));
// in parallel we need node type
UInt nb_proc = mesh.getCommunicator().getNbProc();
if (nb_proc > 1) {
registerField("nodes_type",
std::make_shared<dumpers::NodalField<NodeFlag, true>>(
mesh.getNodesFlags(), 0, 0, &nodes_filter));
}
}
/* -------------------------------------------------------------------------- */
void DumperText::setBaseName(const std::string & basename) {
AKANTU_DEBUG_IN();
DumperIOHelper::setBaseName(basename);
static_cast<iohelper::DumperText *>(this->dumper.get())
->setDataSubDirectory(this->filename + "-DataFiles");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DumperText::setPrecision(UInt prec) {
AKANTU_DEBUG_IN();
static_cast<iohelper::DumperText *>(this->dumper.get())->setPrecision(prec);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/io/dumper/dumper_text.hh b/src/io/dumper/dumper_text.hh
index b1d19a604..efdb4e1db 100644
--- a/src/io/dumper/dumper_text.hh
+++ b/src/io/dumper/dumper_text.hh
@@ -1,86 +1,86 @@
/**
* @file dumper_text.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief to dump into a text file
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DUMPER_TEXT_HH__
-#define __AKANTU_DUMPER_TEXT_HH__
+#ifndef AKANTU_DUMPER_TEXT_HH_
+#define AKANTU_DUMPER_TEXT_HH_
/* -------------------------------------------------------------------------- */
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DumperText : public DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperText(const std::string & basename = "dumper_text",
iohelper::TextDumpMode mode = iohelper::_tdm_space,
bool parallel = true);
~DumperText() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void
registerMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined) override;
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined) override;
void registerFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined) override;
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined) override;
void setBaseName(const std::string & basename) override;
private:
void registerNodeTypeField();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
void setPrecision(UInt prec);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
-#endif /* __AKANTU_DUMPER_TEXT_HH__ */
+#endif /* AKANTU_DUMPER_TEXT_HH_ */
diff --git a/src/io/dumper/dumper_type_traits.hh b/src/io/dumper/dumper_type_traits.hh
index 91817194d..cb608b329 100644
--- a/src/io/dumper/dumper_type_traits.hh
+++ b/src/io/dumper/dumper_type_traits.hh
@@ -1,89 +1,89 @@
/**
* @file dumper_type_traits.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Wed Nov 08 2017
*
* @brief Type traits for field properties
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_DUMPER_TYPE_TRAITS_HH__
-#define __AKANTU_DUMPER_TYPE_TRAITS_HH__
+#ifndef AKANTU_DUMPER_TYPE_TRAITS_HH_
+#define AKANTU_DUMPER_TYPE_TRAITS_HH_
/* -------------------------------------------------------------------------- */
#include "element_type_map.hh"
#include "element_type_map_filter.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* ------------------------------------------------------------------------ */
template <class data, class ret, class field> struct TypeTraits {
//! the stored data (real, int, uint, ...)
using data_type = data;
//! the type returned by the operator *
using return_type = ret;
//! the field type (ElementTypeMap or ElementTypeMapFilter)
using field_type = field;
//! the type over which we iterate
using it_type = typename field_type::type;
//! the type of array (Array<T> or ArrayFilter<T>)
using array_type = typename field_type::array_type;
//! the iterator over the array
using array_iterator = typename array_type::const_vector_iterator;
};
/* ------------------------------------------------------------------------ */
// specialization for the case in which input and output types are the same
template <class T, template <class> class ret, bool filtered>
struct SingleType : public TypeTraits<T, ret<T>, ElementTypeMapArray<T>> {};
/* ------------------------------------------------------------------------ */
// same as before but for filtered data
template <class T, template <class> class ret>
struct SingleType<T, ret, true>
: public TypeTraits<T, ret<T>, ElementTypeMapArrayFilter<T>> {};
/* ------------------------------------------------------------------------ */
// specialization for the case in which input and output types are different
template <class it_type, class data_type, template <class> class ret,
bool filtered>
struct DualType : public TypeTraits<data_type, ret<data_type>,
ElementTypeMapArray<it_type>> {};
/* ------------------------------------------------------------------------ */
// same as before but for filtered data
template <class it_type, class data_type, template <class> class ret>
struct DualType<it_type, data_type, ret, true>
: public TypeTraits<data_type, ret<data_type>,
ElementTypeMapArrayFilter<it_type>> {};
/* ------------------------------------------------------------------------ */
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_DUMPER_TYPE_TRAITS_HH__ */
+#endif /* AKANTU_DUMPER_TYPE_TRAITS_HH_ */
diff --git a/src/io/dumper/dumper_variable.hh b/src/io/dumper/dumper_variable.hh
index f9ea3250b..49d4524fa 100644
--- a/src/io/dumper/dumper_variable.hh
+++ b/src/io/dumper/dumper_variable.hh
@@ -1,119 +1,119 @@
/**
* @file dumper_variable.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Jun 04 2013
* @date last modification: Wed Nov 08 2017
*
* @brief template of variable
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include <type_traits>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH__
-#define __AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH__
+#ifndef AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH_
+#define AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* --------------------------------------------------------------------------
*/
/// Variable interface
class VariableBase {
public:
VariableBase() = default;
virtual ~VariableBase() = default;
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) = 0;
};
/* --------------------------------------------------------------------------
*/
template <typename T, bool is_scal = std::is_arithmetic<T>::value>
class Variable : public VariableBase {
public:
Variable(const T & t) : vari(t) {}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addVariable(id, *this);
}
const T & operator[](UInt i) const { return vari[i]; }
UInt getDim() { return vari.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const T & vari;
};
/* --------------------------------------------------------------------------
*/
template <typename T> class Variable<Vector<T>, false> : public VariableBase {
public:
Variable(const Vector<T> & t) : vari(t) {}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addVariable(id, *this);
}
const T & operator[](UInt i) const { return vari[i]; }
UInt getDim() { return vari.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const Vector<T> & vari;
};
/* --------------------------------------------------------------------------
*/
template <typename T> class Variable<T, true> : public VariableBase {
public:
Variable(const T & t) : vari(t) {}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addVariable(id, *this);
}
const T & operator[](__attribute__((unused)) UInt i) const { return vari; }
UInt getDim() { return 1; }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const T & vari;
};
} // namespace dumper
} // namespace akantu
-#endif /* __AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH__ */
+#endif /* AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH_ */
diff --git a/src/io/mesh_io.cc b/src/io/mesh_io.cc
index 5008b168d..001575922 100644
--- a/src/io/mesh_io.cc
+++ b/src/io/mesh_io.cc
@@ -1,138 +1,139 @@
/**
* @file mesh_io.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Feb 01 2018
*
* @brief common part for all mesh io classes
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
#include "aka_common.hh"
#include "aka_iterators.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIO::MeshIO() {
canReadSurface = false;
canReadExtendedData = false;
}
/* -------------------------------------------------------------------------- */
MeshIO::~MeshIO() = default;
/* -------------------------------------------------------------------------- */
std::unique_ptr<MeshIO> MeshIO::getMeshIO(const std::string & filename,
const MeshIOType & type) {
MeshIOType t = type;
if (type == _miot_auto) {
std::string::size_type idx = filename.rfind('.');
std::string ext;
if (idx != std::string::npos) {
ext = filename.substr(idx + 1);
}
if (ext == "msh") {
t = _miot_gmsh;
} else if (ext == "diana") {
t = _miot_diana;
- } else
+ } else {
AKANTU_EXCEPTION("Cannot guess the type of file of "
<< filename << " (ext " << ext << "). "
<< "Please provide the MeshIOType to the read function");
+ }
}
switch (t) {
case _miot_gmsh:
return std::make_unique<MeshIOMSH>();
#if defined(AKANTU_STRUCTURAL_MECHANICS)
case _miot_gmsh_struct:
return std::make_unique<MeshIOMSHStruct>();
#endif
case _miot_diana:
return std::make_unique<MeshIODiana>();
default:
return nullptr;
}
}
/* -------------------------------------------------------------------------- */
void MeshIO::read(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
std::unique_ptr<MeshIO> mesh_io = getMeshIO(filename, type);
mesh_io->read(filename, mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIO::write(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
std::unique_ptr<MeshIO> mesh_io = getMeshIO(filename, type);
mesh_io->write(filename, mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIO::constructPhysicalNames(const std::string & tag_name, Mesh & mesh) {
- if (!physical_names.empty()) {
+ if (not physical_names.empty()) {
for (auto type : mesh.elementTypes()) {
auto & name_vec =
mesh.getDataPointer<std::string>("physical_names", type);
const auto & tags_vec = mesh.getData<UInt>(tag_name, type);
- for (auto pair : zip(tags_vec, name_vec)) {
+ for (auto && pair : zip(tags_vec, name_vec)) {
auto tag = std::get<0>(pair);
auto & name = std::get<1>(pair);
auto map_it = physical_names.find(tag);
if (map_it == physical_names.end()) {
std::stringstream sstm;
sstm << tag;
name = sstm.str();
} else {
name = map_it->second;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void MeshIO::printself(std::ostream & stream, int indent) const {
- std::string space(AKANTU_INDENT, indent);
+ std::string space(indent, AKANTU_INDENT);
- if (physical_names.size()) {
+ if (not physical_names.empty()) {
stream << space << "Physical map:" << std::endl;
- for (auto & pair : physical_names) {
+ for (const auto & pair : physical_names) {
stream << space << pair.first << ": " << pair.second << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/mesh_io.hh b/src/io/mesh_io.hh
index d7146ad65..b0de9ca2d 100644
--- a/src/io/mesh_io.hh
+++ b/src/io/mesh_io.hh
@@ -1,115 +1,113 @@
/**
* @file mesh_io.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Aug 09 2017
*
* @brief interface of a mesh io class, reader and writer
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_IO_HH__
-#define __AKANTU_MESH_IO_HH__
+#ifndef AKANTU_MESH_IO_HH_
+#define AKANTU_MESH_IO_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIO();
virtual ~MeshIO();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
- void read(const std::string & filename, Mesh & mesh, const MeshIOType & type);
- void write(const std::string & filename, Mesh & mesh,
- const MeshIOType & type);
+ static void read(const std::string & filename, Mesh & mesh,
+ const MeshIOType & type);
+ static void write(const std::string & filename, Mesh & mesh,
+ const MeshIOType & type);
/// read a mesh from the file
- virtual void read(__attribute__((unused)) const std::string & filename,
- __attribute__((unused)) Mesh & mesh) {}
+ virtual void read(const std::string & /*filename*/, Mesh & /*mesh*/) {}
/// write a mesh to a file
- virtual void write(__attribute__((unused)) const std::string & filename,
- __attribute__((unused)) const Mesh & mesh) {}
+ virtual void write(const std::string & /*filename*/, const Mesh & /*mesh*/) {}
/// function to request the manual construction of the physical names maps
virtual void constructPhysicalNames(const std::string & tag_name,
Mesh & mesh);
/// method to permit to be printed to a generic stream
virtual void printself(std::ostream & stream, int indent = 0) const;
/// static contruction of a meshio object
static std::unique_ptr<MeshIO> getMeshIO(const std::string & filename,
const MeshIOType & type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
auto & getPhysicalNames() { return this->physical_names; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
- bool canReadSurface;
-
- bool canReadExtendedData;
+ bool canReadSurface{false};
+ bool canReadExtendedData{false};
/// correspondance between a tag and physical names (if applicable)
std::map<int, std::string> physical_names;
};
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream, const MeshIO & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "mesh_io_diana.hh"
#include "mesh_io_msh.hh"
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "mesh_io_msh_struct.hh"
#endif
-#endif /* __AKANTU_MESH_IO_HH__ */
+#endif /* AKANTU_MESH_IO_HH_ */
diff --git a/src/io/mesh_io/mesh_io_diana.cc b/src/io/mesh_io/mesh_io_diana.cc
index 5f4c09a65..d2acb15a0 100644
--- a/src/io/mesh_io/mesh_io_diana.cc
+++ b/src/io/mesh_io/mesh_io_diana.cc
@@ -1,596 +1,610 @@
/**
* @file mesh_io_diana.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
*
* @date creation: Sat Mar 26 2011
* @date last modification: Tue Feb 20 2018
*
* @brief handles diana meshes
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_io_diana.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <string.h>
/* -------------------------------------------------------------------------- */
#include <stdio.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIODiana::MeshIODiana() {
canReadSurface = true;
canReadExtendedData = true;
_diana_to_akantu_element_types["T9TM"] = _triangle_3;
_diana_to_akantu_element_types["CT6CM"] = _triangle_6;
_diana_to_akantu_element_types["Q12TM"] = _quadrangle_4;
_diana_to_akantu_element_types["CQ8CM"] = _quadrangle_8;
_diana_to_akantu_element_types["TP18L"] = _pentahedron_6;
_diana_to_akantu_element_types["CTP45"] = _pentahedron_15;
_diana_to_akantu_element_types["TE12L"] = _tetrahedron_4;
_diana_to_akantu_element_types["HX24L"] = _hexahedron_8;
_diana_to_akantu_element_types["CHX60"] = _hexahedron_20;
_diana_to_akantu_mat_prop["YOUNG"] = "E";
_diana_to_akantu_mat_prop["DENSIT"] = "rho";
_diana_to_akantu_mat_prop["POISON"] = "nu";
std::map<std::string, ElementType>::iterator it;
for (it = _diana_to_akantu_element_types.begin();
it != _diana_to_akantu_element_types.end(); ++it) {
UInt nb_nodes = Mesh::getNbNodesPerElement(it->second);
auto * tmp = new UInt[nb_nodes];
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->second) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 8;
tmp[2] = 0;
tmp[3] = 6;
tmp[4] = 1;
tmp[5] = 7;
tmp[6] = 11;
tmp[7] = 9;
tmp[8] = 10;
tmp[9] = 5;
tmp[10] = 14;
tmp[11] = 3;
tmp[12] = 12;
tmp[13] = 4;
tmp[14] = 13;
break;
case _hexahedron_20:
tmp[0] = 5;
tmp[1] = 16;
tmp[2] = 4;
tmp[3] = 19;
tmp[4] = 7;
tmp[5] = 18;
tmp[6] = 6;
tmp[7] = 17;
tmp[8] = 13;
tmp[9] = 12;
tmp[10] = 15;
tmp[11] = 14;
tmp[12] = 1;
tmp[13] = 8;
tmp[14] = 0;
tmp[15] = 11;
tmp[16] = 3;
tmp[17] = 10;
tmp[18] = 2;
tmp[19] = 9;
break;
default:
// nothing to change
break;
}
_read_order[it->second] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIODiana::~MeshIODiana() = default;
/* -------------------------------------------------------------------------- */
inline void my_getline(std::ifstream & infile, std::string & line) {
std::getline(infile, line); // read the line
size_t pos = line.find('\r'); /// remove the extra \\r if needed
line = line.substr(0, pos);
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::read(const std::string & filename, Mesh & mesh) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt first_node_number = std::numeric_limits<UInt>::max();
diana_element_number_to_elements.clear();
if (!infile.good()) {
AKANTU_ERROR("Cannot open file " << filename);
}
while (infile.good()) {
my_getline(infile, line);
/// read all nodes
if (line == "'COORDINATES'") {
line = readCoordinates(infile, mesh, first_node_number);
}
/// read all elements
if (line == "'ELEMENTS'") {
line = readElements(infile, mesh, first_node_number);
}
/// read the material properties and write a .dat file
if (line == "'MATERIALS'") {
line = readMaterial(infile, filename);
}
/// read the material properties and write a .dat file
if (line == "'GROUPS'") {
line = readGroups(infile, mesh, first_node_number);
}
}
infile.close();
mesh_accessor.setNbGlobalNodes(mesh.getNbNodes());
MeshUtils::fillElementToSubElementsData(mesh);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::write(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) const Mesh & mesh) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
-std::string MeshIODiana::readCoordinates(std::ifstream & infile, Mesh & mesh,
- UInt & first_node_number) {
+std::string MeshIODiana::
+ readCoordinates( // NOLINT(readability-convert-member-functions-to-static)
+ std::ifstream & infile, Mesh & mesh, UInt & first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
std::string line;
UInt index;
Vector<Real> coord(3);
do {
my_getline(infile, line);
- if ("'ELEMENTS'" == line)
+ if ("'ELEMENTS'" == line) {
break;
+ }
std::stringstream sstr_node(line);
sstr_node >> index >> coord(0) >> coord(1) >> coord(2);
first_node_number = first_node_number < index ? first_node_number : index;
nodes.push_back(coord);
} while (true);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
-UInt MeshIODiana::readInterval(std::stringstream & line,
- std::set<UInt> & interval) {
+UInt MeshIODiana::
+ readInterval( // NOLINT(readability-convert-member-functions-to-static)
+ std::stringstream & line, std::set<UInt> & interval) {
UInt first;
line >> first;
if (line.fail()) {
return 0;
}
interval.insert(first);
UInt second;
int dash;
dash = line.get();
if (dash == '-') {
line >> second;
interval.insert(second);
return 2;
}
- if (line.fail())
+ if (line.fail()) {
line.clear(std::ios::eofbit); // in case of get at end of the line
- else
+ } else {
line.unget();
+ }
return 1;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readGroups(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
bool reading_nodes_group = false;
while (line != "'SUPPORTS'") {
if (line == "NODES") {
reading_nodes_group = true;
my_getline(infile, line);
}
if (line == "ELEMEN") {
reading_nodes_group = false;
my_getline(infile, line);
}
auto * str = new std::stringstream(line);
UInt id;
std::string name;
char c;
*str >> id >> name >> c;
auto * list_ids = new Array<UInt>(0, 1, name);
UInt s = 1;
bool end = false;
while (!end) {
while (!str->eof() && s != 0) {
std::set<UInt> interval;
s = readInterval(*str, interval);
auto it = interval.begin();
- if (s == 1)
+ if (s == 1) {
list_ids->push_back(*it);
+ }
if (s == 2) {
UInt first = *it;
++it;
UInt second = *it;
for (UInt i = first; i <= second; ++i) {
list_ids->push_back(i);
}
}
}
- if (str->fail())
+ if (str->fail()) {
end = true;
- else {
+ } else {
my_getline(infile, line);
delete str;
str = new std::stringstream(line);
}
}
delete str;
if (reading_nodes_group) {
NodeGroup & ng = mesh.createNodeGroup(name);
for (UInt i = 0; i < list_ids->size(); ++i) {
UInt node = (*list_ids)(i)-first_node_number;
ng.add(node, false);
}
delete list_ids;
} else {
ElementGroup & eg = mesh.createElementGroup(name);
for (UInt i = 0; i < list_ids->size(); ++i) {
Element & elem = diana_element_number_to_elements[(*list_ids)(i)];
- if (elem.type != _not_defined)
+ if (elem.type != _not_defined) {
eg.add(elem, false, false);
+ }
}
eg.optimize();
delete list_ids;
}
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readElements(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
if ("CONNECTIVITY" == line) {
line = readConnectivity(infile, mesh, first_node_number);
}
/// read the line corresponding to the materials
if ("MATERIALS" == line) {
line = readMaterialElement(infile, mesh);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readConnectivity(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Int index;
std::string lline;
std::string diana_type;
- ElementType akantu_type, akantu_type_old = _not_defined;
+ ElementType akantu_type;
+ ElementType akantu_type_old = _not_defined;
Array<UInt> * connectivity = nullptr;
UInt node_per_element = 0;
Element elem;
UInt * read_order = nullptr;
while (true) {
my_getline(infile, lline);
// std::cerr << lline << std::endl;
std::stringstream sstr_elem(lline);
- if (lline == "MATERIALS")
+ if (lline == "MATERIALS") {
break;
+ }
/// traiter les coordonnees
sstr_elem >> index;
sstr_elem >> diana_type;
akantu_type = _diana_to_akantu_element_types[diana_type];
- if (akantu_type == _not_defined)
+ if (akantu_type == _not_defined) {
continue;
+ }
if (akantu_type != akantu_type_old) {
connectivity = &(mesh_accessor.getConnectivity(akantu_type));
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
read_order = _read_order[akantu_type];
}
Vector<UInt> local_connect(node_per_element);
// used if element is written on two lines
UInt j_last = 0;
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
// check s'il y a pas plus rien après un certain point
if (sstr_elem.fail()) {
sstr_elem.clear();
sstr_elem.ignore();
break;
}
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
j_last = j;
}
// check if element is written in two lines
if (j_last != (node_per_element - 1)) {
// if this is the case, read on more line
my_getline(infile, lline);
std::stringstream sstr_elem(lline);
for (UInt j = (j_last + 1); j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
}
}
connectivity->push_back(local_connect);
elem.type = akantu_type;
elem.element = connectivity->size() - 1;
diana_element_number_to_elements[index] = elem;
akantu_number_to_diana_number[elem] = index;
}
AKANTU_DEBUG_OUT();
return lline;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterialElement(std::ifstream & infile,
Mesh & mesh) {
AKANTU_DEBUG_IN();
std::string line;
for (auto type : mesh.elementTypes()) {
UInt nb_element = mesh.getNbElement(type);
mesh.getDataPointer<UInt>("material", type, _not_ghost, 1)
.resize(nb_element);
}
my_getline(infile, line);
while (line != "'MATERIALS'") {
line =
line.substr(line.find('/') + 1,
std::string::npos); // erase the first slash / of the line
char tutu[250] = {'\0'};
strncpy(tutu, line.c_str(), 249);
AKANTU_DEBUG_WARNING("reading line " << line);
Array<UInt> temp_id(0, 2);
UInt mat;
while (true) {
std::stringstream sstr_intervals_elements(line);
Vector<UInt> id(2);
char temp;
while (sstr_intervals_elements.good()) {
sstr_intervals_elements >> id(0) >> temp >> id(1); // >> "/" >> mat;
- if (!sstr_intervals_elements.fail())
+ if (!sstr_intervals_elements.fail()) {
temp_id.push_back(id);
+ }
}
if (sstr_intervals_elements.fail()) {
sstr_intervals_elements.clear();
sstr_intervals_elements.ignore();
sstr_intervals_elements >> mat;
break;
}
my_getline(infile, line);
}
// loop over elements
// UInt * temp_id_val = temp_id.storage();
- for (UInt i = 0; i < temp_id.size(); ++i)
+ for (UInt i = 0; i < temp_id.size(); ++i) {
for (UInt j = temp_id(i, 0); j <= temp_id(i, 1); ++j) {
Element & element = diana_element_number_to_elements[j];
- if (element.type == _not_defined)
+ if (element.type == _not_defined) {
continue;
+ }
UInt elem = element.element;
ElementType type = element.type;
Array<UInt> & data =
mesh.getDataPointer<UInt>("material", type, _not_ghost);
data(elem) = mat;
}
+ }
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterial(std::ifstream & infile,
const std::string & filename) {
AKANTU_DEBUG_IN();
std::stringstream mat_file_name;
mat_file_name << "material_" << filename;
std::ofstream material_file;
material_file.open(mat_file_name.str().c_str()); // mat_file_name.str());
UInt mat_index;
std::string line;
bool first_mat = true;
bool end = false;
UInt mat_id = 0;
using MatProp = std::map<std::string, Real>;
MatProp mat_prop;
do {
my_getline(infile, line);
std::stringstream sstr_material(line);
if (("'GROUPS'" == line) || ("'END'" == line)) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
- for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it)
+ for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it) {
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
+ }
material_file << "]" << std::endl;
mat_prop.clear();
}
end = true;
} else {
/// traiter les caractéristiques des matériaux
sstr_material >> mat_index;
if (!sstr_material.fail()) {
if (!first_mat) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
- for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it)
+ for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it) {
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
+ }
material_file << "]" << std::endl;
mat_prop.clear();
}
}
first_mat = false;
} else {
sstr_material.clear();
}
std::string prop_name;
sstr_material >> prop_name;
std::map<std::string, std::string>::iterator it;
it = _diana_to_akantu_mat_prop.find(prop_name);
if (it != _diana_to_akantu_mat_prop.end()) {
Real value;
sstr_material >> value;
mat_prop[it->second] = value;
} else {
AKANTU_DEBUG_INFO("In material reader, property " << prop_name
<< "not recognized");
}
}
} while (!end);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_diana.hh b/src/io/mesh_io/mesh_io_diana.hh
index fc3574f8e..c145a1024 100644
--- a/src/io/mesh_io/mesh_io_diana.hh
+++ b/src/io/mesh_io/mesh_io_diana.hh
@@ -1,107 +1,107 @@
/**
* @file mesh_io_diana.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief diana mesh reader description
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_IO_DIANA_HH__
-#define __AKANTU_MESH_IO_DIANA_HH__
+#ifndef AKANTU_MESH_IO_DIANA_HH_
+#define AKANTU_MESH_IO_DIANA_HH_
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIODiana : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIODiana();
~MeshIODiana() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
void write(const std::string & filename, const Mesh & mesh) override;
private:
std::string readCoordinates(std::ifstream & infile, Mesh & mesh,
UInt & first_node_number);
std::string readElements(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readGroups(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readConnectivity(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readMaterialElement(std::ifstream & infile, Mesh & mesh);
std::string readMaterial(std::ifstream & infile,
const std::string & filename);
UInt readInterval(std::stringstream & line, std::set<UInt> & interval);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
std::map<std::string, ElementType> _diana_to_akantu_element_types;
std::map<std::string, std::string> _diana_to_akantu_mat_prop;
/// order in witch element as to be read, akantu_node_order =
/// _read_order[diana_node_order]
std::map<ElementType, UInt *> _read_order;
std::map<UInt, Element> diana_element_number_to_elements;
std::map<Element, UInt> akantu_number_to_diana_number;
};
} // namespace akantu
-#endif /* __AKANTU_MESH_IO_DIANA_HH__ */
+#endif /* AKANTU_MESH_IO_DIANA_HH_ */
diff --git a/src/io/mesh_io/mesh_io_msh.cc b/src/io/mesh_io/mesh_io_msh.cc
index 460fbf0f9..9549a66a8 100644
--- a/src/io/mesh_io/mesh_io_msh.cc
+++ b/src/io/mesh_io/mesh_io_msh.cc
@@ -1,1099 +1,1123 @@
/**
* @file mesh_io_msh.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Read/Write for MSH files generated by gmsh
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -----------------------------------------------------------------------------
Version (Legacy) 1.0
$NOD
number-of-nodes
node-number x-coord y-coord z-coord
...
$ENDNOD
$ELM
number-of-elements
elm-number elm-type reg-phys reg-elem number-of-nodes node-number-list
...
$ENDELM
-----------------------------------------------------------------------------
Version 2.1
$MeshFormat
version-number file-type data-size
$EndMeshFormat
$Nodes
number-of-nodes
node-number x-coord y-coord z-coord
...
$EndNodes
$Elements
number-of-elements
elm-number elm-type number-of-tags < tag > ... node-number-list
...
$EndElements
$PhysicalNames
number-of-names
physical-dimension physical-number "physical-name"
...
$EndPhysicalNames
$NodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
node-number value ...
...
$EndNodeData
$ElementData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number value ...
...
$EndElementData
$ElementNodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number number-of-nodes-per-element value ...
...
$ElementEndNodeData
-----------------------------------------------------------------------------
elem-type
1: 2-node line.
2: 3-node triangle.
3: 4-node quadrangle.
4: 4-node tetrahedron.
5: 8-node hexahedron.
6: 6-node prism.
7: 5-node pyramid.
8: 3-node second order line
9: 6-node second order triangle
10: 9-node second order quadrangle
11: 10-node second order tetrahedron
12: 27-node second order hexahedron
13: 18-node second order prism
14: 14-node second order pyramid
15: 1-node point.
16: 8-node second order quadrangle
17: 20-node second order hexahedron
18: 15-node second order prism
19: 13-node second order pyramid
20: 9-node third order incomplete triangle
21: 10-node third order triangle
22: 12-node fourth order incomplete triangle
23: 15-node fourth order triangle
24: 15-node fifth order incomplete triangle
25: 21-node fifth order complete triangle
26: 4-node third order edge
27: 5-node fourth order edge
28: 6-node fifth order edge
29: 20-node third order tetrahedron
30: 35-node fourth order tetrahedron
31: 56-node fifth order tetrahedron
-------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIOMSH::MeshIOMSH() {
canReadSurface = true;
canReadExtendedData = true;
_msh_nodes_per_elem[_msh_not_defined] = 0;
_msh_nodes_per_elem[_msh_segment_2] = 2;
_msh_nodes_per_elem[_msh_triangle_3] = 3;
_msh_nodes_per_elem[_msh_quadrangle_4] = 4;
_msh_nodes_per_elem[_msh_tetrahedron_4] = 4;
_msh_nodes_per_elem[_msh_hexahedron_8] = 8;
_msh_nodes_per_elem[_msh_prism_1] = 6;
_msh_nodes_per_elem[_msh_pyramid_1] = 1;
_msh_nodes_per_elem[_msh_segment_3] = 3;
_msh_nodes_per_elem[_msh_triangle_6] = 6;
_msh_nodes_per_elem[_msh_quadrangle_9] = 9;
_msh_nodes_per_elem[_msh_tetrahedron_10] = 10;
_msh_nodes_per_elem[_msh_hexahedron_27] = 27;
_msh_nodes_per_elem[_msh_hexahedron_20] = 20;
_msh_nodes_per_elem[_msh_prism_18] = 18;
_msh_nodes_per_elem[_msh_prism_15] = 15;
_msh_nodes_per_elem[_msh_pyramid_14] = 14;
_msh_nodes_per_elem[_msh_point] = 1;
_msh_nodes_per_elem[_msh_quadrangle_8] = 8;
_msh_to_akantu_element_types[_msh_not_defined] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2] = _segment_2;
_msh_to_akantu_element_types[_msh_triangle_3] = _triangle_3;
_msh_to_akantu_element_types[_msh_quadrangle_4] = _quadrangle_4;
_msh_to_akantu_element_types[_msh_tetrahedron_4] = _tetrahedron_4;
_msh_to_akantu_element_types[_msh_hexahedron_8] = _hexahedron_8;
_msh_to_akantu_element_types[_msh_prism_1] = _pentahedron_6;
_msh_to_akantu_element_types[_msh_pyramid_1] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_3] = _segment_3;
_msh_to_akantu_element_types[_msh_triangle_6] = _triangle_6;
_msh_to_akantu_element_types[_msh_quadrangle_9] = _not_defined;
_msh_to_akantu_element_types[_msh_tetrahedron_10] = _tetrahedron_10;
_msh_to_akantu_element_types[_msh_hexahedron_27] = _not_defined;
_msh_to_akantu_element_types[_msh_hexahedron_20] = _hexahedron_20;
_msh_to_akantu_element_types[_msh_prism_18] = _not_defined;
_msh_to_akantu_element_types[_msh_prism_15] = _pentahedron_15;
_msh_to_akantu_element_types[_msh_pyramid_14] = _not_defined;
_msh_to_akantu_element_types[_msh_point] = _point_1;
_msh_to_akantu_element_types[_msh_quadrangle_8] = _quadrangle_8;
_akantu_to_msh_element_types[_not_defined] = _msh_not_defined;
_akantu_to_msh_element_types[_segment_2] = _msh_segment_2;
_akantu_to_msh_element_types[_segment_3] = _msh_segment_3;
_akantu_to_msh_element_types[_triangle_3] = _msh_triangle_3;
_akantu_to_msh_element_types[_triangle_6] = _msh_triangle_6;
_akantu_to_msh_element_types[_tetrahedron_4] = _msh_tetrahedron_4;
_akantu_to_msh_element_types[_tetrahedron_10] = _msh_tetrahedron_10;
_akantu_to_msh_element_types[_quadrangle_4] = _msh_quadrangle_4;
_akantu_to_msh_element_types[_quadrangle_8] = _msh_quadrangle_8;
_akantu_to_msh_element_types[_hexahedron_8] = _msh_hexahedron_8;
_akantu_to_msh_element_types[_hexahedron_20] = _msh_hexahedron_20;
_akantu_to_msh_element_types[_pentahedron_6] = _msh_prism_1;
_akantu_to_msh_element_types[_pentahedron_15] = _msh_prism_15;
_akantu_to_msh_element_types[_point_1] = _msh_point;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
_akantu_to_msh_element_types[_bernoulli_beam_2] = _msh_segment_2;
_akantu_to_msh_element_types[_bernoulli_beam_3] = _msh_segment_2;
_akantu_to_msh_element_types[_discrete_kirchhoff_triangle_18] =
_msh_triangle_3;
#endif
std::map<ElementType, MSHElementType>::iterator it;
for (it = _akantu_to_msh_element_types.begin();
it != _akantu_to_msh_element_types.end(); ++it) {
UInt nb_nodes = _msh_nodes_per_elem[it->second];
std::vector<UInt> tmp(nb_nodes);
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->first) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_6:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
tmp[6] = 8;
tmp[8] = 11;
tmp[9] = 6;
tmp[10] = 9;
tmp[11] = 10;
tmp[12] = 14;
tmp[14] = 12;
break;
case _hexahedron_20:
tmp[9] = 11;
tmp[10] = 12;
tmp[11] = 9;
tmp[12] = 13;
tmp[13] = 10;
tmp[17] = 19;
tmp[18] = 17;
tmp[19] = 18;
break;
default:
// nothing to change
break;
}
_read_order[it->first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIOMSH::~MeshIOMSH() = default;
/* -------------------------------------------------------------------------- */
namespace {
struct File {
std::string filename;
std::ifstream infile;
std::string line;
size_t current_line{0};
size_t first_node_number{std::numeric_limits<UInt>::max()},
last_node_number{0};
bool has_physical_names{false};
std::unordered_map<size_t, size_t> node_tags;
std::unordered_map<size_t, Element> element_tags;
double version{0};
int size_of_size_t{0};
Mesh & mesh;
MeshAccessor mesh_accessor;
std::multimap<std::pair<int, int>, int> entity_tag_to_physical_tags;
File(const std::string & filename, Mesh & mesh)
: filename(filename), mesh(mesh), mesh_accessor(mesh) {
infile.open(filename.c_str());
if (not infile.good()) {
AKANTU_EXCEPTION("Cannot open file " << filename);
}
}
~File() { infile.close(); }
auto good() { return infile.good(); }
std::stringstream get_line() {
std::string tmp_str;
if (infile.eof()) {
AKANTU_EXCEPTION("Reached the end of the file " << filename);
}
std::getline(infile, tmp_str);
line = trim(tmp_str);
++current_line;
return std::stringstream(line);
}
template <typename... Ts> void read_line(Ts &&... ts) {
auto && sstr = get_line();
(void)std::initializer_list<int>{
(sstr >> std::forward<decltype(ts)>(ts), 0)...};
}
};
} // namespace
/* -------------------------------------------------------------------------- */
template <typename File, typename Readers>
void MeshIOMSH::populateReaders2(File & file, Readers & readers) {
- readers["$NOD"] = readers["$Nodes"] = [&](const std::string &) {
+ readers["$NOD"] = readers["$Nodes"] = [&](const std::string & /*unused*/) {
UInt nb_nodes;
file.read_line(nb_nodes);
Array<Real> & nodes = file.mesh_accessor.getNodes();
nodes.resize(nb_nodes);
file.mesh_accessor.setNbGlobalNodes(nb_nodes);
size_t index;
Vector<double> coord(3);
/// for each node, read the coordinates
for (auto && data : enumerate(make_view(nodes, nodes.getNbComponent()))) {
file.read_line(index, coord(0), coord(1), coord(2));
if (index > std::numeric_limits<UInt>::max()) {
AKANTU_EXCEPTION(
"There are more nodes in this files than the index type of akantu "
"can handle, consider recompiling with a bigger index type");
}
file.first_node_number = std::min(file.first_node_number, index);
file.last_node_number = std::max(file.last_node_number, index);
for (auto && coord_data : zip(std::get<1>(data), coord)) {
std::get<0>(coord_data) = std::get<1>(coord_data);
}
file.node_tags[index] = std::get<0>(data);
}
};
- readers["$ELM"] = readers["$Elements"] = [&](const std::string &) {
+ readers["$ELM"] = readers["$Elements"] = [&](const std::string & /*unused*/) {
UInt nb_elements;
file.read_line(nb_elements);
Int index;
UInt msh_type;
ElementType akantu_type;
for (UInt i = 0; i < nb_elements; ++i) {
auto && sstr_elem = file.get_line();
sstr_elem >> index;
sstr_elem >> msh_type;
/// get the connectivity vector depending on the element type
akantu_type =
this->_msh_to_akantu_element_types[MSHElementType(msh_type)];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind "
<< msh_type << " at line " << file.current_line);
continue;
}
Element elem{akantu_type, 0, _not_ghost};
auto & connectivity = file.mesh_accessor.getConnectivity(akantu_type);
auto node_per_element = connectivity.getNbComponent();
auto & read_order = this->_read_order[akantu_type];
/// read tags informations
if (file.version < 2) {
- Int tag0, tag1, nb_nodes; // reg-phys, reg-elem, number-of-nodes
+ Int tag0;
+ Int tag1;
+ Int nb_nodes; // reg-phys, reg-elem, number-of-nodes
sstr_elem >> tag0 >> tag1 >> nb_nodes;
auto & data0 =
file.mesh_accessor.template getData<UInt>("tag_0", akantu_type);
data0.push_back(tag0);
auto & data1 =
file.mesh_accessor.template getData<UInt>("tag_1", akantu_type);
data1.push_back(tag1);
} else if (file.version < 4) {
UInt nb_tags;
sstr_elem >> nb_tags;
for (UInt j = 0; j < nb_tags; ++j) {
Int tag;
sstr_elem >> tag;
auto & data = file.mesh_accessor.template getData<UInt>(
"tag_" + std::to_string(j), akantu_type);
data.push_back(tag);
}
}
Vector<UInt> local_connect(node_per_element);
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
AKANTU_DEBUG_ASSERT(node_index <= file.last_node_number,
"Node number not in range : line "
<< file.current_line);
local_connect(read_order[j]) = file.node_tags[node_index];
}
connectivity.push_back(local_connect);
elem.element = connectivity.size() - 1;
file.element_tags[index] = elem;
}
};
- readers["$Periodic"] = [&](const std::string &) {
+ readers["$Periodic"] = [&](const std::string & /*unused*/) {
UInt nb_periodic_entities;
file.read_line(nb_periodic_entities);
file.mesh_accessor.getNodesFlags().resize(file.mesh.getNbNodes(),
NodeFlag::_normal);
for (UInt p = 0; p < nb_periodic_entities; ++p) {
// dimension slave-tag master-tag
UInt dimension;
file.read_line(dimension);
// transformation
file.get_line();
// nb nodes
UInt nb_nodes;
file.read_line(nb_nodes);
for (UInt n = 0; n < nb_nodes; ++n) {
// slave master
auto && sstr = file.get_line();
// The info in the mesh seem inconsistent so they are ignored for now.
continue;
if (dimension == file.mesh.getSpatialDimension() - 1) {
- UInt slave, master;
+ UInt slave;
+ UInt master;
sstr >> slave;
sstr >> master;
file.mesh_accessor.addPeriodicSlave(file.node_tags[slave],
file.node_tags[master]);
}
}
}
// mesh_accessor.markMeshPeriodic();
};
}
/* -------------------------------------------------------------------------- */
template <typename File, typename Readers>
void MeshIOMSH::populateReaders4(File & file, Readers & readers) {
static std::map<int, std::string> entity_type{
{0, "points"},
{1, "curve"},
{2, "surface"},
{3, "volume"},
};
- readers["$Entities"] = [&](const std::string &) {
+ readers["$Entities"] = [&](const std::string & /*unused*/) {
size_t num_entity[4];
file.read_line(num_entity[0], num_entity[1], num_entity[2], num_entity[3]);
for (auto entity_dim : arange(4)) {
for (auto _ [[gnu::unused]] : arange(num_entity[entity_dim])) {
auto && sstr = file.get_line();
int tag;
- double min_x, min_y, min_z, max_x, max_y, max_z;
+ double min_x;
+ double min_y;
+ double min_z;
+ double max_x;
+ double max_y;
+ double max_z;
size_t num_physical_tags;
sstr >> tag >> min_x >> min_y >> min_z;
if (entity_dim > 0 or file.version < 4.1) {
sstr >> max_x >> max_y >> max_z;
}
sstr >> num_physical_tags;
for (auto _ [[gnu::unused]] : arange(num_physical_tags)) {
int phys_tag;
sstr >> phys_tag;
std::string physical_name;
if (this->physical_names.find(phys_tag) ==
this->physical_names.end()) {
physical_name = "msh_block_" + std::to_string(phys_tag);
} else {
physical_name = this->physical_names[phys_tag];
}
if (not file.mesh.elementGroupExists(physical_name)) {
file.mesh.createElementGroup(physical_name, entity_dim);
} else {
file.mesh.getElementGroup(physical_name).addDimension(entity_dim);
}
file.entity_tag_to_physical_tags.insert(
std::make_pair(std::make_pair(tag, entity_dim), phys_tag));
}
}
}
};
- readers["$Nodes"] = [&](const std::string &) {
- size_t num_blocks, num_nodes;
+ readers["$Nodes"] = [&](const std::string & /*unused*/) {
+ size_t num_blocks;
+ size_t num_nodes;
if (file.version >= 4.1) {
file.read_line(num_blocks, num_nodes, file.first_node_number,
file.last_node_number);
} else {
file.read_line(num_blocks, num_nodes);
}
auto & nodes = file.mesh_accessor.getNodes();
nodes.reserve(num_nodes);
file.mesh_accessor.setNbGlobalNodes(num_nodes);
if (num_nodes > std::numeric_limits<UInt>::max()) {
AKANTU_EXCEPTION(
"There are more nodes in this files than the index type of akantu "
"can handle, consider recompiling with a bigger index type");
}
size_t node_id{0};
for (auto block [[gnu::unused]] : arange(num_blocks)) {
- int entity_dim, entity_tag, parametric;
+ int entity_dim;
+ int entity_tag;
+ int parametric;
size_t num_nodes_in_block;
Vector<double> pos(3);
Vector<double> real_pos(nodes.getNbComponent());
if (file.version >= 4.1) {
file.read_line(entity_dim, entity_tag, parametric, num_nodes_in_block);
if (parametric) {
AKANTU_EXCEPTION(
"Akantu does not support parametric nodes in msh files");
}
for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
size_t tag;
file.read_line(tag);
file.node_tags[tag] = node_id;
++node_id;
}
for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
file.read_line(pos(_x), pos(_y), pos(_z));
for (auto && data : zip(real_pos, pos)) {
std::get<0>(data) = std::get<1>(data);
}
nodes.push_back(real_pos);
}
} else {
file.read_line(entity_tag, entity_dim, parametric, num_nodes_in_block);
for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
size_t tag;
file.read_line(tag, pos(_x), pos(_y), pos(_z));
if (file.version < 4.1) {
file.first_node_number = std::min(file.first_node_number, tag);
file.last_node_number = std::max(file.last_node_number, tag);
}
for (auto && data : zip(real_pos, pos)) {
std::get<0>(data) = std::get<1>(data);
}
nodes.push_back(real_pos);
file.node_tags[tag] = node_id;
++node_id;
}
}
}
};
- readers["$Elements"] = [&](const std::string &) {
- size_t num_blocks, num_elements;
+ readers["$Elements"] = [&](const std::string & /*unused*/) {
+ size_t num_blocks;
+ size_t num_elements;
file.read_line(num_blocks, num_elements);
for (auto block [[gnu::unused]] : arange(num_blocks)) {
- int entity_dim, entity_tag, element_type;
+ int entity_dim;
+ int entity_tag;
+ int element_type;
size_t num_elements_in_block;
if (file.version >= 4.1) {
file.read_line(entity_dim, entity_tag, element_type,
num_elements_in_block);
} else {
file.read_line(entity_tag, entity_dim, element_type,
num_elements_in_block);
}
/// get the connectivity vector depending on the element type
auto && akantu_type =
this->_msh_to_akantu_element_types[(MSHElementType)element_type];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind " << element_type
<< " at line "
<< file.current_line);
continue;
}
Element elem{akantu_type, 0, _not_ghost};
auto & connectivity = file.mesh_accessor.getConnectivity(akantu_type);
Vector<UInt> local_connect(connectivity.getNbComponent());
auto && read_order = this->_read_order[akantu_type];
auto & data0 =
file.mesh_accessor.template getData<UInt>("tag_0", akantu_type);
data0.resize(data0.size() + num_elements_in_block, 0);
auto & physical_data = file.mesh_accessor.template getData<std::string>(
"physical_names", akantu_type);
physical_data.resize(physical_data.size() + num_elements_in_block, "");
for (auto _ [[gnu::unused]] : arange(num_elements_in_block)) {
auto && sstr_elem = file.get_line();
size_t elem_tag;
sstr_elem >> elem_tag;
for (auto && c : arange(connectivity.getNbComponent())) {
size_t node_tag;
sstr_elem >> node_tag;
AKANTU_DEBUG_ASSERT(node_tag <= file.last_node_number,
"Node number not in range : line "
<< file.current_line);
node_tag = file.node_tags[node_tag];
local_connect(read_order[c]) = node_tag;
}
connectivity.push_back(local_connect);
elem.element = connectivity.size() - 1;
file.element_tags[elem_tag] = elem;
auto range = file.entity_tag_to_physical_tags.equal_range(
std::make_pair(entity_tag, entity_dim));
bool first = true;
for (auto it = range.first; it != range.second; ++it) {
auto phys_it = this->physical_names.find(it->second);
if (first) {
data0(elem.element) =
it->second; // for compatibility with version 2
- if (phys_it != this->physical_names.end())
+ if (phys_it != this->physical_names.end()) {
physical_data(elem.element) = phys_it->second;
+ }
first = false;
}
- if (phys_it != this->physical_names.end())
+ if (phys_it != this->physical_names.end()) {
file.mesh.getElementGroup(phys_it->second).add(elem, true, false);
+ }
}
}
}
for (auto && element_group : file.mesh.iterateElementGroups()) {
element_group.getNodeGroup().optimize();
}
};
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::read(const std::string & filename, Mesh & mesh) {
File file(filename, mesh);
std::map<std::string, std::function<void(const std::string &)>> readers;
- readers["$MeshFormat"] = [&](const std::string &) {
+ readers["$MeshFormat"] = [&](const std::string & /*unused*/) {
auto && sstr = file.get_line();
int format;
sstr >> file.version >> format;
- if (format != 0)
+ if (format != 0) {
AKANTU_ERROR("This reader can only read ASCII files.");
+ }
if (file.version > 2) {
sstr >> file.size_of_size_t;
if (file.size_of_size_t > int(sizeof(UInt))) {
AKANTU_DEBUG_INFO("The size of the indexes in akantu might be to small "
"to read this file (akantu "
<< sizeof(UInt) << " vs. msh file "
<< file.size_of_size_t << ")");
}
}
if (file.version < 4) {
this->populateReaders2(file, readers);
} else {
this->populateReaders4(file, readers);
}
};
auto && read_data = [&](auto && entity_tags, auto && get_data,
auto && read_data) {
auto read_data_tags = [&](auto x) {
UInt number_of_tags{0};
file.read_line(number_of_tags);
std::vector<decltype(x)> tags(number_of_tags);
for (auto && tag : tags) {
file.read_line(tag);
}
return tags;
};
auto && string_tags = read_data_tags(std::string{});
auto && real_tags [[gnu::unused]] = read_data_tags(double{});
auto && int_tags = read_data_tags(int{});
for (auto & s : string_tags) {
s = trim(s, '"');
}
auto id = string_tags[0];
auto size = int_tags[2];
auto nb_component = int_tags[1];
auto & data = get_data(id, size, nb_component);
for (auto n [[gnu::unused]] : arange(size)) {
auto && sstr = file.get_line();
size_t tag;
sstr >> tag;
const auto & entity = entity_tags[tag];
read_data(entity, sstr, data, nb_component);
}
};
- readers["$NodeData"] = [&](const std::string &) {
+ readers["$NodeData"] = [&](const std::string & /*unused*/) {
/* $NodeData
numStringTags(ASCII int)
stringTag(string) ...
numRealTags(ASCII int)
realTag(ASCII double) ...
numIntegerTags(ASCII int)
integerTag(ASCII int) ...
nodeTag(size_t) value(double) ...
...
$EndNodeData */
- read_data(file.node_tags,
- [&](auto && id, auto && size [[gnu::unused]],
- auto && nb_component [[gnu::unused]]) -> Array<double> & {
- auto & data =
- file.mesh.template getNodalData<double>(id, nb_component);
- data.resize(size);
- return data;
- },
- [&](auto && node, auto && sstr, auto && data,
- auto && nb_component [[gnu::unused]]) {
- for (auto c : arange(nb_component)) {
- sstr >> data(node, c);
- }
- });
+ read_data(
+ file.node_tags,
+ [&](auto && id, auto && size [[gnu::unused]],
+ auto && nb_component [[gnu::unused]]) -> Array<double> & {
+ auto & data =
+ file.mesh.template getNodalData<double>(id, nb_component);
+ data.resize(size);
+ return data;
+ },
+ [&](auto && node, auto && sstr, auto && data,
+ auto && nb_component [[gnu::unused]]) {
+ for (auto c : arange(nb_component)) {
+ sstr >> data(node, c);
+ }
+ });
};
- readers["$ElementData"] = [&](const std::string &) {
+ readers["$ElementData"] = [&](const std::string & /*unused*/) {
/* $ElementData
numStringTags(ASCII int)
stringTag(string) ...
numRealTags(ASCII int)
realTag(ASCII double) ...
numIntegerTags(ASCII int)
integerTag(ASCII int) ...
elementTag(size_t) value(double) ...
...
$EndElementData
*/
read_data(
file.element_tags,
[&](auto && id, auto && size [[gnu::unused]],
auto && nb_component
[[gnu::unused]]) -> ElementTypeMapArray<double> & {
file.mesh.template getElementalData<double>(id);
return file.mesh.template getElementalData<double>(id);
},
[&](auto && element, auto && sstr, auto && data, auto && nb_component) {
if (not data.exists(element.type)) {
data.alloc(mesh.getNbElement(element.type), nb_component,
element.type, element.ghost_type);
}
auto & data_array = data(element.type);
for (auto c : arange(nb_component)) {
sstr >> data_array(element.element, c);
}
});
};
- readers["$ElementNodeData"] = [&](const std::string &) {
+ readers["$ElementNodeData"] = [&](const std::string & /*unused*/) {
/* $ElementNodeData
numStringTags(ASCII int)
stringTag(string) ...
numRealTags(ASCII int)
realTag(ASCII double) ...
numIntegerTags(ASCII int)
integerTag(ASCII int) ...
elementTag(size_t) value(double) ...
...
$EndElementNodeData
*/
read_data(
file.element_tags,
[&](auto && id, auto && size [[gnu::unused]],
auto && nb_component
[[gnu::unused]]) -> ElementTypeMapArray<double> & {
file.mesh.template getElementalData<double>(id);
auto & data = file.mesh.template getElementalData<double>(id);
data.isNodal(true);
return data;
},
[&](auto && element, auto && sstr, auto && data, auto && nb_component) {
int nb_nodes_per_element;
sstr >> nb_nodes_per_element;
if (not data.exists(element.type)) {
data.alloc(mesh.getNbElement(element.type),
nb_component * nb_nodes_per_element, element.type,
element.ghost_type);
}
auto & data_array = data(element.type);
for (auto c : arange(nb_component)) {
sstr >> data_array(element.element, c);
}
});
};
- readers["$PhysicalNames"] = [&](const std::string &) {
+ readers["$PhysicalNames"] = [&](const std::string & /*unused*/) {
file.has_physical_names = true;
int num_of_phys_names;
file.read_line(num_of_phys_names); /// the format line
for (auto k [[gnu::unused]] : arange(num_of_phys_names)) {
int phys_name_id;
int phys_dim;
std::string phys_name;
file.read_line(phys_dim, phys_name_id, std::quoted(phys_name));
this->physical_names[phys_name_id] = phys_name;
}
};
readers["Unsupported"] = [&](const std::string & _block) {
std::string block = _block.substr(1);
AKANTU_DEBUG_WARNING("Unsupported block_kind " << block << " at line "
<< file.current_line);
auto && end_block = "$End" + block;
while (file.line != end_block) {
file.get_line();
}
};
while (file.good()) {
std::string block;
file.read_line(block);
auto && it = readers.find(block);
if (it != readers.end()) {
it->second(block);
std::string end_block;
file.read_line(end_block);
block = block.substr(1);
if (end_block != "$End" + block) {
AKANTU_EXCEPTION("The reader failed to properly read the block "
<< block << ". Expected a $End" << block << " at line "
<< file.current_line);
}
- } else if (block.size() != 0) {
+ } else if (not block.empty()) {
readers["Unsupported"](block);
}
}
// mesh.updateTypesOffsets(_not_ghost);
if (file.version < 4) {
this->constructPhysicalNames("tag_0", mesh);
- if (file.has_physical_names)
+ if (file.has_physical_names) {
mesh.createGroupsFromMeshData<std::string>("physical_names");
+ }
}
MeshUtils::fillElementToSubElementsData(mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::write(const std::string & filename, const Mesh & mesh) {
std::ofstream outfile;
const Array<Real> & nodes = mesh.getNodes();
outfile.open(filename.c_str());
outfile << "$MeshFormat"
<< "\n";
outfile << "2.2 0 8"
<< "\n";
outfile << "$EndMeshFormat"
<< "\n";
outfile << std::setprecision(std::numeric_limits<Real>::digits10);
outfile << "$Nodes"
<< "\n";
outfile << nodes.size() << "\n";
outfile << std::uppercase;
for (UInt i = 0; i < nodes.size(); ++i) {
Int offset = i * nodes.getNbComponent();
outfile << i + 1;
for (UInt j = 0; j < nodes.getNbComponent(); ++j) {
outfile << " " << nodes.storage()[offset + j];
}
- for (UInt p = nodes.getNbComponent(); p < 3; ++p)
+ for (UInt p = nodes.getNbComponent(); p < 3; ++p) {
outfile << " " << 0.;
+ }
outfile << "\n";
;
}
outfile << std::nouppercase;
outfile << "$EndNodes"
<< "\n";
outfile << "$Elements"
<< "\n";
Int nb_elements = 0;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
nb_elements += connectivity.size();
}
outfile << nb_elements << "\n";
std::map<Element, size_t> element_to_msh_element;
UInt element_idx = 1;
Element element;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
element.type = type;
UInt * tag[2] = {nullptr, nullptr};
if (mesh.hasData<UInt>("tag_0", type, _not_ghost)) {
const auto & data_tag_0 = mesh.getData<UInt>("tag_0", type, _not_ghost);
tag[0] = data_tag_0.storage();
}
if (mesh.hasData<UInt>("tag_1", type, _not_ghost)) {
const auto & data_tag_1 = mesh.getData<UInt>("tag_1", type, _not_ghost);
tag[1] = data_tag_1.storage();
}
for (auto && data :
enumerate(make_view(connectivity, connectivity.getNbComponent()))) {
element.element = std::get<0>(data);
const auto & conn = std::get<1>(data);
element_to_msh_element[element] = element_idx;
outfile << element_idx << " " << _akantu_to_msh_element_types[type]
<< " 2";
/// \todo write the real data in the file
- for (UInt t = 0; t < 2; ++t)
- if (tag[t])
+ for (UInt t = 0; t < 2; ++t) {
+ if (tag[t] != nullptr) {
outfile << " " << tag[t][element.element];
- else
+ } else {
outfile << " 0";
+ }
+ }
for (auto && c : conn) {
outfile << " " << c + 1;
}
outfile << "\n";
element_idx++;
}
}
outfile << "$EndElements"
<< "\n";
if (mesh.hasData(MeshDataType::_nodal)) {
auto && tags = mesh.getTagNames();
for (auto && tag : tags) {
auto type = mesh.getTypeCode(tag, MeshDataType::_nodal);
if (type != MeshDataTypeCode::_real) {
AKANTU_DEBUG_WARNING(
"The field "
<< tag << " is ignored by the MSH writer, msh files do not support "
<< type << " data");
continue;
}
auto && data = mesh.getNodalData<double>(tag);
outfile << "$NodeData"
<< "\n";
outfile << "1"
<< "\n";
outfile << "\"" << tag << "\"\n";
outfile << "1\n0.0"
<< "\n";
outfile << "3\n0"
<< "\n";
outfile << data.getNbComponent() << "\n";
outfile << data.size() << "\n";
for (auto && d : enumerate(make_view(data, data.getNbComponent()))) {
outfile << std::get<0>(d) + 1;
for (auto && v : std::get<1>(d)) {
outfile << " " << v;
}
outfile << "\n";
}
outfile << "$EndNodeData"
<< "\n";
}
}
if (mesh.hasData(MeshDataType::_elemental)) {
auto && tags = mesh.getTagNames();
for (auto && tag : tags) {
auto && data = mesh.getElementalData<double>(tag);
auto type = mesh.getTypeCode(tag, MeshDataType::_elemental);
if (type != MeshDataTypeCode::_real) {
AKANTU_DEBUG_WARNING(
"The field "
<< tag << " is ignored by the MSH writer, msh files do not support "
<< type << " data");
continue;
}
- if (data.isNodal())
+ if (data.isNodal()) {
continue;
+ }
auto size = data.size();
- if (size == 0)
+ if (size == 0) {
continue;
+ }
auto && nb_components = data.getNbComponents();
auto nb_component = nb_components(*(data.elementTypes().begin()));
outfile << "$ElementData"
<< "\n";
outfile << "1"
<< "\n";
outfile << "\"" << tag << "\"\n";
outfile << "1\n0.0"
<< "\n";
outfile << "3\n0"
<< "\n";
outfile << nb_component << "\n";
outfile << size << "\n";
Element element;
for (auto type : data.elementTypes()) {
element.type = type;
for (auto && _ :
enumerate(make_view(data(type), nb_components(type)))) {
element.element = std::get<0>(_);
outfile << element_to_msh_element[element];
for (auto && v : std::get<1>(_)) {
outfile << " " << v;
}
outfile << "\n";
}
}
outfile << "$EndElementData"
<< "\n";
}
}
outfile.close();
}
/* --------------------------------------------------------------------------
*/
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_msh.hh b/src/io/mesh_io/mesh_io_msh.hh
index a6f796437..56f2927a4 100644
--- a/src/io/mesh_io/mesh_io_msh.hh
+++ b/src/io/mesh_io/mesh_io_msh.hh
@@ -1,115 +1,115 @@
/**
* @file mesh_io_msh.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Read/Write for MSH files
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_IO_MSH_HH__
-#define __AKANTU_MESH_IO_MSH_HH__
+#ifndef AKANTU_MESH_IO_MSH_HH_
+#define AKANTU_MESH_IO_MSH_HH_
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIOMSH : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSH();
~MeshIOMSH() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
void write(const std::string & filename, const Mesh & mesh) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// MSH element types
enum MSHElementType {
_msh_not_defined = 0,
_msh_segment_2 = 1, // 2-node line.
_msh_triangle_3 = 2, // 3-node triangle.
_msh_quadrangle_4 = 3, // 4-node quadrangle.
_msh_tetrahedron_4 = 4, // 4-node tetrahedron.
_msh_hexahedron_8 = 5, // 8-node hexahedron.
_msh_prism_1 = 6, // 6-node prism.
_msh_pyramid_1 = 7, // 5-node pyramid.
_msh_segment_3 = 8, // 3-node second order line
_msh_triangle_6 = 9, // 6-node second order triangle
_msh_quadrangle_9 = 10, // 9-node second order quadrangle
_msh_tetrahedron_10 = 11, // 10-node second order tetrahedron
_msh_hexahedron_27 = 12, // 27-node second order hexahedron
_msh_prism_18 = 13, // 18-node second order prism
_msh_pyramid_14 = 14, // 14-node second order pyramid
_msh_point = 15, // 1-node point.
_msh_quadrangle_8 = 16, // 8-node second order quadrangle
_msh_hexahedron_20 = 17, // 20-node second order hexahedron
_msh_prism_15 = 18 // 15-node second order prism
};
#define MAX_NUMBER_OF_NODE_PER_ELEMENT 10 // tetrahedron of second order
/// order in witch element as to be read
std::map<ElementType, std::vector<UInt>> _read_order;
/// number of nodes per msh element
std::map<MSHElementType, UInt> _msh_nodes_per_elem;
/// correspondence between msh element types and akantu element types
std::map<MSHElementType, ElementType> _msh_to_akantu_element_types;
/// correspondence between akantu element types and msh element types
std::map<ElementType, MSHElementType> _akantu_to_msh_element_types;
protected:
template <typename File, typename Readers>
void populateReaders2(File & file, Readers & readers);
template <typename File, typename Readers>
void populateReaders4(File & file, Readers & readers);
};
} // namespace akantu
-#endif /* __AKANTU_MESH_IO_MSH_HH__ */
+#endif /* AKANTU_MESH_IO_MSH_HH_ */
diff --git a/src/io/mesh_io/mesh_io_msh_struct.cc b/src/io/mesh_io/mesh_io_msh_struct.cc
index 5c0830295..789f9b80a 100644
--- a/src/io/mesh_io/mesh_io_msh_struct.cc
+++ b/src/io/mesh_io/mesh_io_msh_struct.cc
@@ -1,79 +1,79 @@
/**
* @file mesh_io_msh_struct.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Jan 26 2018
*
* @brief Read/Write for MSH files generated by gmsh
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_io_msh_struct.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
-MeshIOMSHStruct::MeshIOMSHStruct() : MeshIOMSH() {
+MeshIOMSHStruct::MeshIOMSHStruct() {
canReadSurface = true;
canReadExtendedData = true;
_msh_to_akantu_element_types.clear();
_msh_to_akantu_element_types[_msh_not_defined] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2] = _bernoulli_beam_2;
_msh_to_akantu_element_types[_msh_triangle_3] =
_discrete_kirchhoff_triangle_18;
_akantu_to_msh_element_types.clear();
_akantu_to_msh_element_types[_not_defined] = _msh_not_defined;
_akantu_to_msh_element_types[_bernoulli_beam_2] = _msh_segment_2;
_akantu_to_msh_element_types[_bernoulli_beam_3] = _msh_segment_2;
_akantu_to_msh_element_types[_discrete_kirchhoff_triangle_18] =
_msh_triangle_3;
for (auto & kv_pair : _akantu_to_msh_element_types) {
UInt nb_nodes = _msh_nodes_per_elem[kv_pair.second];
std::vector<UInt> tmp(nb_nodes);
std::iota(tmp.begin(), tmp.end(), 0);
_read_order[kv_pair.first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
void MeshIOMSHStruct::read(const std::string & filename, Mesh & mesh) {
if (mesh.getSpatialDimension() == 2) {
_msh_to_akantu_element_types[_msh_segment_2] = _bernoulli_beam_2;
} else if (mesh.getSpatialDimension() == 3) {
_msh_to_akantu_element_types[_msh_segment_2] = _bernoulli_beam_3;
AKANTU_DEBUG_WARNING("The MeshIOMSHStruct is reading bernoulli beam 3D be "
"sure to provide the missing normals with the element "
"data \"extra_normal\"");
}
MeshIOMSH::read(filename, mesh);
}
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_msh_struct.hh b/src/io/mesh_io/mesh_io_msh_struct.hh
index 06e67a5ce..7c3f64aa8 100644
--- a/src/io/mesh_io/mesh_io_msh_struct.hh
+++ b/src/io/mesh_io/mesh_io_msh_struct.hh
@@ -1,53 +1,53 @@
/**
* @file mesh_io_msh_struct.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Jan 26 2018
*
* @brief Read/Write for MSH files
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_IO_MSH_STRUCT_HH__
-#define __AKANTU_MESH_IO_MSH_STRUCT_HH__
+#ifndef AKANTU_MESH_IO_MSH_STRUCT_HH_
+#define AKANTU_MESH_IO_MSH_STRUCT_HH_
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIOMSHStruct : public MeshIOMSH {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSHStruct();
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
};
} // namespace akantu
-#endif /* __AKANTU_MESH_IO_MSH_STRUCT_HH__ */
+#endif /* AKANTU_MESH_IO_MSH_STRUCT_HH_ */
diff --git a/src/io/parser/algebraic_parser.hh b/src/io/parser/algebraic_parser.hh
index e2287371c..870c3d963 100644
--- a/src/io/parser/algebraic_parser.hh
+++ b/src/io/parser/algebraic_parser.hh
@@ -1,511 +1,515 @@
/**
* @file algebraic_parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Wed Nov 08 2017
*
* @brief algebraic_parser definition of the grammar
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
// Boost
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/phoenix.hpp>
#include <boost/spirit/include/qi.hpp>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ALGEBRAIC_PARSER_HH__
-#define __AKANTU_ALGEBRAIC_PARSER_HH__
+#ifndef AKANTU_ALGEBRAIC_PARSER_HH_
+#define AKANTU_ALGEBRAIC_PARSER_HH_
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
namespace akantu {
namespace parser {
struct algebraic_error_handler_ {
template <typename, typename, typename> struct result {
using type = void;
};
template <typename Iterator>
void operator()(qi::info const & what, Iterator err_pos,
Iterator last) const {
AKANTU_EXCEPTION(
"Error! Expecting "
<< what // what failed?
<< " here: \""
<< std::string(err_pos, last) // iterators to error-pos, end
<< "\"");
}
};
static Real my_min(Real a, Real b) { return std::min(a, b); }
static Real my_max(Real a, Real b) { return std::max(a, b); }
static Real my_pow(Real a, Real b) { return std::pow(a, b); }
static Real eval_param(const ID & a, const ParserSection & section) {
return section.getParameter(a, _ppsc_current_and_parent_scope);
}
static Real unary_func(Real (*func)(Real), Real a) { return func(a); }
static Real binary_func(Real (*func)(Real, Real), Real a, Real b) {
return func(a, b);
}
template <class Iterator, typename Skipper = spirit::unused_type>
struct AlgebraicGrammar : qi::grammar<Iterator, Real(), Skipper> {
AlgebraicGrammar(const ParserSection & section)
: AlgebraicGrammar::base_type(start, "algebraic_grammar"),
section(section) {
// phx::function<lazy_pow_> lazy_pow;
// phx::function<lazy_unary_func_> lazy_unary_func;
// phx::function<lazy_binary_func_> lazy_binary_func;
// phx::function<lazy_eval_param_> lazy_eval_param;
/* clang-format off */
start
= expr.alias()
;
expr
= term [ lbs::_val = lbs::_1 ]
>> *( ('+' > term [ lbs::_val += lbs::_1 ])
| ('-' > term [ lbs::_val -= lbs::_1 ])
)
;
term
= factor [ lbs::_val = lbs::_1 ]
>> *( ('*' > factor [ lbs::_val *= lbs::_1 ])
| ('/' > factor [ lbs::_val /= lbs::_1 ])
)
;
factor
= number [ lbs::_val = lbs::_1 ]
>> *("**" > number [ lbs::_val = phx::bind(&my_pow, lbs::_val, lbs::_1) ])
;
number
= real [ lbs::_val = lbs::_1 ]
| ('-' > number [ lbs::_val = -lbs::_1 ])
| ('+' > number [ lbs::_val = lbs::_1 ])
| constant [ lbs::_val = lbs::_1 ]
| function [ lbs::_val = lbs::_1 ]
| ('(' > expr > ')') [ lbs::_val = lbs::_1 ]
| variable [ lbs::_val = lbs::_1 ]
;
function
= (qi::no_case[unary_function]
> '('
> expr
> ')') [ lbs::_val = phx::bind(&unary_func, lbs::_1, lbs::_2) ]
| (qi::no_case[binary_function]
> '(' >> expr
> ',' >> expr
> ')') [ lbs::_val = phx::bind(&binary_func ,lbs::_1, lbs::_2, lbs::_3) ]
;
variable
= key [ lbs::_val = phx::bind(&eval_param, lbs::_1, section) ]
;
key
= qi::no_skip[qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")] // coming from the InputFileGrammar
;
#ifndef M_PI
# define M_PI 3.14159265358979323846
#endif
#ifndef M_E
# define M_E 2.7182818284590452354
#endif
constant.add
("pi", M_PI)
("e", M_E);
unary_function.add
("abs" , &std::abs )
("acos" , &std::acos )
("asin" , &std::asin )
("atan" , &std::atan )
("ceil" , &std::ceil )
("cos" , &std::cos )
("cosh" , &std::cosh )
("exp" , &std::exp )
("floor" , &std::floor )
("log10" , &std::log10 )
("log" , &std::log )
("sin" , &std::sin )
("sinh" , &std::sinh )
("sqrt" , &std::sqrt )
("tan" , &std::tan )
("tanh" , &std::tanh )
("acosh" , &std::acosh )
("asinh" , &std::asinh )
("atanh" , &std::atanh )
("exp2" , &std::exp2 )
("expm1" , &std::expm1 )
("log1p" , &std::log1p )
("log2" , &std::log2 )
("erf" , &std::erf )
("erfc" , &std::erfc )
("lgamma", &std::lgamma)
("tgamma", &std::tgamma)
("trunc" , &std::trunc )
("round" , &std::round )
// ("crbt" , &std::crbt )
;
binary_function.add
("pow" , &std::pow )
("min" , &parser::my_min)
("max" , &parser::my_max)
("atan2", &std::atan2 )
("fmod" , &std::fmod )
("hypot", &std::hypot )
;
#if !defined(AKANTU_NDEBUG)
phx::function<algebraic_error_handler_> const error_handler = algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
expr .name("expression");
term .name("term");
factor .name("factor");
number .name("numerical-value");
variable.name("variable");
function.name("function");
constant.name("constants-list");
unary_function.name("unary-functions-list");
binary_function.name("binary-functions-list");
#if !defined AKANTU_NDEBUG
if(AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(expr);
qi::debug(term);
qi::debug(factor);
qi::debug(number);
qi::debug(variable);
qi::debug(function);
}
#endif
}
/* clang-format on */
private:
qi::rule<Iterator, Real(), Skipper> start;
qi::rule<Iterator, Real(), Skipper> expr;
qi::rule<Iterator, Real(), Skipper> term;
qi::rule<Iterator, Real(), Skipper> factor;
qi::rule<Iterator, Real(), Skipper> number;
qi::rule<Iterator, Real(), Skipper> variable;
qi::rule<Iterator, Real(), Skipper> function;
qi::rule<Iterator, std::string(), Skipper> key;
qi::real_parser<Real, qi::real_policies<Real>> real;
qi::symbols<char, Real> constant;
qi::symbols<char, Real (*)(Real)> unary_function;
qi::symbols<char, Real (*)(Real, Real)> binary_function;
const ParserSection & section;
};
/* ---------------------------------------------------------------------- */
/* Vector Parser */
/* ---------------------------------------------------------------------- */
struct parsable_vector {
operator Vector<Real>() {
Vector<Real> tmp(_cells.size());
auto it = _cells.begin();
- for (UInt i = 0; it != _cells.end(); ++it, ++i)
+ for (UInt i = 0; it != _cells.end(); ++it, ++i) {
tmp(i) = *it;
+ }
return tmp;
}
std::vector<Real> _cells;
};
inline std::ostream & operator<<(std::ostream & stream,
const parsable_vector & pv) {
stream << "pv[";
auto it = pv._cells.begin();
if (it != pv._cells.end()) {
stream << *it;
- for (++it; it != pv._cells.end(); ++it)
+ for (++it; it != pv._cells.end(); ++it) {
stream << ", " << *it;
+ }
}
stream << "]";
return stream;
}
struct parsable_matrix {
operator Matrix<Real>() {
size_t cols = 0;
auto it_rows = _cells.begin();
- for (; it_rows != _cells.end(); ++it_rows)
+ for (; it_rows != _cells.end(); ++it_rows) {
cols = std::max(cols, it_rows->_cells.size());
+ }
Matrix<Real> tmp(_cells.size(), _cells[0]._cells.size(), 0.);
it_rows = _cells.begin();
for (UInt i = 0; it_rows != _cells.end(); ++it_rows, ++i) {
auto it_cols = it_rows->_cells.begin();
for (UInt j = 0; it_cols != it_rows->_cells.end(); ++it_cols, ++j) {
tmp(i, j) = *it_cols;
}
}
return tmp;
}
std::vector<parsable_vector> _cells;
};
inline std::ostream & operator<<(std::ostream & stream,
const parsable_matrix & pm) {
stream << "pm[";
auto it = pm._cells.begin();
if (it != pm._cells.end()) {
stream << *it;
- for (++it; it != pm._cells.end(); ++it)
+ for (++it; it != pm._cells.end(); ++it) {
stream << ", " << *it;
+ }
}
stream << "]";
return stream;
}
/* ---------------------------------------------------------------------- */
template <typename T1, typename T2>
static void cont_add(T1 & cont, T2 & value) {
cont._cells.push_back(value);
}
/* ---------------------------------------------------------------------- */
template <class Iterator, typename Skipper = spirit::unused_type>
struct VectorGrammar : qi::grammar<Iterator, parsable_vector(), Skipper> {
VectorGrammar(const ParserSection & section)
: VectorGrammar::base_type(start, "vector_algebraic_grammar"),
number(section) {
start = '[' > vector > ']';
vector =
(number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)] >>
*(',' >> number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)]))[lbs::_val = lbs::_a];
#if !defined(AKANTU_NDEBUG)
phx::function<algebraic_error_handler_> const error_handler =
algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start.name("start");
vector.name("vector");
number.name("value");
#if !defined AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(start);
qi::debug(vector);
}
#endif
}
private:
qi::rule<Iterator, parsable_vector(), Skipper> start;
qi::rule<Iterator, parsable_vector(), qi::locals<parsable_vector>, Skipper>
vector;
qi::rule<Iterator, Real(), Skipper> value;
AlgebraicGrammar<Iterator, Skipper> number;
};
/* ---------------------------------------------------------------------- */
static inline bool vector_eval(const ID & a, const ParserSection & section,
parsable_vector & result) {
std::string value = section.getParameter(a, _ppsc_current_and_parent_scope);
std::string::const_iterator b = value.begin();
std::string::const_iterator e = value.end();
parser::VectorGrammar<std::string::const_iterator, qi::space_type> grammar(
section);
return qi::phrase_parse(b, e, grammar, qi::space, result);
}
/* ---------------------------------------------------------------------- */
template <class Iterator, typename Skipper = spirit::unused_type>
struct MatrixGrammar : qi::grammar<Iterator, parsable_matrix(), Skipper> {
MatrixGrammar(const ParserSection & section)
: MatrixGrammar::base_type(start, "matrix_algebraic_grammar"),
vector(section) {
start = '[' >> matrix >> ']';
matrix =
(rows[phx::bind(&cont_add<parsable_matrix, parsable_vector>, lbs::_a,
lbs::_1)] >>
*(',' >> rows[phx::bind(&cont_add<parsable_matrix, parsable_vector>,
lbs::_a, lbs::_1)]))[lbs::_val = lbs::_a];
rows = eval_vector | vector;
eval_vector = (key[lbs::_pass = phx::bind(&vector_eval, lbs::_1, section,
lbs::_a)])[lbs::_val = lbs::_a];
key = qi::char_("a-zA-Z_") >>
*qi::char_("a-zA-Z_0-9") // coming from the InputFileGrammar
;
#if !defined(AKANTU_NDEBUG)
phx::function<algebraic_error_handler_> const error_handler =
algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start.name("matrix");
matrix.name("all_rows");
rows.name("rows");
vector.name("vector");
eval_vector.name("eval_vector");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(start);
qi::debug(matrix);
qi::debug(rows);
qi::debug(eval_vector);
qi::debug(key);
}
#endif
}
private:
qi::rule<Iterator, parsable_matrix(), Skipper> start;
qi::rule<Iterator, parsable_matrix(), qi::locals<parsable_matrix>, Skipper>
matrix;
qi::rule<Iterator, parsable_vector(), Skipper> rows;
qi::rule<Iterator, parsable_vector(), qi::locals<parsable_vector>, Skipper>
eval_vector;
qi::rule<Iterator, std::string(), Skipper> key;
VectorGrammar<Iterator, Skipper> vector;
};
/* ---------------------------------------------------------------------- */
/* Randon Generator */
/* ---------------------------------------------------------------------- */
struct ParsableRandomGenerator {
ParsableRandomGenerator(
Real base = Real(),
const RandomDistributionType & type = _rdt_not_defined,
const parsable_vector & parameters = parsable_vector())
: base(base), type(type), parameters(parameters) {}
Real base;
RandomDistributionType type;
parsable_vector parameters;
};
inline std::ostream & operator<<(std::ostream & stream,
const ParsableRandomGenerator & prg) {
stream << "prg[" << prg.base << " " << UInt(prg.type) << " "
<< prg.parameters << "]";
return stream;
}
/* ---------------------------------------------------------------------- */
template <class Iterator, typename Skipper = spirit::unused_type>
struct RandomGeneratorGrammar
: qi::grammar<Iterator, ParsableRandomGenerator(), Skipper> {
RandomGeneratorGrammar(const ParserSection & section)
: RandomGeneratorGrammar::base_type(start, "random_generator_grammar"),
number(section) {
start = generator.alias();
generator =
qi::hold[distribution[lbs::_val = lbs::_1]] |
number[lbs::_val = phx::construct<ParsableRandomGenerator>(lbs::_1)];
distribution = (number >> generator_type >> '[' >> generator_params >>
']')[lbs::_val = phx::construct<ParsableRandomGenerator>(
lbs::_1, lbs::_2, lbs::_3)];
generator_params =
(number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)] >>
*(',' > number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)]))[lbs::_val = lbs::_a];
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_ADD(r, data, elem) \
(BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 0, elem)), \
AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(BOOST_PP_TUPLE_ELEM(2, 0, elem)))
generator_type.add BOOST_PP_SEQ_FOR_EACH(
AKANTU_RANDOM_DISTRIBUTION_TYPE_ADD, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES);
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_ADD
#if !defined(AKANTU_NDEBUG)
phx::function<algebraic_error_handler_> const error_handler =
algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start.name("random-generator");
generator.name("random-generator");
distribution.name("random-distribution");
generator_type.name("generator-type");
generator_params.name("generator-parameters");
number.name("number");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(generator);
qi::debug(distribution);
qi::debug(generator_params);
}
#endif
}
private:
qi::rule<Iterator, ParsableRandomGenerator(), Skipper> start;
qi::rule<Iterator, ParsableRandomGenerator(), Skipper> generator;
qi::rule<Iterator, ParsableRandomGenerator(), Skipper> distribution;
qi::rule<Iterator, parsable_vector(), qi::locals<parsable_vector>, Skipper>
generator_params;
AlgebraicGrammar<Iterator, Skipper> number;
qi::symbols<char, RandomDistributionType> generator_type;
};
} // namespace parser
} // namespace akantu
-#endif /* __AKANTU_ALGEBRAIC_PARSER_HH__ */
+#endif /* AKANTU_ALGEBRAIC_PARSER_HH_ */
diff --git a/src/io/parser/cppargparse/cppargparse.cc b/src/io/parser/cppargparse/cppargparse.cc
index d9e7df3ed..95fadd974 100644
--- a/src/io/parser/cppargparse/cppargparse.cc
+++ b/src/io/parser/cppargparse/cppargparse.cc
@@ -1,522 +1,536 @@
/**
* @file cppargparse.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
* @date last modification: Wed Nov 08 2017
*
* @brief implementation of the ArgumentParser
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cppargparse.hh"
#include <cstdlib>
#include <cstring>
#include <libgen.h>
#include <algorithm>
#include <iomanip>
#include <iostream>
#include <queue>
#include <sstream>
#include <string>
#include <exception>
#include <stdexcept>
#include <string.h>
namespace cppargparse {
/* -------------------------------------------------------------------------- */
static inline std::string to_upper(const std::string & str) {
std::string lstr = str;
std::transform(lstr.begin(), lstr.end(), lstr.begin(),
(int (*)(int))std::toupper);
return lstr;
}
/* -------------------------------------------------------------------------- */
/* ArgumentParser */
/* -------------------------------------------------------------------------- */
ArgumentParser::ArgumentParser() {
this->addArgument("-h;--help", "show this help message and exit", 0, _boolean,
false, true);
}
/* -------------------------------------------------------------------------- */
ArgumentParser::~ArgumentParser() {
for (auto it = arguments.begin(); it != arguments.end(); ++it) {
delete it->second;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::setParallelContext(int prank, int psize) {
this->prank = prank;
this->psize = psize;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::_exit(const std::string & msg, int status) {
if (prank == 0) {
- if (msg != "") {
+ if (not msg.empty()) {
std::cerr << msg << std::endl;
std::cerr << std::endl;
}
this->print_help(std::cerr);
}
- if (external_exit)
+ if (external_exit != nullptr) {
(*external_exit)(status);
- else {
+ } else {
exit(status);
}
}
/* -------------------------------------------------------------------------- */
-const ArgumentParser::Argument & ArgumentParser::
-operator[](const std::string & name) const {
+const ArgumentParser::Argument &
+ArgumentParser::operator[](const std::string & name) const {
auto it = success_parsed.find(name);
if (it != success_parsed.end()) {
return *(it->second);
- } else {
- throw std::range_error("No argument named \'" + name +
- "\' was found in the parsed argument," +
- " make sur to specify it \'required\'" +
- " or to give it a default value");
}
+ throw std::range_error("No argument named \'" + name +
+ "\' was found in the parsed argument," +
+ " make sur to specify it \'required\'" +
+ " or to give it a default value");
}
/* -------------------------------------------------------------------------- */
bool ArgumentParser::has(const std::string & name) const {
return (success_parsed.find(name) != success_parsed.end());
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type) {
_addArgument(name_or_flag, help, nargs, type);
}
/* -------------------------------------------------------------------------- */
-ArgumentParser::_Argument &
+ArgumentParser::Argument_ &
ArgumentParser::_addArgument(const std::string & name, const std::string & help,
int nargs, ArgumentType type) {
- _Argument * arg = nullptr;
+ Argument_ * arg = nullptr;
switch (type) {
case _string: {
arg = new ArgumentStorage<std::string>();
break;
}
case _float: {
arg = new ArgumentStorage<double>();
break;
}
case _integer: {
arg = new ArgumentStorage<long int>();
break;
}
case _boolean: {
arg = new ArgumentStorage<bool>();
break;
}
}
arg->help = help;
arg->nargs = nargs;
arg->type = type;
std::stringstream sstr(name);
std::string item;
std::vector<std::string> tmp_keys;
while (std::getline(sstr, item, ';')) {
tmp_keys.push_back(item);
}
int long_key = -1;
int short_key = -1;
- bool problem = (tmp_keys.size() > 2) || (name == "");
+ bool problem = (tmp_keys.size() > 2) || name.empty();
for (auto it = tmp_keys.begin(); it != tmp_keys.end(); ++it) {
if (it->find("--") == 0) {
problem |= (long_key != -1);
long_key = it - tmp_keys.begin();
} else if (it->find("-") == 0) {
problem |= (long_key != -1);
short_key = it - tmp_keys.begin();
}
}
problem |= ((tmp_keys.size() == 2) && (long_key == -1 || short_key == -1));
if (problem) {
delete arg;
throw std::invalid_argument("Synthax of name or flags is not correct. "
"Possible synthax are \'-f\', \'-f;--foo\', "
"\'--foo\', \'bar\'");
}
if (long_key != -1) {
arg->name = tmp_keys[long_key];
arg->name.erase(0, 2);
} else if (short_key != -1) {
arg->name = tmp_keys[short_key];
arg->name.erase(0, 1);
} else {
arg->name = tmp_keys[0];
pos_args.push_back(arg);
arg->required = (nargs != _one_if_possible);
arg->is_positional = true;
}
arguments[arg->name] = arg;
if (!arg->is_positional) {
if (short_key != -1) {
std::string key = tmp_keys[short_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
if (long_key != -1) {
std::string key = tmp_keys[long_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
}
return *arg;
}
#if not HAVE_STRDUP
static char * strdup(const char * str) {
size_t len = strlen(str);
auto * x = (char *)malloc(len + 1); /* 1 for the null terminator */
- if (!x)
- return nullptr; /* malloc could not allocate memory */
+ if (x == nullptr) {
+ return nullptr; /* malloc could not allocate memory */
+ }
+
memcpy(x, str, len + 1); /* copy the string into the new buffer */
return x;
}
#endif
/* -------------------------------------------------------------------------- */
void ArgumentParser::parse(int & argc, char **& argv, int flags,
bool parse_help) {
- bool stop_in_not_parsed = flags & _stop_on_not_parsed;
- bool remove_parsed = flags & _remove_parsed;
+ bool stop_in_not_parsed = (flags & _stop_on_not_parsed) != 0;
+ bool remove_parsed = (flags & _remove_parsed) != 0;
std::vector<std::string> argvs;
argvs.reserve(argc);
for (int i = 0; i < argc; ++i) {
argvs.emplace_back(argv[i]);
}
unsigned int current_position = 0;
- if (this->program_name == "" && argc > 0) {
+ if (this->program_name.empty() and argc > 0) {
std::string prog = argvs[current_position];
const char * c_prog = prog.c_str();
char * c_prog_tmp = strdup(c_prog);
std::string base_prog(basename(c_prog_tmp));
this->program_name = base_prog;
std::free(c_prog_tmp);
}
- std::queue<_Argument *> positional_queue;
- for (auto it = pos_args.begin(); it != pos_args.end(); ++it)
+ std::queue<Argument_ *> positional_queue;
+ for (auto it = pos_args.begin(); it != pos_args.end(); ++it) {
positional_queue.push(*it);
+ }
std::vector<int> argvs_to_remove;
++current_position; // consume argv[0]
while (current_position < argvs.size()) {
std::string arg = argvs[current_position];
++current_position;
auto key_it = key_args.find(arg);
bool is_positional = false;
- _Argument * argument_ptr = nullptr;
+ Argument_ * argument_ptr = nullptr;
if (key_it == key_args.end()) {
if (positional_queue.empty()) {
- if (stop_in_not_parsed)
+ if (stop_in_not_parsed) {
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
+ }
continue;
- } else {
- argument_ptr = positional_queue.front();
- is_positional = true;
- --current_position;
}
+
+ argument_ptr = positional_queue.front();
+ is_positional = true;
+ --current_position;
+
} else {
argument_ptr = key_it->second;
}
if (remove_parsed && !is_positional && argument_ptr->name != "help") {
argvs_to_remove.push_back(current_position - 1);
}
- _Argument & argument = *argument_ptr;
+ Argument_ & argument = *argument_ptr;
+
+ unsigned int min_nb_val{};
+ unsigned int max_nb_val{};
- unsigned int min_nb_val = 0, max_nb_val = 0;
switch (argument.nargs) {
case _one_if_possible:
max_nb_val = 1;
break; // "?"
case _at_least_one:
min_nb_val = 1; // "+"
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it*/
case _any:
max_nb_val = argc - current_position;
break; // "*"
default:
min_nb_val = max_nb_val = argument.nargs; // "N"
}
std::vector<std::string> values;
unsigned int arg_consumed = 0;
if (max_nb_val <= (argc - current_position)) {
for (; arg_consumed < max_nb_val; ++arg_consumed) {
std::string v = argvs[current_position];
++current_position;
bool is_key = key_args.find(v) != key_args.end();
bool is_good_type = checkType(argument.type, v);
if (!is_key && is_good_type) {
values.push_back(v);
- if (remove_parsed)
+ if (remove_parsed) {
argvs_to_remove.push_back(current_position - 1);
+ }
} else {
// unconsume not parsed argument for optional
- if (!is_positional || is_key)
+ if (!is_positional || is_key) {
--current_position;
+ }
break;
}
}
}
if (arg_consumed < min_nb_val) {
if (!is_positional) {
this->_exit("Not enought values for the argument " + argument.name +
" where provided",
EXIT_FAILURE);
} else {
- if (stop_in_not_parsed)
+ if (stop_in_not_parsed) {
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
+ }
}
} else {
- if (is_positional)
+ if (is_positional) {
positional_queue.pop();
+ }
if (!argument.parsed) {
success_parsed[argument.name] = &argument;
argument.parsed = true;
if ((argument.nargs == _one_if_possible || argument.nargs == 0) &&
arg_consumed == 0) {
- if (argument.has_const)
+ if (argument.has_const) {
argument.setToConst();
- else if (argument.has_default)
+ } else if (argument.has_default) {
argument.setToDefault();
+ }
} else {
argument.setValues(values);
}
} else {
this->_exit("Argument " + argument.name +
" already present in the list of argument",
EXIT_FAILURE);
}
}
}
for (auto ait = arguments.begin(); ait != arguments.end(); ++ait) {
- _Argument & argument = *(ait->second);
+ Argument_ & argument = *(ait->second);
if (!argument.parsed) {
if (argument.has_default) {
argument.setToDefault();
success_parsed[argument.name] = &argument;
}
if (argument.required) {
this->_exit("Argument " + argument.name + " required but not given!",
EXIT_FAILURE);
}
}
}
// removing the parsed argument if remove_parsed is true
- if (argvs_to_remove.size()) {
+ if (not argvs_to_remove.empty()) {
std::vector<int>::const_iterator next_to_remove = argvs_to_remove.begin();
for (int i = 0, c = 0; i < argc; ++i) {
if (next_to_remove == argvs_to_remove.end() || i != *next_to_remove) {
argv[c] = argv[i];
++c;
} else {
- if (next_to_remove != argvs_to_remove.end())
+ if (next_to_remove != argvs_to_remove.end()) {
++next_to_remove;
+ }
}
}
argc -= argvs_to_remove.size();
}
this->argc = &argc;
this->argv = &argv;
if (this->arguments["help"]->parsed && parse_help) {
this->_exit();
}
}
/* -------------------------------------------------------------------------- */
-bool ArgumentParser::checkType(ArgumentType type,
- const std::string & value) const {
+bool ArgumentParser::checkType(ArgumentType type, const std::string & value) {
std::stringstream sstr(value);
switch (type) {
case _string: {
std::string s;
sstr >> s;
break;
}
case _float: {
double d;
sstr >> d;
break;
}
case _integer: {
long int i;
sstr >> i;
break;
}
case _boolean: {
bool b;
sstr >> b;
break;
}
}
- return (sstr.fail() == false);
+ return (not sstr.fail());
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::printself(std::ostream & stream) const {
for (auto it = success_parsed.begin(); it != success_parsed.end(); ++it) {
const Argument & argument = *(it->second);
argument.printself(stream);
stream << std::endl;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage(std::ostream & stream) const {
stream << "Usage: " << this->program_name;
// print shorten usage
for (auto it = arguments.begin(); it != arguments.end(); ++it) {
- const _Argument & argument = *(it->second);
+ const Argument_ & argument = *(it->second);
if (!argument.is_positional) {
- if (!argument.required)
+ if (!argument.required) {
stream << " [";
+ }
stream << argument.keys[0];
- this->print_usage_nargs(stream, argument);
- if (!argument.required)
+ ArgumentParser::print_usage_nargs(stream, argument);
+ if (!argument.required) {
stream << "]";
+ }
}
}
for (auto it = pos_args.begin(); it != pos_args.end(); ++it) {
- const _Argument & argument = **it;
- this->print_usage_nargs(stream, argument);
+ const Argument_ & argument = **it;
+ ArgumentParser::print_usage_nargs(stream, argument);
}
stream << std::endl;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage_nargs(std::ostream & stream,
- const _Argument & argument) const {
+ const Argument_ & argument) {
std::string u_name = to_upper(argument.name);
switch (argument.nargs) {
case _one_if_possible:
stream << " [" << u_name << "]";
break;
case _at_least_one:
stream << " " << u_name;
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it */
case _any:
stream << " [" << u_name << " ...]";
break;
default:
for (int i = 0; i < argument.nargs; ++i) {
stream << " " << u_name;
}
}
}
void ArgumentParser::print_help(std::ostream & stream) const {
this->print_usage(stream);
if (!pos_args.empty()) {
stream << std::endl;
stream << "positional arguments:" << std::endl;
for (auto it = pos_args.begin(); it != pos_args.end(); ++it) {
- const _Argument & argument = **it;
+ const Argument_ & argument = **it;
this->print_help_argument(stream, argument);
}
}
if (!key_args.empty()) {
stream << std::endl;
stream << "optional arguments:" << std::endl;
for (auto it = arguments.begin(); it != arguments.end(); ++it) {
- const _Argument & argument = *(it->second);
+ const Argument_ & argument = *(it->second);
if (!argument.is_positional) {
this->print_help_argument(stream, argument);
}
}
}
}
void ArgumentParser::print_help_argument(std::ostream & stream,
- const _Argument & argument) const {
- std::string key("");
- if (argument.is_positional)
+ const Argument_ & argument) const {
+ std::string key;
+ if (argument.is_positional) {
key = argument.name;
- else {
+ } else {
std::stringstream sstr;
for (unsigned int i = 0; i < argument.keys.size(); ++i) {
- if (i != 0)
+ if (i != 0) {
sstr << ", ";
+ }
sstr << argument.keys[i];
this->print_usage_nargs(sstr, argument);
}
key = sstr.str();
}
stream << " " << std::left << std::setw(15) << key << " " << argument.help;
argument.printDefault(stream);
stream << std::endl;
}
} // namespace cppargparse
diff --git a/src/io/parser/cppargparse/cppargparse.hh b/src/io/parser/cppargparse/cppargparse.hh
index 8ab19ffc1..b6fe478c3 100644
--- a/src/io/parser/cppargparse/cppargparse.hh
+++ b/src/io/parser/cppargparse/cppargparse.hh
@@ -1,200 +1,200 @@
/**
* @file cppargparse.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
* @date last modification: Sun Dec 03 2017
*
* @brief Get the commandline options and store them as short, long and others
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <map>
#include <string>
#include <vector>
-#ifndef __CPPARGPARSE_HH__
-#define __CPPARGPARSE_HH__
+#ifndef CPPARGPARSE_HH_
+#define CPPARGPARSE_HH_
/* -------------------------------------------------------------------------- */
namespace cppargparse {
/// define the types of the arguments
enum ArgumentType { _string, _integer, _float, _boolean };
/// Defines how many arguments to expect
enum ArgumentNargs { _one_if_possible = -1, _at_least_one = -2, _any = -3 };
/// Flags for the parse function of ArgumentParser
enum ParseFlags {
_no_flags = 0x0, ///< Default behavior
_stop_on_not_parsed = 0x1, ///< Stop on unknown arguments
_remove_parsed = 0x2 ///< Remove parsed arguments from argc argv
};
/// Helps to combine parse flags
inline ParseFlags operator|(const ParseFlags & a, const ParseFlags & b) {
auto tmp = ParseFlags(int(a) | int(b));
return tmp;
}
/* -------------------------------------------------------------------------- */
/**
* ArgumentParser is a class that mimics the Python argparse module
*/
class ArgumentParser {
public:
/// public definition of an argument
class Argument {
public:
Argument() : name(std::string()) {}
virtual ~Argument() = default;
virtual void printself(std::ostream & stream) const = 0;
template <class T> operator T() const;
std::string name;
};
/// constructor
ArgumentParser();
/// destroy everything
~ArgumentParser();
/// add an argument with a description
void addArgument(const std::string & name_or_flag, const std::string & help,
int nargs = 1, ArgumentType type = _string);
/// add an argument with an help and a default value
template <class T>
void addArgument(const std::string & name_or_flag, const std::string & help,
int nargs, ArgumentType type, T def);
/// add an argument with an help and a default + const value
template <class T>
void addArgument(const std::string & name_or_flag, const std::string & help,
int nargs, ArgumentType type, T def, T cons);
/// parse argc, argv
void parse(int & argc, char **& argv, int flags = _stop_on_not_parsed,
bool parse_help = true);
/// get the last argc parsed
int & getArgC() { return *(this->argc); }
/// get the last argv parsed
char **& getArgV() { return *(this->argv); }
/// print the content in the stream
void printself(std::ostream & stream) const;
/// print the help text
void print_help(std::ostream & stream = std::cout) const;
/// print the usage text
void print_usage(std::ostream & stream = std::cout) const;
/// set an external function to replace the exit function from the stdlib
void setExternalExitFunction(void (*external_exit)(int)) {
this->external_exit = external_exit;
}
/// accessor for a registered argument that was parsed, throw an exception if
/// the argument does not exist or was not set (parsed or default value)
const Argument & operator[](const std::string & name) const;
/// is the argument present
- bool has(const std::string &) const;
+ bool has(const std::string & /*name*/) const;
/// set the parallel context to avoid multiple help messages in
/// multiproc/thread cases
void setParallelContext(int prank, int psize);
public:
/// Internal class describing the arguments
- struct _Argument;
+ struct Argument_;
/// Stores that value of an argument
template <class T> class ArgumentStorage;
private:
/// Internal function to be used by the public addArgument
- _Argument & _addArgument(const std::string & name_or_flag,
- const std::string & description, int nargs,
+ Argument_ & _addArgument(const std::string & name_or_flag,
+ const std::string & help, int nargs,
ArgumentType type);
void _exit(const std::string & msg = "", int status = 0);
- bool checkType(ArgumentType type, const std::string & value) const;
+ static bool checkType(ArgumentType type, const std::string & value);
/// function to help to print help
- void print_usage_nargs(std::ostream & stream,
- const _Argument & argument) const;
+ static void print_usage_nargs(std::ostream & stream,
+ const Argument_ & argument);
/// function to help to print help
void print_help_argument(std::ostream & stream,
- const _Argument & argument) const;
+ const Argument_ & argument) const;
private:
/// public arguments storage
using Arguments = std::map<std::string, Argument *>;
/// internal arguments storage
- using _Arguments = std::map<std::string, _Argument *>;
+ using Arguments_ = std::map<std::string, Argument_ *>;
/// association key argument
- using ArgumentKeyMap = std::map<std::string, _Argument *>;
+ using ArgumentKeyMap = std::map<std::string, Argument_ *>;
/// position arguments
- using PositionalArgument = std::vector<_Argument *>;
+ using PositionalArgument = std::vector<Argument_ *>;
/// internal storage of arguments declared by the user
- _Arguments arguments;
+ Arguments_ arguments;
/// list of arguments successfully parsed
Arguments success_parsed;
/// keys associated to arguments
ArgumentKeyMap key_args;
/// positional arguments
PositionalArgument pos_args;
/// program name
std::string program_name;
/// exit function to use
void (*external_exit)(int){nullptr};
/// Parallel context, rank and size of communicator
int prank{0}, psize{1};
/// The last argc parsed (those are the modified version after parse)
int * argc;
/// The last argv parsed (those are the modified version after parse)
char *** argv;
};
inline std::ostream & operator<<(std::ostream & stream,
const ArgumentParser & argparse) {
argparse.printself(stream);
return stream;
}
} // namespace cppargparse
-#endif /* __CPPARGPARSE_HH__ */
+#endif /* CPPARGPARSE_HH_ */
#include "cppargparse_tmpl.hh"
diff --git a/src/io/parser/cppargparse/cppargparse_tmpl.hh b/src/io/parser/cppargparse/cppargparse_tmpl.hh
index ec71057b2..7e138944e 100644
--- a/src/io/parser/cppargparse/cppargparse_tmpl.hh
+++ b/src/io/parser/cppargparse/cppargparse_tmpl.hh
@@ -1,241 +1,241 @@
/**
* @file cppargparse_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
* @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the templated part of the commandline argument
* parser
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include <stdexcept>
-#ifndef __CPPARGPARSE_TMPL_HH__
-#define __CPPARGPARSE_TMPL_HH__
+#ifndef CPPARGPARSE_TMPL_HH_
+#define CPPARGPARSE_TMPL_HH_
namespace cppargparse {
/* -------------------------------------------------------------------------- */
/* Argument */
/* -------------------------------------------------------------------------- */
/// internal description of arguments
-struct ArgumentParser::_Argument : public Argument {
- _Argument() : Argument(), help(std::string()) {}
- ~_Argument() override = default;
+struct ArgumentParser::Argument_ : public Argument {
+ Argument_() = default;
+ ~Argument_() override = default;
void setValues(std::vector<std::string> & values) {
for (auto it = values.begin(); it != values.end(); ++it) {
this->addValue(*it);
}
}
virtual void addValue(std::string & value) = 0;
virtual void setToDefault() = 0;
virtual void setToConst() = 0;
std::ostream & printDefault(std::ostream & stream) const {
stream << std::boolalpha;
if (has_default) {
stream << " (default: ";
this->_printDefault(stream);
stream << ")";
}
if (has_const) {
stream << " (const: ";
this->_printConst(stream);
stream << ")";
}
return stream;
}
virtual std::ostream & _printDefault(std::ostream & stream) const = 0;
virtual std::ostream & _printConst(std::ostream & stream) const = 0;
std::string help;
int nargs{1};
ArgumentType type{_string};
bool required{false};
bool parsed{false};
bool has_default{false};
bool has_const{false};
std::vector<std::string> keys;
bool is_positional{false};
};
/* -------------------------------------------------------------------------- */
/// typed storage of the arguments
template <class T>
-class ArgumentParser::ArgumentStorage : public ArgumentParser::_Argument {
+class ArgumentParser::ArgumentStorage : public ArgumentParser::Argument_ {
public:
ArgumentStorage() : _default(T()), _const(T()), values(std::vector<T>()) {}
void addValue(std::string & value) override {
std::stringstream sstr(value);
T t;
sstr >> t;
values.push_back(t);
}
void setToDefault() override {
values.clear();
values.push_back(_default);
}
void setToConst() override {
values.clear();
values.push_back(_const);
}
void printself(std::ostream & stream) const override {
stream << this->name << " =";
stream << std::boolalpha; // for boolean
for (auto vit = this->values.begin(); vit != this->values.end(); ++vit) {
stream << " " << *vit;
}
}
std::ostream & _printDefault(std::ostream & stream) const override {
stream << _default;
return stream;
}
std::ostream & _printConst(std::ostream & stream) const override {
stream << _const;
return stream;
}
T _default;
T _const;
std::vector<T> values;
};
/* -------------------------------------------------------------------------- */
template <>
inline void
ArgumentParser::ArgumentStorage<std::string>::addValue(std::string & value) {
values.push_back(value);
}
template <class T> struct is_vector {
enum { value = false };
};
template <class T> struct is_vector<std::vector<T>> {
enum { value = true };
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_vector = cppargparse::is_vector<T>::value>
struct cast_helper {
static T cast(const ArgumentParser::Argument & arg) {
const auto & _arg =
dynamic_cast<const ArgumentParser::ArgumentStorage<T> &>(arg);
if (_arg.values.size() == 1) {
return _arg.values[0];
- } else {
- throw std::length_error("Not enougth or too many argument where passed "
- "for the command line argument: " +
- arg.name);
}
+ throw std::length_error("Not enougth or too many argument where passed "
+ "for the command line argument: " +
+ arg.name);
}
};
template <class T> struct cast_helper<T, true> {
static T cast(const ArgumentParser::Argument & arg) {
const auto & _arg =
dynamic_cast<const ArgumentParser::ArgumentStorage<T> &>(arg);
return _arg.values;
}
};
/* -------------------------------------------------------------------------- */
template <class T> ArgumentParser::Argument::operator T() const {
return cast_helper<T>::cast(*this);
}
#if !defined(DOXYGEN)
-template <> inline ArgumentParser::Argument::operator const std::string() const {
+template <>
+inline ArgumentParser::Argument::operator std::string() const {
return cast_helper<std::string>::cast(*this);
}
template <> inline ArgumentParser::Argument::operator unsigned int() const {
return cast_helper<int>::cast(*this);
}
#endif
template <class T>
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, T def) {
- _Argument & arg = _addArgument(name_or_flag, help, nargs, type);
+ Argument_ & arg = _addArgument(name_or_flag, help, nargs, type);
dynamic_cast<ArgumentStorage<T> &>(arg)._default = def;
arg.has_default = true;
}
template <class T>
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, T def, T cons) {
- _Argument & arg = _addArgument(name_or_flag, help, nargs, type);
+ Argument_ & arg = _addArgument(name_or_flag, help, nargs, type);
dynamic_cast<ArgumentStorage<T> &>(arg)._default = def;
arg.has_default = true;
dynamic_cast<ArgumentStorage<T> &>(arg)._const = cons;
arg.has_const = true;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ArgumentParser::addArgument<const char *>(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, const char * def) {
this->addArgument<std::string>(name_or_flag, help, nargs, type, def);
}
template <>
inline void
ArgumentParser::addArgument<unsigned int>(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, unsigned int def) {
this->addArgument<int>(name_or_flag, help, nargs, type, def);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ArgumentParser::addArgument<const char *>(
const std::string & name_or_flag, const std::string & help, int nargs,
ArgumentType type, const char * def, const char * cons) {
this->addArgument<std::string>(name_or_flag, help, nargs, type, def, cons);
}
template <>
inline void ArgumentParser::addArgument<unsigned int>(
const std::string & name_or_flag, const std::string & help, int nargs,
ArgumentType type, unsigned int def, unsigned int cons) {
this->addArgument<int>(name_or_flag, help, nargs, type, def, cons);
}
} // namespace cppargparse
-#endif /* __AKANTU_CPPARGPARSE_TMPL_HH__ */
+#endif /* AKANTU_CPPARGPARSE_TMPL_HH_ */
diff --git a/src/io/parser/input_file_parser.hh b/src/io/parser/input_file_parser.hh
index e52655656..72f3b21a4 100644
--- a/src/io/parser/input_file_parser.hh
+++ b/src/io/parser/input_file_parser.hh
@@ -1,267 +1,269 @@
/**
* @file input_file_parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Mon Dec 18 2017
*
* @brief Grammar definition for the input files
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// Boost
/* -------------------------------------------------------------------------- */
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/phoenix_bind.hpp>
#include <boost/spirit/include/phoenix_core.hpp>
#include <boost/spirit/include/phoenix_fusion.hpp>
#include <boost/spirit/include/phoenix_operator.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/variant/recursive_variant.hpp>
-#ifndef __AKANTU_INPUT_FILE_PARSER_HH__
-#define __AKANTU_INPUT_FILE_PARSER_HH__
+#ifndef AKANTU_INPUT_FILE_PARSER_HH_
+#define AKANTU_INPUT_FILE_PARSER_HH_
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
namespace akantu {
namespace parser {
struct error_handler_ {
template <typename, typename, typename, typename> struct result {
using type = void;
};
template <typename Iterator>
void operator()(qi::info const & what, Iterator err_pos, Iterator /*first*/,
Iterator /*last*/) const {
spirit::classic::file_position pos = err_pos.get_position();
AKANTU_EXCEPTION("Parse error [ "
<< "Expecting " << what << " instead of \"" << *err_pos
<< "\" ]"
<< " in file " << pos.file << " line " << pos.line
<< " column " << pos.column << std::endl
<< "'" << err_pos.get_currentline() << "'" << std::endl
<< std::setw(pos.column) << " "
<< "^- here");
}
private:
};
static ParserSection & create_subsection(
const ParserType & type, const boost::optional<std::string> & opt_name,
const boost::optional<std::string> & opt_option, ParserSection & sect) {
- std::string option = "";
- if (opt_option)
+ std::string option;
+ if (opt_option) {
option = *opt_option;
+ }
static size_t id = 12;
std::string name = "anonymous_" + std::to_string(id++);
- if (opt_name)
+ if (opt_name) {
name = *opt_name;
+ }
ParserSection sect_tmp(name, type, option, sect);
return sect.addSubSection(sect_tmp);
}
template <typename Iter>
static bool create_parameter(boost::iterator_range<Iter> & rng,
std::string & value, ParserSection & sect) {
try {
std::string name(rng.begin(), rng.end());
name = trim(name);
spirit::classic::file_position pos = rng.begin().get_position();
ParserParameter param_tmp(name, value, sect);
param_tmp.setDebugInfo(pos.file, pos.line, pos.column);
sect.addParameter(param_tmp);
} catch (debug::Exception & e) {
return false;
}
return true;
}
static std::string concatenate(const std::string & t1,
const std::string & t2) {
return (t1 + t2);
}
/* ---------------------------------------------------------------------- */
/* Grammars definitions */
/* ---------------------------------------------------------------------- */
template <class Iterator>
struct InputFileGrammar
: qi::grammar<Iterator, void(), typename Skipper<Iterator>::type> {
InputFileGrammar(ParserSection * sect)
: InputFileGrammar::base_type(start, "input_file_grammar"),
parent_section(sect) {
/* clang-format off */
start
= mini_section(parent_section)
;
mini_section
= *(
entry (lbs::_r1)
| section(lbs::_r1)
)
;
entry
= (
qi::raw[key]
>> '='
> value
) [ lbs::_pass = phx::bind(&create_parameter<Iterator>,
lbs::_1,
lbs::_2,
*lbs::_r1) ]
;
section
= (
qi::no_case[section_type]
> qi::lexeme
[
-section_name
> -section_option
]
) [ lbs::_a = &phx::bind(&create_subsection,
lbs::_1,
phx::at_c<0>(lbs::_2),
phx::at_c<1>(lbs::_2),
*lbs::_r1) ]
> '['
> mini_section(lbs::_a)
> ']'
;
section_name
= qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")
;
section_option
= (+ascii::space >> section_name) [ lbs::_val = lbs::_2 ]
;
key
= qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")
;
value
= (
mono_line_value [ lbs::_a = phx::bind(&concatenate, lbs::_a, lbs::_1) ]
> *(
'\\' > mono_line_value [ lbs::_a = phx::bind(&concatenate, lbs::_a, lbs::_1) ]
)
) [ lbs::_val = lbs::_a ]
;
mono_line_value
= qi::lexeme
[
+(qi::char_ - (qi::char_('=') | spirit::eol | '#' | ';' | '\\'))
]
;
skipper
= ascii::space
| "#" >> *(qi::char_ - spirit::eol)
;
/* clang-format on */
#define AKANTU_SECTION_TYPE_ADD(r, data, elem) \
(BOOST_PP_STRINGIZE(elem), BOOST_PP_CAT(ParserType::_, elem))
section_type.add BOOST_PP_SEQ_FOR_EACH(AKANTU_SECTION_TYPE_ADD, _,
AKANTU_SECTION_TYPES);
#undef AKANTU_SECTION_TYPE_ADD
#if !defined(AKANTU_NDEBUG)
phx::function<error_handler_> const error_handler = error_handler_();
qi::on_error<qi::fail>(start,
error_handler(lbs::_4, lbs::_3, lbs::_1, lbs::_2));
#endif
section.name("section");
section_name.name("section-name");
section_option.name("section-option");
mini_section.name("section-content");
entry.name("parameter");
key.name("parameter-name");
value.name("parameter-value");
section_type.name("section-types-list");
mono_line_value.name("mono-line-value");
#if !defined AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
// qi::debug(section);
qi::debug(section_name);
qi::debug(section_option);
// qi::debug(mini_section);
// qi::debug(entry);
qi::debug(key);
qi::debug(value);
qi::debug(mono_line_value);
}
#endif
}
const std::string & getErrorMessage() const { return error_message; };
using skipper_type = typename Skipper<Iterator>::type;
skipper_type skipper;
private:
std::string error_message;
qi::rule<Iterator, void(ParserSection *), skipper_type> mini_section;
qi::rule<Iterator, void(ParserSection *), qi::locals<ParserSection *>,
skipper_type>
section;
qi::rule<Iterator, void(), skipper_type> start;
qi::rule<Iterator, std::string()> section_name;
qi::rule<Iterator, std::string()> section_option;
qi::rule<Iterator, void(ParserSection *), skipper_type> entry;
qi::rule<Iterator, std::string(), skipper_type> key;
qi::rule<Iterator, std::string(), qi::locals<std::string>, skipper_type>
value;
qi::rule<Iterator, std::string(), skipper_type> mono_line_value;
qi::symbols<char, ParserType> section_type;
ParserSection * parent_section;
};
} // namespace parser
} // namespace akantu
-#endif /* __AKANTU_INPUT_FILE_PARSER_HH__ */
+#endif /* AKANTU_INPUT_FILE_PARSER_HH_ */
diff --git a/src/io/parser/parameter_registry.cc b/src/io/parser/parameter_registry.cc
index d9c852707..008c7613d 100644
--- a/src/io/parser/parameter_registry.cc
+++ b/src/io/parser/parameter_registry.cc
@@ -1,151 +1,154 @@
/**
* @file parameter_registry.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed May 04 2016
* @date last modification: Thu Feb 01 2018
*
* @brief Parameter Registry and derived classes implementation
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <utility>
#include "parameter_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
-Parameter::Parameter() : name(""), description("") {}
+Parameter::Parameter() = default;
/* -------------------------------------------------------------------------- */
Parameter::Parameter(std::string name, std::string description,
ParameterAccessType param_type)
: name(std::move(name)), description(std::move(description)),
param_type(param_type) {}
/* -------------------------------------------------------------------------- */
-bool Parameter::isWritable() const { return param_type & _pat_writable; }
+bool Parameter::isWritable() const { return (param_type & _pat_writable) != 0; }
/* -------------------------------------------------------------------------- */
-bool Parameter::isReadable() const { return param_type & _pat_readable; }
+bool Parameter::isReadable() const { return (param_type & _pat_readable) != 0; }
/* -------------------------------------------------------------------------- */
-bool Parameter::isInternal() const { return param_type & _pat_internal; }
+bool Parameter::isInternal() const { return (param_type & _pat_internal) != 0; }
/* -------------------------------------------------------------------------- */
-bool Parameter::isParsable() const { return param_type & _pat_parsable; }
+bool Parameter::isParsable() const { return (param_type & _pat_parsable) != 0; }
/* -------------------------------------------------------------------------- */
void Parameter::setAccessType(ParameterAccessType ptype) {
this->param_type = ptype;
}
/* -------------------------------------------------------------------------- */
void Parameter::printself(std::ostream & stream) const {
stream << " ";
- if (isInternal())
+ if (isInternal()) {
stream << "iii";
- else {
- if (isReadable())
+ } else {
+ if (isReadable()) {
stream << "r";
- else
+ } else {
stream << "-";
+ }
- if (isWritable())
+ if (isWritable()) {
stream << "w";
- else
+ } else {
stream << "-";
+ }
- if (isParsable())
+ if (isParsable()) {
stream << "p";
- else
+ } else {
stream << "-";
+ }
}
stream << " ";
std::stringstream sstr;
sstr << name;
UInt width = std::max(int(10 - sstr.str().length()), 0);
sstr.width(width);
- if (description != "") {
+ if (not description.empty()) {
sstr << " [" << description << "]";
}
stream << sstr.str();
width = std::max(int(50 - sstr.str().length()), 0);
stream.width(width);
stream << " : ";
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
ParameterRegistry::ParameterRegistry() = default;
/* -------------------------------------------------------------------------- */
ParameterRegistry::~ParameterRegistry() {
- std::map<std::string, Parameter *>::iterator it, end;
- for (it = params.begin(); it != params.end(); ++it) {
- delete it->second;
- it->second = NULL;
+ for (auto && data : params) {
+ delete data.second;
+ data.second = NULL;
}
this->params.clear();
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
Parameters::const_iterator it;
for (it = params.begin(); it != params.end(); ++it) {
stream << space;
it->second->printself(stream);
}
SubRegisteries::const_iterator sub_it;
for (sub_it = sub_registries.begin(); sub_it != sub_registries.end();
++sub_it) {
stream << space << "Registry [" << std::endl;
sub_it->second->printself(stream, indent + 1);
stream << space << "]";
}
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::registerSubRegistry(const ID & id,
ParameterRegistry & registry) {
sub_registries[id] = &registry;
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::setParameterAccessType(const std::string & name,
ParameterAccessType ptype) {
auto it = params.find(name);
- if (it == params.end())
+ if (it == params.end()) {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
+ }
Parameter & param = *(it->second);
param.setAccessType(ptype);
}
} // namespace akantu
diff --git a/src/io/parser/parameter_registry.hh b/src/io/parser/parameter_registry.hh
index af7dfccc1..5dbd40df1 100644
--- a/src/io/parser/parameter_registry.hh
+++ b/src/io/parser/parameter_registry.hh
@@ -1,223 +1,225 @@
/**
* @file parameter_registry.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
* @date last modification: Tue Jan 30 2018
*
* @brief Interface of the parameter registry
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PARAMETER_REGISTRY_HH__
-#define __AKANTU_PARAMETER_REGISTRY_HH__
+#ifndef AKANTU_PARAMETER_REGISTRY_HH_
+#define AKANTU_PARAMETER_REGISTRY_HH_
namespace akantu {
class ParserParameter;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Defines the access modes of parsable parameters
enum ParameterAccessType {
_pat_internal = 0x0001,
_pat_writable = 0x0010,
_pat_readable = 0x0100,
_pat_modifiable = 0x0110, //<_pat_readable | _pat_writable,
_pat_parsable = 0x1000,
_pat_parsmod = 0x1110 //< _pat_parsable | _pat_modifiable
};
/// Bit-wise operator between access modes
inline ParameterAccessType operator|(const ParameterAccessType & a,
const ParameterAccessType & b) {
auto tmp = ParameterAccessType(UInt(a) | UInt(b));
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T> class ParameterTyped;
/**
* Interface for the Parameter
*/
class Parameter {
public:
Parameter();
Parameter(std::string name, std::string description,
ParameterAccessType param_type);
virtual ~Parameter() = default;
/* ------------------------------------------------------------------------ */
bool isInternal() const;
bool isWritable() const;
bool isReadable() const;
bool isParsable() const;
void setAccessType(ParameterAccessType ptype);
/* ------------------------------------------------------------------------ */
template <typename T, typename V> void set(const V & value);
virtual void setAuto(const ParserParameter & param);
template <typename T> T & get();
template <typename T> const T & get() const;
virtual inline operator Real() const { throw std::bad_cast(); };
template <typename T> inline operator T() const;
/* ------------------------------------------------------------------------ */
virtual void printself(std::ostream & stream) const;
virtual const std::type_info & type() const = 0;
protected:
/// Returns const instance of templated sub-class ParameterTyped
template <typename T> const ParameterTyped<T> & getParameterTyped() const;
/// Returns instance of templated sub-class ParameterTyped
template <typename T> ParameterTyped<T> & getParameterTyped();
protected:
/// Name of parameter
std::string name;
private:
/// Description of parameter
std::string description;
/// Type of access
ParameterAccessType param_type{_pat_internal};
};
/* -------------------------------------------------------------------------- */
/* Typed Parameter */
/* -------------------------------------------------------------------------- */
/**
* Type parameter transfering a ParserParameter (string: string) to a typed
* parameter in the memory of the p
*/
template <typename T> class ParameterTyped : public Parameter {
public:
- ParameterTyped(std::string name, std::string description,
+ ParameterTyped(const std::string & name, const std::string & description,
ParameterAccessType param_type, T & param);
/* ------------------------------------------------------------------------ */
template <typename V> void setTyped(const V & value);
- void setAuto(const ParserParameter & param) override;
+ void setAuto(const ParserParameter & value) override;
T & getTyped();
const T & getTyped() const;
void printself(std::ostream & stream) const override;
inline operator Real() const override;
inline const std::type_info & type() const override { return typeid(T); }
private:
/// Value of parameter
T & param;
};
/* -------------------------------------------------------------------------- */
/* Parsable Interface */
/* -------------------------------------------------------------------------- */
/// Defines interface for classes to manipulate parsable parameters
class ParameterRegistry {
public:
ParameterRegistry();
virtual ~ParameterRegistry();
/* ------------------------------------------------------------------------ */
/// Add parameter to the params map
template <typename T>
- void registerParam(std::string name, T & variable, ParameterAccessType type,
+ void registerParam(const std::string & name, T & variable, ParameterAccessType type,
const std::string & description = "");
/// Add parameter to the params map (with default value)
template <typename T>
- void registerParam(std::string name, T & variable, const T & default_value,
+ void registerParam(const std::string &name, T & variable, const T & default_value,
ParameterAccessType type,
const std::string & description = "");
/*------------------------------------------------------------------------- */
protected:
void registerSubRegistry(const ID & id, ParameterRegistry & registry);
/* ------------------------------------------------------------------------ */
public:
/// Set value to a parameter (with possible different type)
template <typename T, typename V>
void setMixed(const std::string & name, const V & value);
/// Set value to a parameter
template <typename T> void set(const std::string & name, const T & value);
/// Get value of a parameter
inline const Parameter & get(const std::string & name) const;
/// Get value of a parameter
inline Parameter & get(const std::string & name);
std::vector<ID> listParameters() const {
std::vector<ID> params;
- for (auto & pair : this->params)
+ for (const auto & pair : this->params) {
params.push_back(pair.first);
+ }
return params;
}
std::vector<ID> listSubRegisteries() const {
std::vector<ID> subs;
- for (auto & pair : this->sub_registries)
+ for (const auto & pair : this->sub_registries) {
subs.push_back(pair.first);
+ }
return subs;
}
protected:
template <typename T> T & get_(const std::string & name);
protected:
void setParameterAccessType(const std::string & name,
ParameterAccessType ptype);
/* ------------------------------------------------------------------------ */
virtual void printself(std::ostream & stream, int indent) const;
protected:
/// Parameters map
using Parameters = std::map<std::string, Parameter *>;
Parameters params;
/// list of sub-registries
using SubRegisteries = std::map<std::string, ParameterRegistry *>;
SubRegisteries sub_registries;
/// should accessor check in sub registries
bool consisder_sub{true};
};
} // namespace akantu
#include "parameter_registry_tmpl.hh"
-#endif /* __AKANTU_PARAMETER_REGISTRY_HH__ */
+#endif /* AKANTU_PARAMETER_REGISTRY_HH_ */
diff --git a/src/io/parser/parameter_registry_tmpl.hh b/src/io/parser/parameter_registry_tmpl.hh
index f471d3564..ad6cc226f 100644
--- a/src/io/parser/parameter_registry_tmpl.hh
+++ b/src/io/parser/parameter_registry_tmpl.hh
@@ -1,455 +1,457 @@
/**
* @file parameter_registry_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed May 04 2016
* @date last modification: Tue Jan 30 2018
*
* @brief implementation of the templated part of ParameterRegistry class and
* the derivated ones
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_error.hh"
#include "aka_iterators.hh"
//#include "parameter_registry.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <set>
#include <string>
#include <vector>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PARAMETER_REGISTRY_TMPL_HH__
-#define __AKANTU_PARAMETER_REGISTRY_TMPL_HH__
+#ifndef AKANTU_PARAMETER_REGISTRY_TMPL_HH_
+#define AKANTU_PARAMETER_REGISTRY_TMPL_HH_
namespace akantu {
namespace debug {
class ParameterException : public Exception {
public:
ParameterException(const std::string & name, const std::string & message)
: Exception(message), name(name) {}
const std::string & name;
};
class ParameterUnexistingException : public ParameterException {
public:
ParameterUnexistingException(const std::string & name,
const ParameterRegistry & registery)
: ParameterException(name, "Parameter " + name +
" does not exists in this scope") {
auto && params = registery.listParameters();
this->_info =
std::accumulate(params.begin(), params.end(),
this->_info + "\n Possible parameters are: ",
[](auto && str, auto && param) {
static auto first = true;
auto ret = str + (first ? " " : ", ") + param;
first = false;
return ret;
});
}
};
class ParameterAccessRightException : public ParameterException {
public:
ParameterAccessRightException(const std::string & name,
const std::string & perm)
: ParameterException(name, "Parameter " + name + " is not " + perm) {}
};
class ParameterWrongTypeException : public ParameterException {
public:
ParameterWrongTypeException(const std::string & name,
const std::type_info & wrong_type,
const std::type_info & type)
: ParameterException(name, "Parameter " + name +
" type error, cannot convert " +
debug::demangle(type.name()) + " to " +
debug::demangle(wrong_type.name())) {}
};
} // namespace debug
/* -------------------------------------------------------------------------- */
template <typename T>
const ParameterTyped<T> & Parameter::getParameterTyped() const {
try {
const auto & tmp = aka::as_type<ParameterTyped<T>>(*this);
return tmp;
} catch (std::bad_cast &) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterWrongTypeException(name, typeid(T), this->type()));
}
}
/* -------------------------------------------------------------------------- */
template <typename T> ParameterTyped<T> & Parameter::getParameterTyped() {
try {
auto & tmp = aka::as_type<ParameterTyped<T>>(*this);
return tmp;
} catch (std::bad_cast &) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterWrongTypeException(name, typeid(T), this->type()));
}
}
/* ------------------------------------------------------------------------ */
template <typename T, typename V> void Parameter::set(const V & value) {
- if (!(isWritable()))
+ if (not isWritable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "writable"));
+ }
ParameterTyped<T> & typed_param = getParameterTyped<T>();
typed_param.setTyped(value);
}
/* ------------------------------------------------------------------------ */
-inline void Parameter::setAuto(__attribute__((unused))
- const ParserParameter & value) {
- if (!(isParsable()))
+inline void Parameter::setAuto(const ParserParameter & /*value*/) {
+ if (not isParsable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "parsable"));
+ }
}
/* -------------------------------------------------------------------------- */
template <typename T> const T & Parameter::get() const {
- if (!(isReadable()))
+ if (not isReadable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "readable"));
+ }
const ParameterTyped<T> & typed_param = getParameterTyped<T>();
return typed_param.getTyped();
}
/* -------------------------------------------------------------------------- */
template <typename T> T & Parameter::get() {
ParameterTyped<T> & typed_param = getParameterTyped<T>();
- if (!(isReadable()) || !(this->isWritable()))
+ if (not isReadable() or not this->isWritable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "accessible"));
+ }
return typed_param.getTyped();
}
/* -------------------------------------------------------------------------- */
template <typename T> inline Parameter::operator T() const {
return this->get<T>();
}
/* -------------------------------------------------------------------------- */
template <typename T>
-ParameterTyped<T>::ParameterTyped(std::string name, std::string description,
+ParameterTyped<T>::ParameterTyped(const std::string & name,
+ const std::string & description,
ParameterAccessType param_type, T & param)
: Parameter(name, description, param_type), param(param) {}
/* -------------------------------------------------------------------------- */
template <typename T>
template <typename V>
void ParameterTyped<T>::setTyped(const V & value) {
param = value;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParameterTyped<T>::setAuto(const ParserParameter & value) {
Parameter::setAuto(value);
param = static_cast<T>(value);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<std::string>::setAuto(const ParserParameter & value) {
Parameter::setAuto(value);
param = value.getValue();
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<Vector<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Vector<Real> tmp = in_param;
if (param.size() == 0) {
param = tmp;
} else {
for (UInt i = 0; i < param.size(); ++i) {
param(i) = tmp(i);
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<Matrix<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Matrix<Real> tmp = in_param;
if (param.size() == 0) {
param = tmp;
} else {
for (UInt i = 0; i < param.rows(); ++i) {
for (UInt j = 0; j < param.cols(); ++j) {
param(i, j) = tmp(i, j);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T> const T & ParameterTyped<T>::getTyped() const {
return param;
}
/* -------------------------------------------------------------------------- */
template <typename T> T & ParameterTyped<T>::getTyped() { return param; }
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParameterTyped<T>::printself(std::ostream & stream) const {
Parameter::printself(stream);
stream << param << "\n";
}
/* -------------------------------------------------------------------------- */
template <typename T> class ParameterTyped<std::vector<T>> : public Parameter {
public:
- ParameterTyped(std::string name, std::string description,
+ ParameterTyped(const std::string & name, const std::string & description,
ParameterAccessType param_type, std::vector<T> & param)
: Parameter(name, description, param_type), param(param) {}
/* ------------------------------------------------------------------------
*/
- template <typename V>
- void setTyped(const V & value) {
- param = value;
- }
+ template <typename V> void setTyped(const V & value) { param = value; }
void setAuto(const ParserParameter & value) override {
Parameter::setAuto(value);
- param.clear();
+ param.zero();
const std::vector<T> & tmp = value;
for (auto && z : tmp) {
param.emplace_back(z);
}
}
std::vector<T> & getTyped() { return param; }
const std::vector<T> & getTyped() const { return param; }
void printself(std::ostream & stream) const override {
Parameter::printself(stream);
stream << "[ ";
- for (auto && v : param)
+ for (auto && v : param) {
stream << v << " ";
+ }
stream << "]\n";
}
inline const std::type_info & type() const override {
return typeid(std::vector<T>);
}
private:
/// Value of parameter
std::vector<T> & param;
};
/* -------------------------------------------------------------------------- */
template <typename T> class ParameterTyped<std::set<T>> : public Parameter {
public:
- ParameterTyped(std::string name, std::string description,
+ ParameterTyped(const std::string & name, const std::string & description,
ParameterAccessType param_type, std::set<T> & param)
: Parameter(name, description, param_type), param(param) {}
/* ------------------------------------------------------------------------
*/
- template <typename V>
- void setTyped(const V & value) {
- param = value;
- }
+ template <typename V> void setTyped(const V & value) { param = value; }
void setAuto(const ParserParameter & value) override {
Parameter::setAuto(value);
param.clear();
const std::set<T> & tmp = value;
for (auto && z : tmp) {
param.emplace(z);
}
}
std::set<T> & getTyped() { return param; }
const std::set<T> & getTyped() const { return param; }
void printself(std::ostream & stream) const override {
Parameter::printself(stream);
stream << "[ ";
- for (auto && v : param)
+ for (auto && v : param) {
stream << v << " ";
+ }
stream << "]\n";
}
inline const std::type_info & type() const override {
return typeid(std::set<T>);
}
private:
/// Value of parameter
std::set<T> & param;
};
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<bool>::printself(std::ostream & stream) const {
Parameter::printself(stream);
stream << std::boolalpha << param << "\n";
}
/* -------------------------------------------------------------------------- */
template <typename T>
-void ParameterRegistry::registerParam(std::string name, T & variable,
+void ParameterRegistry::registerParam(const std::string & name, T & variable,
ParameterAccessType type,
const std::string & description) {
auto it = params.find(name);
- if (it != params.end())
+ if (it != params.end()) {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterException(
name, "Parameter named " + name + " already registered."));
+ }
auto * param = new ParameterTyped<T>(name, description, type, variable);
params[name] = param;
}
/* -------------------------------------------------------------------------- */
template <typename T>
-void ParameterRegistry::registerParam(std::string name, T & variable,
+void ParameterRegistry::registerParam(const std::string & name, T & variable,
const T & default_value,
ParameterAccessType type,
const std::string & description) {
variable = default_value;
registerParam(name, variable, type, description);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename V>
void ParameterRegistry::setMixed(const std::string & name, const V & value) {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
it->second->setMixed<T>(name, value);
}
} else {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
} else {
Parameter & param = *(it->second);
param.set<T>(value);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::set(const std::string & name, const T & value) {
this->template setMixed<T>(name, value);
}
/* -------------------------------------------------------------------------- */
template <typename T> T & ParameterRegistry::get_(const std::string & name) {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
try {
return it->second->get_<T>(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
Parameter & param = *(it->second);
return param.get<T>();
}
/* -------------------------------------------------------------------------- */
const Parameter & ParameterRegistry::get(const std::string & name) const {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
try {
return it->second->get(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
Parameter & param = *(it->second);
return param;
}
/* -------------------------------------------------------------------------- */
Parameter & ParameterRegistry::get(const std::string & name) {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
try {
return it->second->get(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
Parameter & param = *(it->second);
return param;
}
/* -------------------------------------------------------------------------- */
namespace {
namespace details {
template <class T, class R, class Enable = void> struct CastHelper {
- static R convert(const T &) { throw std::bad_cast(); }
+ static R convert(const T & /*unused*/) { throw std::bad_cast(); }
};
template <class T, class R>
struct CastHelper<T, R,
std::enable_if_t<std::is_convertible<T, R>::value>> {
static R convert(const T & val) { return val; }
};
} // namespace details
} // namespace
template <typename T> inline ParameterTyped<T>::operator Real() const {
- if (not isReadable())
+ if (not isReadable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "accessible"));
+ }
return details::CastHelper<T, Real>::convert(param);
}
} // namespace akantu
-#endif /* __AKANTU_PARAMETER_REGISTRY_TMPL_HH__ */
+#endif /* AKANTU_PARAMETER_REGISTRY_TMPL_HH_ */
diff --git a/src/io/parser/parsable.cc b/src/io/parser/parsable.cc
index 8c939f542..9e6dfff6d 100644
--- a/src/io/parser/parsable.cc
+++ b/src/io/parser/parsable.cc
@@ -1,109 +1,110 @@
/**
* @file parsable.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Feb 08 2018
*
* @brief Parsable implementation
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "parsable.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Parsable::Parsable(const ParserType & section_type, const ID & id)
: section_type(section_type), pid(id) {
this->consisder_sub = false;
}
/* -------------------------------------------------------------------------- */
Parsable::~Parsable() = default;
/* -------------------------------------------------------------------------- */
void Parsable::registerSubSection(const ParserType & type,
const std::string & name,
Parsable & sub_section) {
SubSectionKey key(type, name);
sub_sections[key] = &sub_section;
this->registerSubRegistry(name, sub_section);
}
/* -------------------------------------------------------------------------- */
void Parsable::parseParam(const ParserParameter & in_param) {
auto it = params.find(in_param.getName());
if (it == params.end()) {
if (Parser::isPermissive()) {
AKANTU_DEBUG_WARNING("No parameter named " << in_param.getName()
<< " registered in " << pid
<< ".");
return;
- } else
- AKANTU_EXCEPTION("No parameter named " << in_param.getName()
- << " registered in " << pid
- << ".");
+ }
+
+ AKANTU_EXCEPTION("No parameter named " << in_param.getName()
+ << " registered in " << pid << ".");
}
Parameter & param = *(it->second);
param.setAuto(in_param);
}
/* -------------------------------------------------------------------------- */
void Parsable::parseSection(const ParserSection & section) {
- if (section_type != section.getType())
+ if (section_type != section.getType()) {
AKANTU_EXCEPTION("The object "
<< pid << " is meant to parse section of type "
<< section_type << ", so it cannot parse section of type "
<< section.getType());
+ }
auto params = section.getParameters();
auto it = params.first;
for (; it != params.second; ++it) {
parseParam(*it);
}
auto sit = section.getSubSections().first;
for (; sit != section.getSubSections().second; ++sit) {
parseSubSection(*sit);
}
}
/* -------------------------------------------------------------------------- */
void Parsable::parseSubSection(const ParserSection & section) {
SubSectionKey key(section.getType(), section.getName());
auto it = sub_sections.find(key);
if (it != sub_sections.end()) {
it->second->parseSection(section);
} else if (!Parser::isPermissive()) {
AKANTU_EXCEPTION("No parsable defined for sub sections of type <"
<< key.first << "," << key.second << "> in " << pid);
} else {
AKANTU_DEBUG_WARNING("No parsable defined for sub sections of type <"
<< key.first << "," << key.second << "> in " << pid);
}
}
} // namespace akantu
diff --git a/src/io/parser/parsable.hh b/src/io/parser/parsable.hh
index ade1df6cd..d01694238 100644
--- a/src/io/parser/parsable.hh
+++ b/src/io/parser/parsable.hh
@@ -1,72 +1,72 @@
/**
* @file parsable.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
* @date last modification: Fri Dec 08 2017
*
* @brief Interface of the parameter registry
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parameter_registry.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PARSABLE_HH__
-#define __AKANTU_PARSABLE_HH__
+#ifndef AKANTU_PARSABLE_HH_
+#define AKANTU_PARSABLE_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Parsable Interface */
/* -------------------------------------------------------------------------- */
/// Defines interface for classes to manipulate parsable parameters
class Parsable : public ParameterRegistry {
public:
Parsable(const ParserType & section_type, const ID & id = std::string());
~Parsable() override;
/// Add subsection to the sub_sections map
void registerSubSection(const ParserType & type, const std::string & name,
Parsable & sub_section);
/* ------------------------------------------------------------------------ */
public:
virtual void parseSection(const ParserSection & section);
virtual void parseSubSection(const ParserSection & section);
- virtual void parseParam(const ParserParameter & parameter);
+ virtual void parseParam(const ParserParameter & in_param);
private:
ParserType section_type;
/// ID of parsable object
ID pid;
using SubSectionKey = std::pair<ParserType, std::string>;
using SubSections = std::map<SubSectionKey, Parsable *>;
/// Subsections map
SubSections sub_sections;
};
} // namespace akantu
-#endif /* __AKANTU_PARSABLE_HH__ */
+#endif /* AKANTU_PARSABLE_HH_ */
diff --git a/src/io/parser/parser.cc b/src/io/parser/parser.cc
index 19e00f3bd..bc4252069 100644
--- a/src/io/parser/parser.cc
+++ b/src/io/parser/parser.cc
@@ -1,96 +1,98 @@
/**
* @file parser.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Feb 01 2018
*
* @brief implementation of the parser
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// STL
#include <fstream>
#include <iomanip>
#include <map>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ParserSection::~ParserSection() { this->clean(); }
/* -------------------------------------------------------------------------- */
ParserParameter & ParserSection::addParameter(const ParserParameter & param) {
- if (parameters.find(param.getName()) != parameters.end())
+ if (parameters.find(param.getName()) != parameters.end()) {
AKANTU_EXCEPTION("The parameter \"" + param.getName() +
"\" is already defined in this section");
+ }
return (parameters
.insert(std::pair<std::string, ParserParameter>(param.getName(),
param))
.first->second);
}
/* -------------------------------------------------------------------------- */
ParserSection & ParserSection::addSubSection(const ParserSection & section) {
return ((sub_sections_by_type.insert(std::pair<ParserType, ParserSection>(
section.getType(), section)))
->second);
}
/* -------------------------------------------------------------------------- */
std::string Parser::getLastParsedFile() const { return last_parsed_file; }
/* -------------------------------------------------------------------------- */
void ParserSection::printself(std::ostream & stream,
unsigned int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Section(" << this->type << ") " << this->name
- << (option != "" ? (" " + option) : "") << " [" << std::endl;
+ << ((not option.empty()) ? (" " + option) : "") << " [" << std::endl;
if (!this->parameters.empty()) {
stream << space << " Parameters [" << std::endl;
auto pit = this->parameters.begin();
for (; pit != this->parameters.end(); ++pit) {
stream << space << " + ";
pit->second.printself(stream, indent);
stream << "\n";
}
stream << space << " ]" << std::endl;
}
if (!this->sub_sections_by_type.empty()) {
stream << space << " Subsections [" << std::endl;
auto sit = this->sub_sections_by_type.begin();
- for (; sit != this->sub_sections_by_type.end(); ++sit)
+ for (; sit != this->sub_sections_by_type.end(); ++sit) {
sit->second.printself(stream, indent + 2);
+ }
stream << std::endl;
stream << space << " ]" << std::endl;
}
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/io/parser/parser.hh b/src/io/parser/parser.hh
index ea5b7ca77..84311b866 100644
--- a/src/io/parser/parser.hh
+++ b/src/io/parser/parser.hh
@@ -1,505 +1,513 @@
/**
* @file parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Fri Dec 08 2017
*
* @brief File parser interface
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PARSER_HH__
-#define __AKANTU_PARSER_HH__
+#ifndef AKANTU_PARSER_HH_
+#define AKANTU_PARSER_HH_
namespace akantu {
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_SECTION_TYPES \
(cohesive_inserter) \
(contact) \
(embedded_interface) \
(friction) \
(global) \
(heat) \
(integration_scheme) \
(material) \
(mesh) \
(model) \
(model_solver) \
(neighborhood) \
(neighborhoods) \
(non_linear_solver) \
(non_local) \
(rules) \
(solver) \
(time_step_solver) \
(user) \
(weight_function) \
(not_defined)
// clang-format on
/// Defines the possible section types
AKANTU_CLASS_ENUM_DECLARE(ParserType, AKANTU_SECTION_TYPES)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(ParserType, AKANTU_SECTION_TYPES)
AKANTU_CLASS_ENUM_INPUT_STREAM(ParserType, AKANTU_SECTION_TYPES)
#endif
/// Defines the possible search contexts/scopes (for parameter search)
enum ParserParameterSearchCxt {
_ppsc_current_scope = 0x1,
_ppsc_parent_scope = 0x2,
_ppsc_current_and_parent_scope = 0x3
};
/* ------------------------------------------------------------------------ */
/* Parameters Class */
/* ------------------------------------------------------------------------ */
class ParserSection;
/// @brief The ParserParameter objects represent the end of tree branches as
/// they
/// are the different informations contained in the input file.
class ParserParameter {
public:
ParserParameter()
: name(std::string()), value(std::string()), dbg_filename(std::string()) {
}
ParserParameter(const std::string & name, const std::string & value,
const ParserSection & parent_section)
: parent_section(&parent_section), name(name), value(value),
dbg_filename(std::string()) {}
ParserParameter(const ParserParameter & param) = default;
virtual ~ParserParameter() = default;
/// Get parameter name
const std::string & getName() const { return name; }
/// Get parameter value
const std::string & getValue() const { return value; }
/// Set info for debug output
void setDebugInfo(const std::string & filename, UInt line, UInt column) {
dbg_filename = filename;
dbg_line = line;
dbg_column = column;
}
template <typename T> inline operator T() const;
// template <typename T> inline operator Vector<T>() const;
// template <typename T> inline operator Matrix<T>() const;
/// Print parameter info in stream
void printself(std::ostream & stream,
__attribute__((unused)) unsigned int indent = 0) const {
stream << name << ": " << value << " (" << dbg_filename << ":" << dbg_line
<< ":" << dbg_column << ")";
}
private:
void setParent(const ParserSection & sect) { parent_section = &sect; }
friend class ParserSection;
private:
/// Pointer to the parent section
const ParserSection * parent_section{nullptr};
/// Name of the parameter
std::string name;
/// Value of the parameter
std::string value;
/// File for debug output
std::string dbg_filename;
/// Position of parameter in parsed file
UInt dbg_line, dbg_column;
};
/* ------------------------------------------------------------------------ */
/* Sections Class */
/* ------------------------------------------------------------------------ */
/// ParserSection represents a branch of the parsing tree.
class ParserSection {
public:
using SubSections = std::multimap<ParserType, ParserSection>;
using Parameters = std::map<std::string, ParserParameter>;
private:
using const_section_iterator_ = SubSections::const_iterator;
public:
/* ------------------------------------------------------------------------ */
/* SubSection iterator */
/* ------------------------------------------------------------------------ */
/// Iterator on sections
class const_section_iterator {
public:
using iterator_category = std::forward_iterator_tag;
using value_type = ParserSection;
using pointer = ParserSection *;
using reference = ParserSection &;
const_section_iterator() = default;
const_section_iterator(const const_section_iterator_ & it) : it(it) {}
const_section_iterator(const const_section_iterator & other) = default;
const_section_iterator &
operator=(const const_section_iterator & other) = default;
const ParserSection & operator*() const { return it->second; }
const ParserSection * operator->() const { return &(it->second); }
bool operator==(const const_section_iterator & other) const {
return it == other.it;
}
bool operator!=(const const_section_iterator & other) const {
return it != other.it;
}
const_section_iterator & operator++() {
++it;
return *this;
}
const_section_iterator operator++(int) {
const_section_iterator tmp = *this;
operator++();
return tmp;
}
private:
const_section_iterator_ it;
};
/* ------------------------------------------------------------------------ */
/* Parameters iterator */
/* ------------------------------------------------------------------------ */
/// Iterator on parameters
class const_parameter_iterator {
public:
const_parameter_iterator(const const_parameter_iterator & other) = default;
const_parameter_iterator(const Parameters::const_iterator & it) : it(it) {}
const_parameter_iterator &
operator=(const const_parameter_iterator & other) {
if (this != &other) {
it = other.it;
}
return *this;
}
+
const ParserParameter & operator*() const { return it->second; }
const ParserParameter * operator->() { return &(it->second); };
+
bool operator==(const const_parameter_iterator & other) const {
return it == other.it;
}
+
bool operator!=(const const_parameter_iterator & other) const {
return it != other.it;
}
+
const_parameter_iterator & operator++() {
++it;
return *this;
}
+
const_parameter_iterator operator++(int) {
const_parameter_iterator tmp = *this;
operator++();
return tmp;
}
private:
Parameters::const_iterator it;
};
/* ---------------------------------------------------------------------- */
ParserSection() : name(std::string()) {}
ParserSection(const std::string & name, ParserType type)
- : parent_section(nullptr), name(name), type(type) {}
+ : name(name), type(type) {}
ParserSection(const std::string & name, ParserType type,
const std::string & option,
const ParserSection & parent_section)
: parent_section(&parent_section), name(name), type(type),
option(option) {}
ParserSection(const ParserSection & section)
: parent_section(section.parent_section), name(section.name),
type(section.type), option(section.option),
parameters(section.parameters),
sub_sections_by_type(section.sub_sections_by_type) {
setChldrenPointers();
}
ParserSection & operator=(const ParserSection & other) {
if (&other != this) {
parent_section = other.parent_section;
name = other.name;
type = other.type;
option = other.option;
parameters = other.parameters;
sub_sections_by_type = other.sub_sections_by_type;
setChldrenPointers();
}
return *this;
}
virtual ~ParserSection();
virtual void printself(std::ostream & stream, unsigned int indent = 0) const;
/* ---------------------------------------------------------------------- */
/* Creation functions */
/* ---------------------------------------------------------------------- */
public:
ParserParameter & addParameter(const ParserParameter & param);
ParserSection & addSubSection(const ParserSection & section);
protected:
/// Clean ParserSection content
void clean() {
parameters.clear();
sub_sections_by_type.clear();
}
private:
void setChldrenPointers() {
- for (auto && param_pair : this->parameters)
+ for (auto && param_pair : this->parameters) {
param_pair.second.setParent(*this);
+ }
- for (auto && sub_sect_pair : this->sub_sections_by_type)
+ for (auto && sub_sect_pair : this->sub_sections_by_type) {
sub_sect_pair.second.setParent(*this);
+ }
}
/* ---------------------------------------------------------------------- */
/* Accessors */
/* ---------------------------------------------------------------------- */
public:
class SubSectionsRange
: public std::pair<const_section_iterator, const_section_iterator> {
public:
SubSectionsRange(const const_section_iterator & first,
const const_section_iterator & second)
: std::pair<const_section_iterator, const_section_iterator>(first,
second) {}
auto begin() { return this->first; }
auto end() { return this->second; }
};
/// Get begin and end iterators on subsections of certain type
auto getSubSections(ParserType type = ParserType::_not_defined) const {
if (type != ParserType::_not_defined) {
auto range = sub_sections_by_type.equal_range(type);
return SubSectionsRange(range.first, range.second);
- } else {
- return SubSectionsRange(sub_sections_by_type.begin(),
- sub_sections_by_type.end());
}
+ return SubSectionsRange(sub_sections_by_type.begin(),
+ sub_sections_by_type.end());
}
/// Get number of subsections of certain type
UInt getNbSubSections(ParserType type = ParserType::_not_defined) const {
if (type != ParserType::_not_defined) {
return this->sub_sections_by_type.count(type);
- } else {
- return this->sub_sections_by_type.size();
}
+ return this->sub_sections_by_type.size();
}
/// Get begin and end iterators on parameters
auto getParameters() const {
return std::pair<const_parameter_iterator, const_parameter_iterator>(
parameters.begin(), parameters.end());
}
/* ---------------------------------------------------------------------- */
/// Get parameter within specified context
const ParserParameter & getParameter(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
Parameters::const_iterator it;
- if (search_ctx & _ppsc_current_scope)
+ if ((search_ctx & _ppsc_current_scope) != 0) {
it = parameters.find(name);
+ }
if (it == parameters.end()) {
- if ((search_ctx & _ppsc_parent_scope) && parent_section)
+ if ((search_ctx & _ppsc_parent_scope) != 0 and
+ parent_section != nullptr) {
return parent_section->getParameter(name, search_ctx);
- else {
- AKANTU_SILENT_EXCEPTION(
- "The parameter " << name
- << " has not been found in the specified context");
}
+
+ AKANTU_SILENT_EXCEPTION(
+ "The parameter " << name
+ << " has not been found in the specified context");
}
return it->second;
}
/* ------------------------------------------------------------------------ */
/// Get parameter within specified context, with a default value in case the
/// parameter does not exists
template <class T>
- const T getParameter(
+ T getParameter(
const std::string & name, const T & default_value,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
try {
T tmp = this->getParameter(name, search_ctx);
return tmp;
} catch (debug::Exception &) {
return default_value;
}
}
/* ------------------------------------------------------------------------ */
/// Check if parameter exists within specified context
bool hasParameter(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
Parameters::const_iterator it;
- if (search_ctx & _ppsc_current_scope)
+ if ((search_ctx & _ppsc_current_scope) != 0) {
it = parameters.find(name);
+ }
if (it == parameters.end()) {
- if ((search_ctx & _ppsc_parent_scope) && parent_section)
+ if ((search_ctx & _ppsc_parent_scope) != 0 and
+ parent_section != nullptr) {
return parent_section->hasParameter(name, search_ctx);
- else {
- return false;
}
+ return false;
}
return true;
}
/* --------------------------------------------------------------------------
*/
/// Get value of given parameter in context
template <class T>
T getParameterValue(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
const ParserParameter & tmp_param = getParameter(name, search_ctx);
T t = tmp_param;
return t;
}
/* --------------------------------------------------------------------------
*/
/// Get section name
- const std::string getName() const { return name; }
+ std::string getName() const { return name; }
/// Get section type
ParserType getType() const { return type; }
/// Get section option
- const std::string getOption(const std::string & def = "") const {
- return option != "" ? option : def;
+ std::string getOption(const std::string & def = "") const {
+ return (not option.empty()) ? option : def;
}
protected:
void setParent(const ParserSection & sect) { parent_section = &sect; }
/* ---------------------------------------------------------------------- */
/* Members */
/* ---------------------------------------------------------------------- */
private:
/// Pointer to the parent section
const ParserSection * parent_section{nullptr};
/// Name of section
std::string name;
/// Type of section, see AKANTU_SECTION_TYPES
ParserType type{ParserType::_not_defined};
/// Section option
std::string option;
/// Map of parameters in section
Parameters parameters;
/// Multi-map of subsections
SubSections sub_sections_by_type;
};
/* ------------------------------------------------------------------------ */
/* Parser Class */
/* ------------------------------------------------------------------------ */
/// Root of parsing tree, represents the global ParserSection
class Parser : public ParserSection {
public:
Parser() : ParserSection("global", ParserType::_global) {}
void parse(const std::string & filename);
std::string getLastParsedFile() const;
static bool isPermissive() { return permissive_parser; }
public:
/// Parse real scalar
static Real parseReal(const std::string & value,
const ParserSection & section);
/// Parse real vector
static Vector<Real> parseVector(const std::string & value,
const ParserSection & section);
/// Parse real matrix
static Matrix<Real> parseMatrix(const std::string & value,
const ParserSection & section);
/// Parse real random parameter
static RandomParameter<Real>
parseRandomParameter(const std::string & value,
const ParserSection & section);
protected:
/// General parse function
template <class T, class Grammar>
static T parseType(const std::string & value, Grammar & grammar);
protected:
// friend class Parsable;
static bool permissive_parser;
std::string last_parsed_file;
};
inline std::ostream & operator<<(std::ostream & stream,
const ParserParameter & _this) {
_this.printself(stream);
return stream;
}
inline std::ostream & operator<<(std::ostream & stream,
const ParserSection & section) {
section.printself(stream);
return stream;
}
} // namespace akantu
namespace std {
template <> struct iterator_traits<::akantu::Parser::const_section_iterator> {
using iterator_category = input_iterator_tag;
using value_type = ::akantu::ParserParameter;
using difference_type = ptrdiff_t;
using pointer = const ::akantu::ParserParameter *;
using reference = const ::akantu::ParserParameter &;
};
} // namespace std
#include "parser_tmpl.hh"
-#endif /* __AKANTU_PARSER_HH__ */
+#endif /* AKANTU_PARSER_HH_ */
diff --git a/src/io/parser/parser_tmpl.hh b/src/io/parser/parser_tmpl.hh
index c116bd277..0e531778d 100644
--- a/src/io/parser/parser_tmpl.hh
+++ b/src/io/parser/parser_tmpl.hh
@@ -1,122 +1,123 @@
/**
* @file parser_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Mon Dec 18 2017
*
* @brief Implementation of the parser templated methods
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <regex>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> inline ParserParameter::operator T() const {
T t;
std::stringstream sstr(value);
sstr >> t;
- if (sstr.bad())
+ if (sstr.bad()) {
AKANTU_EXCEPTION("No known conversion of a ParserParameter \""
<< name << "\" to the type " << typeid(T).name());
+ }
return t;
}
#if !defined(DOXYGEN)
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator const char *() const {
return value.c_str();
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator Real() const {
return Parser::parseReal(value, *parent_section);
}
/* --------------------------------------------------------- -----------------
*/
template <> inline ParserParameter::operator bool() const {
bool b;
std::stringstream sstr(value);
sstr >> std::boolalpha >> b;
if (sstr.fail()) {
sstr.clear();
sstr >> std::noboolalpha >> b;
}
return b;
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator std::vector<std::string>() const {
std::vector<std::string> tmp;
auto string =
std::regex_replace(value, std::regex("[[:space:]]|\\[|\\]"), "");
std::smatch sm;
while (std::regex_search(string, sm, std::regex("[^,]+"))) {
tmp.push_back(sm.str());
string = sm.suffix();
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator std::set<std::string>() const {
std::set<std::string> tmp;
auto string =
std::regex_replace(value, std::regex("[[:space:]]|\\[|\\]"), "");
std::smatch sm;
while (std::regex_search(string, sm, std::regex("[^,]+"))) {
tmp.emplace(sm.str());
string = sm.suffix();
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator Vector<Real>() const {
return Parser::parseVector(value, *parent_section);
}
/* --------------------------------------------------------- ---------------- */
template <> inline ParserParameter::operator Vector<UInt>() const {
Vector<Real> tmp = Parser::parseVector(value, *parent_section);
Vector<UInt> tmp_uint(tmp.size());
for (UInt i = 0; i < tmp.size(); ++i) {
tmp_uint(i) = UInt(tmp(i));
}
return tmp_uint;
}
/* --------------------------------------------------------- ---------------- */
template <> inline ParserParameter::operator Matrix<Real>() const {
return Parser::parseMatrix(value, *parent_section);
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator RandomParameter<Real>() const {
return Parser::parseRandomParameter(value, *parent_section);
}
#endif
} // namespace akantu
diff --git a/src/mesh/element_group.cc b/src/mesh/element_group.cc
index 36d67fadd..58664e486 100644
--- a/src/mesh/element_group.cc
+++ b/src/mesh/element_group.cc
@@ -1,197 +1,204 @@
/**
* @file element_group.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Mon Jan 22 2018
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_csr.hh"
#include "dumpable.hh"
#include "dumpable_inline_impl.hh"
#include "group_manager.hh"
#include "group_manager_inline_impl.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include <algorithm>
#include <iterator>
#include <sstream>
#include "element_group.hh"
#if defined(AKANTU_USE_IOHELPER)
#include "dumper_iohelper_paraview.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
ElementGroup::ElementGroup(const std::string & group_name, const Mesh & mesh,
NodeGroup & node_group, UInt dimension,
const std::string & id, const MemoryID & mem_id)
: Memory(id, mem_id), mesh(mesh), name(group_name),
elements("elements", id, mem_id), node_group(node_group),
dimension(dimension) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_USE_IOHELPER)
this->registerDumper<DumperParaview>("paraview_" + group_name, group_name,
true);
this->addDumpFilteredMesh(mesh, elements, node_group.getNodes(),
_all_dimensions);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementGroup::ElementGroup(const ElementGroup & /*other*/) = default;
/* -------------------------------------------------------------------------- */
-void ElementGroup::empty() { elements.free(); }
+void ElementGroup::clear() { elements.free(); }
+
+/* -------------------------------------------------------------------------- */
+bool ElementGroup::empty() const { return elements.empty(); }
/* -------------------------------------------------------------------------- */
void ElementGroup::append(const ElementGroup & other_group) {
AKANTU_DEBUG_IN();
node_group.append(other_group.node_group);
/// loop on all element types in all dimensions
for (auto ghost_type : ghost_types) {
for (auto type : other_group.elementTypes(_ghost_type = ghost_type,
_element_kind = _ek_not_defined)) {
const Array<UInt> & other_elem_list =
other_group.elements(type, ghost_type);
UInt nb_other_elem = other_elem_list.size();
Array<UInt> * elem_list;
UInt nb_elem = 0;
/// create current type if doesn't exists, otherwise get information
if (elements.exists(type, ghost_type)) {
elem_list = &elements(type, ghost_type);
nb_elem = elem_list->size();
} else {
elem_list = &(elements.alloc(0, 1, type, ghost_type));
}
/// append new elements to current list
elem_list->resize(nb_elem + nb_other_elem);
std::copy(other_elem_list.begin(), other_elem_list.end(),
elem_list->begin() + nb_elem);
/// remove duplicates
std::sort(elem_list->begin(), elem_list->end());
Array<UInt>::iterator<> end =
std::unique(elem_list->begin(), elem_list->end());
elem_list->resize(end - elem_list->begin());
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::printself(std::ostream & stream, int indent) const {
std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
+ for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
+ }
stream << space << "ElementGroup [" << std::endl;
stream << space << " + name: " << name << std::endl;
stream << space << " + dimension: " << dimension << std::endl;
elements.printself(stream, indent + 1);
node_group.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ElementGroup::optimize() {
// increasing the locality of data when iterating on the element of a group
for (auto ghost_type : ghost_types) {
for (auto type : elements.elementTypes(_ghost_type = ghost_type)) {
Array<UInt> & els = elements(type, ghost_type);
std::sort(els.begin(), els.end());
Array<UInt>::iterator<> end = std::unique(els.begin(), els.end());
els.resize(end - els.begin());
}
}
node_group.optimize();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::fillFromNodeGroup() {
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(this->mesh, node_to_elem, this->dimension);
std::set<Element> seen;
Array<UInt>::const_iterator<> itn = this->node_group.begin();
Array<UInt>::const_iterator<> endn = this->node_group.end();
for (; itn != endn; ++itn) {
CSR<Element>::iterator ite = node_to_elem.begin(*itn);
CSR<Element>::iterator ende = node_to_elem.end(*itn);
for (; ite != ende; ++ite) {
const Element & elem = *ite;
if (this->dimension != _all_dimensions &&
- this->dimension != Mesh::getSpatialDimension(elem.type))
+ this->dimension != Mesh::getSpatialDimension(elem.type)) {
continue;
- if (seen.find(elem) != seen.end())
+ }
+ if (seen.find(elem) != seen.end()) {
continue;
+ }
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(elem.type);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
this->mesh.getConnectivity(elem.type, elem.ghost_type)
.begin(nb_nodes_per_element);
const Vector<UInt> & conn = conn_it[elem.element];
UInt count = 0;
for (UInt n = 0; n < conn.size(); ++n) {
count +=
(this->node_group.getNodes().find(conn(n)) != UInt(-1) ? 1 : 0);
}
- if (count == nb_nodes_per_element)
+ if (count == nb_nodes_per_element) {
this->add(elem);
+ }
seen.insert(elem);
}
}
this->optimize();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::addDimension(UInt dimension) {
this->dimension = std::max(dimension, this->dimension);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/mesh/element_group.hh b/src/mesh/element_group.hh
index 90f512568..40cd5826c 100644
--- a/src/mesh/element_group.hh
+++ b/src/mesh/element_group.hh
@@ -1,200 +1,202 @@
/**
* @file element_group.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Wed Nov 08 2017
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_memory.hh"
#include "dumpable.hh"
#include "element_type_map.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_GROUP_HH__
-#define __AKANTU_ELEMENT_GROUP_HH__
+#ifndef AKANTU_ELEMENT_GROUP_HH_
+#define AKANTU_ELEMENT_GROUP_HH_
namespace akantu {
class Mesh;
class Element;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
class ElementGroup : private Memory, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementGroup(const std::string & name, const Mesh & mesh,
NodeGroup & node_group, UInt dimension = _all_dimensions,
const std::string & id = "element_group",
- const MemoryID & memory_id = 0);
+ const MemoryID & mem_id = 0);
- ElementGroup(const ElementGroup &);
+ ElementGroup(const ElementGroup & /*unused*/);
/* ------------------------------------------------------------------------ */
/* Type definitions */
/* ------------------------------------------------------------------------ */
public:
using ElementList = ElementTypeMapArray<UInt>;
using NodeList = Array<UInt>;
/* ------------------------------------------------------------------------ */
/* Element iterator */
/* ------------------------------------------------------------------------ */
using type_iterator = ElementList::type_iterator;
[[deprecated("Use elementTypes instead")]] inline type_iterator
firstType(UInt dim = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & kind = _ek_regular) const;
+ GhostType ghost_type = _not_ghost,
+ ElementKind kind = _ek_regular) const;
[[deprecated("Use elementTypes instead")]] inline type_iterator
lastType(UInt dim = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & kind = _ek_regular) const;
+ GhostType ghost_type = _not_ghost,
+ ElementKind kind = _ek_regular) const;
template <typename... pack>
inline decltype(auto) elementTypes(pack &&... _pack) const {
return elements.elementTypes(_pack...);
}
using const_element_iterator = Array<UInt>::const_iterator<UInt>;
inline const_element_iterator
- begin(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ begin(ElementType type,
+ GhostType ghost_type = _not_ghost) const;
inline const_element_iterator
- end(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ end(ElementType type,
+ GhostType ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// empty the element group
- void empty();
+ void clear();
+
+ bool empty() const __attribute__((warn_unused_result));
/// append another group to this group
/// BE CAREFUL: it doesn't conserve the element order
void append(const ElementGroup & other_group);
/// add an element to the group. By default the it does not add the nodes to
/// the group
inline void add(const Element & el, bool add_nodes = false,
bool check_for_duplicate = true);
/// \todo fix the default for add_nodes : make it coherent with the other
/// method
- inline void add(const ElementType & type, UInt element,
- const GhostType & ghost_type = _not_ghost,
+ inline void add(ElementType type, UInt element,
+ GhostType ghost_type = _not_ghost,
bool add_nodes = true, bool check_for_duplicate = true);
inline void addNode(UInt node_id, bool check_for_duplicate = true);
inline void removeNode(UInt node_id);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// fill the elements based on the underlying node group.
virtual void fillFromNodeGroup();
// sort and remove duplicated values
void optimize();
/// change the dimension if needed
void addDimension(UInt dimension);
private:
- inline void addElement(const ElementType & elem_type, UInt elem_id,
- const GhostType & ghost_type);
+ inline void addElement(ElementType elem_type, UInt elem_id,
+ GhostType ghost_type);
friend class GroupManager;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
const Array<UInt> &
- getElements(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ getElements(ElementType type,
+ GhostType ghost_type = _not_ghost) const;
AKANTU_GET_MACRO(Elements, elements, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO_NOT_CONST(Elements, elements, ElementTypeMapArray<UInt> &);
// AKANTU_GET_MACRO(Nodes, node_group.getNodes(), const Array<UInt> &);
AKANTU_GET_MACRO(NodeGroup, node_group, const NodeGroup &);
AKANTU_GET_MACRO_NOT_CONST(NodeGroup, node_group, NodeGroup &);
AKANTU_GET_MACRO(Dimension, dimension, UInt);
AKANTU_GET_MACRO(Name, name, std::string);
inline UInt getNbNodes() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Mesh to which this group belongs
const Mesh & mesh;
/// name of the group
std::string name;
/// list of elements composing the group
ElementList elements;
/// sub list of nodes which are composing the elements
NodeGroup & node_group;
/// group dimension
UInt dimension{_all_dimensions};
/// empty arry for the iterator to work when an element type not present
Array<UInt> empty_elements;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ElementGroup & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "element.hh"
#include "element_group_inline_impl.hh"
-#endif /* __AKANTU_ELEMENT_GROUP_HH__ */
+#endif /* AKANTU_ELEMENT_GROUP_HH_ */
diff --git a/src/mesh/element_group_inline_impl.hh b/src/mesh/element_group_inline_impl.hh
index eab1978f7..d45a3ffb9 100644
--- a/src/mesh/element_group_inline_impl.hh
+++ b/src/mesh/element_group_inline_impl.hh
@@ -1,145 +1,143 @@
/**
* @file element_group_inline_impl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Sun Aug 13 2017
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_GROUP_INLINE_IMPL_HH__
-#define __AKANTU_ELEMENT_GROUP_INLINE_IMPL_HH__
+#ifndef AKANTU_ELEMENT_GROUP_INLINE_IMPL_HH_
+#define AKANTU_ELEMENT_GROUP_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void ElementGroup::add(const Element & el, bool add_nodes,
bool check_for_duplicate) {
this->add(el.type, el.element, el.ghost_type, add_nodes, check_for_duplicate);
}
/* -------------------------------------------------------------------------- */
-inline void ElementGroup::add(const ElementType & type, UInt element,
- const GhostType & ghost_type, bool add_nodes,
+inline void ElementGroup::add(ElementType type, UInt element,
+ GhostType ghost_type, bool add_nodes,
bool check_for_duplicate) {
addElement(type, element, ghost_type);
if (add_nodes) {
Array<UInt>::const_vector_iterator it =
mesh.getConnectivity(type, ghost_type)
.begin(mesh.getNbNodesPerElement(type)) +
element;
const Vector<UInt> & conn = *it;
- for (UInt i = 0; i < conn.size(); ++i)
+ for (UInt i = 0; i < conn.size(); ++i) {
addNode(conn[i], check_for_duplicate);
+ }
}
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::addNode(UInt node_id, bool check_for_duplicate) {
node_group.add(node_id, check_for_duplicate);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::removeNode(UInt node_id) {
node_group.remove(node_id);
}
/* -------------------------------------------------------------------------- */
-inline void ElementGroup::addElement(const ElementType & elem_type,
+inline void ElementGroup::addElement(ElementType elem_type,
UInt elem_id,
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
if (!(elements.exists(elem_type, ghost_type))) {
elements.alloc(0, 1, elem_type, ghost_type);
}
elements(elem_type, ghost_type).push_back(elem_id);
this->dimension = UInt(
std::max(Int(this->dimension), Int(mesh.getSpatialDimension(elem_type))));
}
/* -------------------------------------------------------------------------- */
inline UInt ElementGroup::getNbNodes() const { return node_group.size(); }
/* -------------------------------------------------------------------------- */
inline ElementGroup::type_iterator
-ElementGroup::firstType(UInt dim, const GhostType & ghost_type,
- const ElementKind & kind) const {
+ElementGroup::firstType(UInt dim, GhostType ghost_type,
+ ElementKind kind) const {
return elements.elementTypes(dim, ghost_type, kind).begin();
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::type_iterator
-ElementGroup::lastType(UInt dim, const GhostType & ghost_type,
- const ElementKind & kind) const {
+ElementGroup::lastType(UInt dim, GhostType ghost_type,
+ ElementKind kind) const {
return elements.elementTypes(dim, ghost_type, kind).end();
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_element_iterator
-ElementGroup::begin(const ElementType & type,
- const GhostType & ghost_type) const {
+ElementGroup::begin(ElementType type,
+ GhostType ghost_type) const {
if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type).begin();
- } else {
- return empty_elements.begin();
}
+ return empty_elements.begin();
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_element_iterator
-ElementGroup::end(const ElementType & type,
- const GhostType & ghost_type) const {
+ElementGroup::end(ElementType type,
+ GhostType ghost_type) const {
if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type).end();
- } else {
- return empty_elements.end();
}
+ return empty_elements.end();
}
/* -------------------------------------------------------------------------- */
inline const Array<UInt> &
-ElementGroup::getElements(const ElementType & type,
- const GhostType & ghost_type) const {
+ElementGroup::getElements(ElementType type,
+ GhostType ghost_type) const {
if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type);
- } else {
- return empty_elements;
}
+ return empty_elements;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_GROUP_INLINE_IMPL_HH__ */
+#endif /* AKANTU_ELEMENT_GROUP_INLINE_IMPL_HH_ */
diff --git a/src/mesh/element_type_map.cc b/src/mesh/element_type_map.cc
index ab31acb0c..1e8a45c53 100644
--- a/src/mesh/element_type_map.cc
+++ b/src/mesh/element_type_map.cc
@@ -1,73 +1,73 @@
/**
* @file element_type_map.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
FEEngineElementTypeMapArrayInitializer::FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine, UInt nb_component, UInt spatial_dimension,
- const GhostType & ghost_type, const ElementKind & element_kind)
+ GhostType ghost_type, ElementKind element_kind)
: MeshElementTypeMapArrayInitializer(
fe_engine.getMesh(), nb_component,
spatial_dimension == UInt(-2)
? fe_engine.getMesh().getSpatialDimension()
: spatial_dimension,
ghost_type, element_kind, true, false),
fe_engine(fe_engine) {}
FEEngineElementTypeMapArrayInitializer::FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine,
const ElementTypeMapArrayInitializer::CompFunc & nb_component,
- UInt spatial_dimension, const GhostType & ghost_type,
- const ElementKind & element_kind)
+ UInt spatial_dimension, GhostType ghost_type,
+ ElementKind element_kind)
: MeshElementTypeMapArrayInitializer(
fe_engine.getMesh(), nb_component,
spatial_dimension == UInt(-2)
? fe_engine.getMesh().getSpatialDimension()
: spatial_dimension,
ghost_type, element_kind, true, false),
fe_engine(fe_engine) {}
UInt FEEngineElementTypeMapArrayInitializer::size(
- const ElementType & type) const {
+ ElementType type) const {
return MeshElementTypeMapArrayInitializer::size(type) *
fe_engine.getNbIntegrationPoints(type, this->ghost_type);
}
FEEngineElementTypeMapArrayInitializer::ElementTypesIteratorHelper
FEEngineElementTypeMapArrayInitializer::elementTypes() const {
return this->fe_engine.elementTypes(spatial_dimension, ghost_type,
element_kind);
}
} // namespace akantu
diff --git a/src/mesh/element_type_map.hh b/src/mesh/element_type_map.hh
index c7f1d5ef6..9eed9937c 100644
--- a/src/mesh/element_type_map.hh
+++ b/src/mesh/element_type_map.hh
@@ -1,478 +1,484 @@
/**
* @file element_type_map.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
* @date last modification: Tue Feb 20 2018
*
* @brief storage class by element type
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_memory.hh"
#include "aka_named_argument.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_TYPE_MAP_HH__
-#define __AKANTU_ELEMENT_TYPE_MAP_HH__
+#ifndef AKANTU_ELEMENT_TYPE_MAP_HH_
+#define AKANTU_ELEMENT_TYPE_MAP_HH_
namespace akantu {
class FEEngine;
} // namespace akantu
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(all_ghost_types);
DECLARE_NAMED_ARGUMENT(default_value);
DECLARE_NAMED_ARGUMENT(element_kind);
DECLARE_NAMED_ARGUMENT(ghost_type);
DECLARE_NAMED_ARGUMENT(nb_component);
DECLARE_NAMED_ARGUMENT(nb_component_functor);
DECLARE_NAMED_ARGUMENT(with_nb_element);
DECLARE_NAMED_ARGUMENT(with_nb_nodes_per_element);
DECLARE_NAMED_ARGUMENT(spatial_dimension);
DECLARE_NAMED_ARGUMENT(do_not_default);
} // namespace
template <class Stored, typename SupportType = ElementType>
class ElementTypeMap;
/* -------------------------------------------------------------------------- */
/* ElementTypeMapBase */
/* -------------------------------------------------------------------------- */
/// Common non templated base class for the ElementTypeMap class
class ElementTypeMapBase {
public:
virtual ~ElementTypeMapBase() = default;
};
/* -------------------------------------------------------------------------- */
/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
class ElementTypeMap : public ElementTypeMapBase {
public:
ElementTypeMap();
~ElementTypeMap() override;
inline static std::string printType(const SupportType & type,
- const GhostType & ghost_type);
+ GhostType ghost_type);
/*! Tests whether a type is present in the object
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return true if the type is present. */
inline bool exists(const SupportType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ GhostType ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline const Stored &
operator()(const SupportType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ GhostType ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline Stored & operator()(const SupportType & type,
- const GhostType & ghost_type = _not_ghost);
+ GhostType ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map. THIS METHOD IS
* NOT ARRAY SAFE, when using ElementTypeMapArray, use setArray instead
* @param data to insert
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
template <typename U>
- inline Stored & operator()(U && data, const SupportType & type,
- const GhostType & ghost_type = _not_ghost);
+ inline Stored & operator()(U && insertee, const SupportType & type,
+ GhostType ghost_type = _not_ghost);
public:
/// print helper
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
/*! iterator allows to iterate over type-data pairs of the map. The interface
* expects the SupportType to be ElementType. */
using DataMap = std::map<SupportType, Stored>;
/// helper class to use in range for constructions
class type_iterator
: private std::iterator<std::forward_iterator_tag, const SupportType> {
public:
using value_type = const SupportType;
using pointer = const SupportType *;
using reference = const SupportType &;
protected:
using DataMapIterator =
typename ElementTypeMap<Stored>::DataMap::const_iterator;
public:
type_iterator(DataMapIterator & list_begin, DataMapIterator & list_end,
UInt dim, ElementKind ek);
type_iterator(const type_iterator & it);
type_iterator() = default;
inline reference operator*();
inline reference operator*() const;
inline type_iterator & operator++();
type_iterator operator++(int);
inline bool operator==(const type_iterator & other) const;
inline bool operator!=(const type_iterator & other) const;
- type_iterator & operator=(const type_iterator & other);
+ type_iterator & operator=(const type_iterator & it);
private:
DataMapIterator list_begin;
DataMapIterator list_end;
UInt dim;
ElementKind kind;
};
/// helper class to use in range for constructions
class ElementTypesIteratorHelper {
public:
using Container = ElementTypeMap<Stored, SupportType>;
using iterator = typename Container::type_iterator;
ElementTypesIteratorHelper(const Container & container, UInt dim,
GhostType ghost_type, ElementKind kind)
: container(std::cref(container)), dim(dim), ghost_type(ghost_type),
kind(kind) {}
template <typename... pack>
- ElementTypesIteratorHelper(const Container & container, use_named_args_t,
- pack &&... _pack)
+ ElementTypesIteratorHelper(const Container & container,
+ use_named_args_t /*unused*/, pack &&... _pack)
: ElementTypesIteratorHelper(
container, OPTIONAL_NAMED_ARG(spatial_dimension, _all_dimensions),
OPTIONAL_NAMED_ARG(ghost_type, _not_ghost),
OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined)) {}
ElementTypesIteratorHelper(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
operator=(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
- operator=(ElementTypesIteratorHelper &&) = default;
+ operator=(ElementTypesIteratorHelper &&) noexcept = default;
iterator begin();
iterator end();
private:
std::reference_wrapper<const Container> container;
UInt dim;
GhostType ghost_type;
ElementKind kind;
};
private:
ElementTypesIteratorHelper
elementTypesImpl(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
template <typename... pack>
ElementTypesIteratorHelper
elementTypesImpl(const use_named_args_t & /*unused*/, pack &&... _pack) const;
public:
/*!
* \param _pack
* \parblock
* represent optional parameters:
* \li \c _spatial_dimension filter for elements of given spatial
* dimension
* \li \c _ghost_type filter for a certain ghost_type
* \li \c _element_kind filter for elements of given kind
* \endparblock
*/
template <typename... pack>
std::enable_if_t<are_named_argument<pack...>::value,
ElementTypesIteratorHelper>
elementTypes(pack &&... _pack) const {
return elementTypesImpl(use_named_args,
std::forward<decltype(_pack)>(_pack)...);
}
template <typename... pack>
std::enable_if_t<not are_named_argument<pack...>::value,
ElementTypesIteratorHelper>
elementTypes(pack &&... _pack) const {
return elementTypesImpl(std::forward<decltype(_pack)>(_pack)...);
}
/*! Get an iterator to the beginning of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the first stored data matching the filters
* or an iterator to the end of the map if none match*/
[[deprecated("Use elementTypes instead")]] inline type_iterator
firstType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
/*! Get an iterator to the end of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the last stored data matching the filters
* or an iterator to the end of the map if none match */
[[deprecated("Use elementTypes instead")]] inline type_iterator
lastType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline DataMap & getData(GhostType ghost_type);
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline const DataMap & getData(GhostType ghost_type) const;
/* ------------------------------------------------------------------------ */
protected:
DataMap data;
DataMap ghost_data;
};
/* -------------------------------------------------------------------------- */
/* Some typedefs */
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
class ElementTypeMapArray : public ElementTypeMap<Array<T> *, SupportType>,
public Memory {
public:
using type = T;
using array_type = Array<T>;
protected:
using parent = ElementTypeMap<Array<T> *, SupportType>;
using DataMap = typename parent::DataMap;
public:
using type_iterator = typename parent::type_iterator;
/// standard assigment (copy) operator
void operator=(const ElementTypeMapArray &) = delete;
- ElementTypeMapArray(const ElementTypeMapArray &);
+ ElementTypeMapArray(const ElementTypeMapArray & /*other*/);
/// explicit copy
void copy(const ElementTypeMapArray & other);
/*! Constructor
* @param id optional: identifier (string)
* @param parent_id optional: parent identifier. for organizational purposes
* only
* @param memory_id optional: choose a specific memory, defaults to memory 0
*/
ElementTypeMapArray(const ID & id = "by_element_type_array",
const ID & parent_id = "no_parent",
const MemoryID & memory_id = 0)
: parent(), Memory(parent_id + ":" + id, memory_id), name(id){};
/*! allocate memory for a new array
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map
* @param ghost_type whether to add the field to the data map or the
* ghost_data map
* @param default_value the default value to use to fill the array
* @return a reference to the allocated array */
inline Array<T> & alloc(UInt size, UInt nb_component,
const SupportType & type,
- const GhostType & ghost_type,
+ GhostType ghost_type,
const T & default_value = T());
/*! allocate memory for a new array in both the data and the ghost_data map
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map
* @param default_value the default value to use to fill the array
*/
inline void alloc(UInt size, UInt nb_component, const SupportType & type,
const T & default_value = T());
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a reference to the array */
inline const Array<T> &
operator()(const SupportType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ GhostType ghost_type = _not_ghost) const;
/// access the data of an element, this combine the map and array accessor
inline const T & operator()(const Element & element,
UInt component = 0) const;
/// access the data of an element, this combine the map and array accessor
inline T & operator()(const Element & element, UInt component = 0);
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a const reference to the array */
inline Array<T> & operator()(const SupportType & type,
- const GhostType & ghost_type = _not_ghost);
+ GhostType ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map.
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @param vect the vector to include into the map
* @return stored data corresponding to type. */
- inline void setArray(const SupportType & type, const GhostType & ghost_type,
+ inline void setArray(const SupportType & type, GhostType ghost_type,
const Array<T> & vect);
/*! frees all memory related to the data*/
inline void free();
- /*! set all values in the ElementTypeMap to zero*/
inline void clear();
+ inline bool empty() const __attribute__((warn_unused_result));
+
+ /*! set all values in the ElementTypeMap to zero*/
+ inline void zero() { this->set(T()); }
+
/*! set all values in the ElementTypeMap to value */
- template <typename ST> inline void set(const ST & value);
+ template<typename ST>
+ inline void set(const ST & value);
+
/*! deletes and reorders entries in the stored arrays
* @param new_numbering a ElementTypeMapArray of new indices. UInt(-1)
* indicates
* deleted entries. */
inline void
onElementsRemoved(const ElementTypeMapArray<UInt> & new_numbering);
/// text output helper
void printself(std::ostream & stream, int indent = 0) const override;
/*! set the id
* @param id the new name
*/
inline void setID(const ID & id) { this->id = id; }
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
ElementTypeMap<UInt> nb_components;
for (auto & type : this->elementTypes(dim, ghost_type, kind)) {
UInt nb_comp = (*this)(type, ghost_type).getNbComponent();
nb_components(type, ghost_type) = nb_comp;
}
return nb_components;
}
/* ------------------------------------------------------------------------ */
/* more evolved allocators */
/* ------------------------------------------------------------------------ */
public:
/// initialize the arrays in accordance to a functor
template <class Func>
void initialize(const Func & f, const T & default_value, bool do_not_default);
/// initialize with sizes and number of components in accordance of a mesh
/// content
template <typename... pack>
void initialize(const Mesh & mesh, pack &&... _pack);
/// initialize with sizes and number of components in accordance of a fe
/// engine content (aka integration points)
template <typename... pack>
void initialize(const FEEngine & fe_engine, pack &&... _pack);
/* ------------------------------------------------------------------------ */
/* Accesssors */
/* ------------------------------------------------------------------------ */
public:
/// get the name of the internal field
AKANTU_GET_MACRO(Name, name, ID);
/**
* get the size of the ElementTypeMapArray<T>
* @param[in] _pack
* \parblock
* optional arguments can be any of:
* \li \c _spatial_dimension the dimension to consider (default:
* _all_dimensions)
* \li \c _ghost_type (default: _not_ghost)
* \li \c _element_kind (default: _ek_not_defined)
* \li \c _all_ghost_types (default: false)
* \endparblock
**/
template <typename... pack> UInt size(pack &&... _pack) const;
bool isNodal() const { return is_nodal; }
void isNodal(bool is_nodal) { this->is_nodal = is_nodal; }
private:
- UInt sizeImpl(UInt spatial_dimension, const GhostType & ghost_type,
- const ElementKind & kind) const;
+ UInt sizeImpl(UInt spatial_dimension, GhostType ghost_type,
+ ElementKind kind) const;
protected:
/// name of the element type map: e.g. connectivity, grad_u
ID name;
/// Is the data stored by node of the element
bool is_nodal{false};
};
/// to store data Array<Real> by element type
using ElementTypeMapReal = ElementTypeMapArray<Real>;
/// to store data Array<Int> by element type
using ElementTypeMapInt = ElementTypeMapArray<Int>;
/// to store data Array<UInt> by element type
using ElementTypeMapUInt = ElementTypeMapArray<UInt, ElementType>;
/// Map of data of type UInt stored in a mesh
using UIntDataMap = std::map<std::string, Array<UInt> *>;
using ElementTypeMapUIntDataMap = ElementTypeMap<UIntDataMap, ElementType>;
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_TYPE_MAP_HH__ */
+#endif /* AKANTU_ELEMENT_TYPE_MAP_HH_ */
diff --git a/src/mesh/element_type_map_filter.hh b/src/mesh/element_type_map_filter.hh
index 695fac32b..6727387f2 100644
--- a/src/mesh/element_type_map_filter.hh
+++ b/src/mesh/element_type_map_filter.hh
@@ -1,299 +1,301 @@
/**
* @file element_type_map_filter.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Sun Dec 03 2017
*
* @brief Filtered version based on a an akantu::ElementGroup of a
* akantu::ElementTypeMap
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_BY_ELEMENT_TYPE_FILTER_HH__
-#define __AKANTU_BY_ELEMENT_TYPE_FILTER_HH__
+#ifndef AKANTU_BY_ELEMENT_TYPE_FILTER_HH_
+#define AKANTU_BY_ELEMENT_TYPE_FILTER_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* ArrayFilter */
/* -------------------------------------------------------------------------- */
template <typename T> class ArrayFilter {
-
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
-
public:
/// standard iterator
template <typename R = T> class iterator {
inline bool operator!=(__attribute__((unused)) iterator<R> & other) {
throw;
};
inline bool operator==(__attribute__((unused)) iterator<R> & other) {
throw;
};
inline iterator<R> & operator++() { throw; };
inline T operator*() {
throw;
return T();
};
};
/// const iterator
template <template <class S> class original_iterator, typename Shape,
typename filter_iterator>
class const_iterator {
public:
UInt getCurrentIndex() {
return (*this->filter_it * this->nb_item_per_elem +
this->sub_element_counter);
}
inline const_iterator() = default;
inline const_iterator(const original_iterator<Shape> & origin_it,
const filter_iterator & filter_it,
UInt nb_item_per_elem)
: origin_it(origin_it), filter_it(filter_it),
nb_item_per_elem(nb_item_per_elem), sub_element_counter(0){};
inline bool operator!=(const_iterator & other) const {
return !((*this) == other);
}
inline bool operator==(const_iterator & other) const {
return (this->origin_it == other.origin_it &&
this->filter_it == other.filter_it &&
this->sub_element_counter == other.sub_element_counter);
}
inline bool operator!=(const const_iterator & other) const {
return !((*this) == other);
}
inline bool operator==(const const_iterator & other) const {
return (this->origin_it == other.origin_it &&
this->filter_it == other.filter_it &&
this->sub_element_counter == other.sub_element_counter);
}
inline const_iterator & operator++() {
++sub_element_counter;
if (sub_element_counter == nb_item_per_elem) {
sub_element_counter = 0;
++filter_it;
}
return *this;
};
inline Shape operator*() {
return origin_it[nb_item_per_elem * (*filter_it) + sub_element_counter];
};
private:
original_iterator<Shape> origin_it;
filter_iterator filter_it;
/// the number of item per element
UInt nb_item_per_elem;
/// counter for every sub element group
UInt sub_element_counter;
};
using vector_iterator = iterator<Vector<T>>;
using array_type = Array<T>;
using const_vector_iterator =
const_iterator<array_type::template const_iterator, Vector<T>,
Array<UInt>::const_iterator<UInt>>;
using value_type = typename array_type::value_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ArrayFilter(const Array<T> & array, const Array<UInt> & filter,
UInt nb_item_per_elem)
: array(array), filter(filter), nb_item_per_elem(nb_item_per_elem){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
const_vector_iterator begin_reinterpret(UInt n, UInt new_size) const {
AKANTU_DEBUG_ASSERT(
n * new_size == this->getNbComponent() * this->size(),
"The new values for size ("
<< new_size << ") and nb_component (" << n
<< ") are not compatible with the one of this array("
<< this->size() << "," << this->getNbComponent() << ")");
UInt new_full_array_size = this->array.size() * array.getNbComponent() / n;
UInt new_nb_item_per_elem = this->nb_item_per_elem;
- if (new_size != 0 && n != 0)
+ if (new_size != 0 && n != 0) {
new_nb_item_per_elem = this->array.getNbComponent() *
this->filter.size() * this->nb_item_per_elem /
(n * new_size);
+ }
return const_vector_iterator(
this->array.begin_reinterpret(n, new_full_array_size),
this->filter.begin(), new_nb_item_per_elem);
};
const_vector_iterator end_reinterpret(UInt n, UInt new_size) const {
AKANTU_DEBUG_ASSERT(
n * new_size == this->getNbComponent() * this->size(),
"The new values for size ("
<< new_size << ") and nb_component (" << n
<< ") are not compatible with the one of this array("
<< this->size() << "," << this->getNbComponent() << ")");
UInt new_full_array_size =
this->array.size() * this->array.getNbComponent() / n;
UInt new_nb_item_per_elem = this->nb_item_per_elem;
- if (new_size != 0 && n != 0)
+ if (new_size != 0 && n != 0) {
new_nb_item_per_elem = this->array.getNbComponent() *
this->filter.size() * this->nb_item_per_elem /
(n * new_size);
+ }
return const_vector_iterator(
this->array.begin_reinterpret(n, new_full_array_size),
this->filter.end(), new_nb_item_per_elem);
};
- vector_iterator begin_reinterpret(UInt, UInt) { throw; };
+ vector_iterator begin_reinterpret(UInt /*unused*/, UInt /*unused*/) {
+ throw;
+ };
- vector_iterator end_reinterpret(UInt, UInt) { throw; };
+ vector_iterator end_reinterpret(UInt /*unused*/, UInt /*unused*/) { throw; };
/// return the size of the filtered array which is the filter size
UInt size() const { return this->filter.size() * this->nb_item_per_elem; };
/// the number of components of the filtered array
UInt getNbComponent() const { return this->array.getNbComponent(); };
+ bool empty() const __attribute__((warn_unused_result)) { return (size() == 0);}
+
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// reference to array of data
const Array<T> & array;
/// reference to the filter used to select elements
const Array<UInt> & filter;
/// the number of item per element
UInt nb_item_per_elem;
};
/* -------------------------------------------------------------------------- */
/* ElementTypeMapFilter */
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType = ElementType>
class ElementTypeMapArrayFilter {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using type = T;
using array_type = ArrayFilter<T>;
using value_type = typename array_type::value_type;
using type_iterator =
typename ElementTypeMapArray<UInt, SupportType>::type_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementTypeMapArrayFilter(
const ElementTypeMapArray<T, SupportType> & array,
const ElementTypeMapArray<UInt, SupportType> & filter,
const ElementTypeMap<UInt, SupportType> & nb_data_per_elem)
: array(array), filter(filter), nb_data_per_elem(nb_data_per_elem) {}
ElementTypeMapArrayFilter(
const ElementTypeMapArray<T, SupportType> & array,
const ElementTypeMapArray<UInt, SupportType> & filter)
: array(array), filter(filter) {}
~ElementTypeMapArrayFilter() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
- inline const ArrayFilter<T>
- operator()(const SupportType & type,
- const GhostType & ghost_type = _not_ghost) const {
+ inline ArrayFilter<T> operator()(const SupportType & type,
+ GhostType ghost_type = _not_ghost) const {
if (filter.exists(type, ghost_type)) {
- if (nb_data_per_elem.exists(type, ghost_type))
+ if (nb_data_per_elem.exists(type, ghost_type)) {
return ArrayFilter<T>(array(type, ghost_type), filter(type, ghost_type),
nb_data_per_elem(type, ghost_type) /
array(type, ghost_type).getNbComponent());
- else
- return ArrayFilter<T>(array(type, ghost_type), filter(type, ghost_type),
- 1);
- } else {
- return ArrayFilter<T>(empty_array, empty_filter, 1);
+ }
+ return ArrayFilter<T>(array(type, ghost_type), filter(type, ghost_type),
+ 1);
}
+ return ArrayFilter<T>(empty_array, empty_filter, 1);
};
template <typename... Args>
decltype(auto) elementTypes(Args &&... args) const {
return filter.elementTypes(std::forward<decltype(args)>(args)...);
}
decltype(auto) getNbComponents(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
return this->array.getNbComponents(dim, ghost_type, kind);
};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
std::string getID() {
return std::string("filtered:" + this->array().getID());
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
const ElementTypeMapArray<T, SupportType> & array;
const ElementTypeMapArray<UInt, SupportType> & filter;
ElementTypeMap<UInt> nb_data_per_elem;
/// Empty array to be able to return consistent filtered arrays
Array<T> empty_array;
Array<UInt> empty_filter;
};
} // namespace akantu
-#endif /* __AKANTU_BY_ELEMENT_TYPE_FILTER_HH__ */
+#endif /* AKANTU_BY_ELEMENT_TYPE_FILTER_HH_ */
diff --git a/src/mesh/element_type_map_tmpl.hh b/src/mesh/element_type_map_tmpl.hh
index f4eee8d7b..438d56f7b 100644
--- a/src/mesh/element_type_map_tmpl.hh
+++ b/src/mesh/element_type_map_tmpl.hh
@@ -1,790 +1,823 @@
/**
* @file element_type_map_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
* @date last modification: Tue Feb 20 2018
*
* @brief implementation of template functions of the ElementTypeMap and
* ElementTypeMapArray classes
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
#include "element_type_map.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include "element_type_conversion.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_TYPE_MAP_TMPL_HH__
-#define __AKANTU_ELEMENT_TYPE_MAP_TMPL_HH__
+#ifndef AKANTU_ELEMENT_TYPE_MAP_TMPL_HH_
+#define AKANTU_ELEMENT_TYPE_MAP_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline std::string
ElementTypeMap<Stored, SupportType>::printType(const SupportType & type,
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
std::stringstream sstr;
sstr << "(" << ghost_type << ":" << type << ")";
return sstr.str();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::exists(
- const SupportType & type, const GhostType & ghost_type) const {
+ const SupportType & type, GhostType ghost_type) const {
return this->getData(ghost_type).find(type) !=
this->getData(ghost_type).end();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline const Stored & ElementTypeMap<Stored, SupportType>::
-operator()(const SupportType & type, const GhostType & ghost_type) const {
+operator()(const SupportType & type, GhostType ghost_type) const {
auto it = this->getData(ghost_type).find(type);
- if (it == this->getData(ghost_type).end())
+ if (it == this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMap::printType(type, ghost_type)
<< " in this ElementTypeMap<"
<< debug::demangle(typeid(Stored).name())
<< "> class");
+ }
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline Stored & ElementTypeMap<Stored, SupportType>::
-operator()(const SupportType & type, const GhostType & ghost_type) {
+operator()(const SupportType & type, GhostType ghost_type) {
return this->getData(ghost_type)[type];
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
template <typename U>
inline Stored & ElementTypeMap<Stored, SupportType>::
operator()(U && insertee, const SupportType & type,
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
auto it = this->getData(ghost_type).find(type);
if (it != this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("Element of type "
<< ElementTypeMap::printType(type, ghost_type)
<< " already in this ElementTypeMap<"
<< debug::demangle(typeid(Stored).name())
<< "> class");
} else {
auto & data = this->getData(ghost_type);
const auto & res =
data.insert(std::make_pair(type, std::forward<U>(insertee)));
it = res.first;
}
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::DataMap &
ElementTypeMap<Stored, SupportType>::getData(GhostType ghost_type) {
- if (ghost_type == _not_ghost)
+ if (ghost_type == _not_ghost) {
return data;
+ }
return ghost_data;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline const typename ElementTypeMap<Stored, SupportType>::DataMap &
ElementTypeMap<Stored, SupportType>::getData(GhostType ghost_type) const {
- if (ghost_type == _not_ghost)
+ if (ghost_type == _not_ghost) {
return data;
+ }
return ghost_data;
}
/* -------------------------------------------------------------------------- */
/// Works only if stored is a pointer to a class with a printself method
template <class Stored, typename SupportType>
void ElementTypeMap<Stored, SupportType>::printself(std::ostream & stream,
int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "ElementTypeMap<" << debug::demangle(typeid(Stored).name())
<< "> [" << std::endl;
for (auto && gt : ghost_types) {
const DataMap & data = getData(gt);
for (auto & pair : data) {
stream << space << space << ElementTypeMap::printType(pair.first, gt)
<< std::endl;
}
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::ElementTypeMap() = default;
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::~ElementTypeMap() = default;
/* -------------------------------------------------------------------------- */
/* ElementTypeMapArray */
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
void ElementTypeMapArray<T, SupportType>::copy(
const ElementTypeMapArray & other) {
for (auto ghost_type : ghost_types) {
for (auto type :
this->elementTypes(_all_dimensions, ghost_type, _ek_not_defined)) {
const auto & array_to_copy = other(type, ghost_type);
auto & array =
this->alloc(0, array_to_copy.getNbComponent(), type, ghost_type);
array.copy(array_to_copy);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
ElementTypeMapArray<T, SupportType>::ElementTypeMapArray(
const ElementTypeMapArray & other)
: parent(), Memory(other.id + "_copy", other.memory_id),
name(other.name + "_copy") {
this->copy(other);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline Array<T> & ElementTypeMapArray<T, SupportType>::alloc(
UInt size, UInt nb_component, const SupportType & type,
- const GhostType & ghost_type, const T & default_value) {
- std::string ghost_id = "";
- if (ghost_type == _ghost)
+ GhostType ghost_type, const T & default_value) {
+ std::string ghost_id;
+ if (ghost_type == _ghost) {
ghost_id = ":ghost";
+ }
Array<T> * tmp;
auto it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end()) {
auto id = this->id + ":" + std::to_string(type) + ghost_id;
tmp = &(Memory::alloc<T>(id, size, nb_component, default_value));
this->getData(ghost_type)[type] = tmp;
} else {
AKANTU_DEBUG_INFO(
"The vector "
<< this->id << this->printType(type, ghost_type)
<< " already exists, it is resized instead of allocated.");
tmp = it->second;
it->second->resize(size);
}
return *tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void
ElementTypeMapArray<T, SupportType>::alloc(UInt size, UInt nb_component,
const SupportType & type,
const T & default_value) {
this->alloc(size, nb_component, type, _not_ghost, default_value);
this->alloc(size, nb_component, type, _ghost, default_value);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::free() {
AKANTU_DEBUG_IN();
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
for (auto & pair : data) {
dealloc(pair.second->getID());
}
data.clear();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::clear() {
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
for (auto & vect : data) {
vect.second->clear();
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
-template <typename ST>
+inline bool ElementTypeMapArray<T, SupportType>::empty() const {
+ bool is_empty = true;
+ for (auto gt : ghost_types) {
+ auto & data = this->getData(gt);
+ for (auto & vect : data) {
+ is_empty &= vect.second->empty();
+ if (not is_empty) {
+ return false;
+ }
+ }
+ }
+ return is_empty;
+}
+
+/* -------------------------------------------------------------------------- */
+template <typename T, typename SupportType>
+template<typename ST>
inline void ElementTypeMapArray<T, SupportType>::set(const ST & value) {
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
for (auto & vect : data) {
vect.second->set(value);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline const Array<T> & ElementTypeMapArray<T, SupportType>::
-operator()(const SupportType & type, const GhostType & ghost_type) const {
+operator()(const SupportType & type, GhostType ghost_type) const {
auto it = this->getData(ghost_type).find(type);
- if (it == this->getData(ghost_type).end())
+ if (it == this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMapArray::printType(type, ghost_type)
<< " in this const ElementTypeMapArray<"
<< debug::demangle(typeid(T).name()) << "> class(\""
<< this->id << "\")");
+ }
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline Array<T> & ElementTypeMapArray<T, SupportType>::
-operator()(const SupportType & type, const GhostType & ghost_type) {
+operator()(const SupportType & type, GhostType ghost_type) {
auto it = this->getData(ghost_type).find(type);
- if (it == this->getData(ghost_type).end())
+ if (it == this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMapArray::printType(type, ghost_type)
<< " in this ElementTypeMapArray<"
<< debug::demangle(typeid(T).name())
<< "> class (\"" << this->id << "\")");
+ }
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void
ElementTypeMapArray<T, SupportType>::setArray(const SupportType & type,
- const GhostType & ghost_type,
+ GhostType ghost_type,
const Array<T> & vect) {
auto it = this->getData(ghost_type).find(type);
if (AKANTU_DEBUG_TEST(dblWarning) && it != this->getData(ghost_type).end() &&
it->second != &vect) {
AKANTU_DEBUG_WARNING(
"The Array "
<< this->printType(type, ghost_type)
<< " is already registred, this call can lead to a memory leak.");
}
this->getData(ghost_type)[type] = &(const_cast<Array<T> &>(vect));
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::onElementsRemoved(
const ElementTypeMapArray<UInt> & new_numbering) {
for (auto gt : ghost_types) {
- for (auto & type :
+ for (auto && type :
new_numbering.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
auto support_type = convertType<ElementType, SupportType>(type);
if (this->exists(support_type, gt)) {
const auto & renumbering = new_numbering(type, gt);
- if (renumbering.size() == 0)
+ if (renumbering.empty()) {
continue;
+ }
auto & vect = this->operator()(support_type, gt);
auto nb_component = vect.getNbComponent();
Array<T> tmp(renumbering.size(), nb_component);
UInt new_size = 0;
for (UInt i = 0; i < vect.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
- memcpy(tmp.storage() + new_i * nb_component,
- vect.storage() + i * nb_component, nb_component * sizeof(T));
+ std::copy_n(vect.storage() + i * nb_component,
+ nb_component,
+ tmp.storage() + new_i * nb_component);
++new_size;
}
}
tmp.resize(new_size);
vect.copy(tmp);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
void ElementTypeMapArray<T, SupportType>::printself(std::ostream & stream,
int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "ElementTypeMapArray<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
for (UInt g = _not_ghost; g <= _ghost; ++g) {
auto gt = (GhostType)g;
const DataMap & data = this->getData(gt);
typename DataMap::const_iterator it;
for (it = data.begin(); it != data.end(); ++it) {
stream << space << space << ElementTypeMapArray::printType(it->first, gt)
<< " [" << std::endl;
it->second->printself(stream, indent + 3);
stream << space << space << " ]" << std::endl;
}
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/* SupportType Iterator */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::type_iterator::type_iterator(
DataMapIterator & list_begin, DataMapIterator & list_end, UInt dim,
ElementKind ek)
: list_begin(list_begin), list_end(list_end), dim(dim), kind(ek) {}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::type_iterator::type_iterator(
const type_iterator & it)
: list_begin(it.list_begin), list_end(it.list_end), dim(it.dim),
kind(it.kind) {}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::type_iterator &
ElementTypeMap<Stored, SupportType>::type_iterator::
operator=(const type_iterator & it) {
if (this != &it) {
list_begin = it.list_begin;
list_end = it.list_end;
dim = it.dim;
kind = it.kind;
}
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator::reference
ElementTypeMap<Stored, SupportType>::type_iterator::operator*() {
return list_begin->first;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator::reference
ElementTypeMap<Stored, SupportType>::type_iterator::operator*() const {
return list_begin->first;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator &
ElementTypeMap<Stored, SupportType>::type_iterator::operator++() {
++list_begin;
while ((list_begin != list_end) &&
(((dim != _all_dimensions) &&
(dim != Mesh::getSpatialDimension(list_begin->first))) ||
((kind != _ek_not_defined) &&
- (kind != Mesh::getKind(list_begin->first)))))
+ (kind != Mesh::getKind(list_begin->first))))) {
++list_begin;
+ }
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::type_iterator
ElementTypeMap<Stored, SupportType>::type_iterator::operator++(int) {
type_iterator tmp(*this);
operator++();
return tmp;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::type_iterator::
operator==(const type_iterator & other) const {
return this->list_begin == other.list_begin;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::type_iterator::
operator!=(const type_iterator & other) const {
return this->list_begin != other.list_begin;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
auto ElementTypeMap<Stored, SupportType>::ElementTypesIteratorHelper::begin()
-> iterator {
auto b = container.get().getData(ghost_type).begin();
auto e = container.get().getData(ghost_type).end();
// loop until the first valid type
while ((b != e) &&
(((dim != _all_dimensions) &&
(dim != Mesh::getSpatialDimension(b->first))) ||
- ((kind != _ek_not_defined) && (kind != Mesh::getKind(b->first)))))
+ ((kind != _ek_not_defined) && (kind != Mesh::getKind(b->first))))) {
++b;
+ }
return iterator(b, e, dim, kind);
}
template <class Stored, typename SupportType>
auto ElementTypeMap<Stored, SupportType>::ElementTypesIteratorHelper::end()
-> iterator {
auto e = container.get().getData(ghost_type).end();
return iterator(e, e, dim, kind);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
auto ElementTypeMap<Stored, SupportType>::elementTypesImpl(
UInt dim, GhostType ghost_type, ElementKind kind) const
-> ElementTypesIteratorHelper {
return ElementTypesIteratorHelper(*this, dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
template <typename... pack>
auto ElementTypeMap<Stored, SupportType>::elementTypesImpl(
const use_named_args_t & unused, pack &&... _pack) const
-> ElementTypesIteratorHelper {
return ElementTypesIteratorHelper(*this, unused, _pack...);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline auto ElementTypeMap<Stored, SupportType>::firstType(
UInt dim, GhostType ghost_type, ElementKind kind) const -> type_iterator {
return elementTypes(dim, ghost_type, kind).begin();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline auto ElementTypeMap<Stored, SupportType>::lastType(
UInt dim, GhostType ghost_type, ElementKind kind) const -> type_iterator {
typename DataMap::const_iterator e;
e = getData(ghost_type).end();
return typename ElementTypeMap<Stored, SupportType>::type_iterator(e, e, dim,
kind);
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Stored, typename SupportType>
inline std::ostream &
operator<<(std::ostream & stream,
const ElementTypeMap<Stored, SupportType> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
class ElementTypeMapArrayInitializer {
protected:
- using CompFunc = std::function<UInt(const ElementType &, const GhostType &)>;
+ using CompFunc = std::function<UInt(ElementType, GhostType)>;
public:
ElementTypeMapArrayInitializer(
const CompFunc & comp_func, UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined)
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined)
: comp_func(comp_func), spatial_dimension(spatial_dimension),
ghost_type(ghost_type), element_kind(element_kind) {}
- const GhostType & ghostType() const { return ghost_type; }
+ GhostType ghostType() const { return ghost_type; }
- virtual UInt nbComponent(const ElementType & type) const {
+ virtual UInt nbComponent(ElementType type) const {
return comp_func(type, ghostType());
}
virtual bool isNodal() const { return false; }
protected:
CompFunc comp_func;
UInt spatial_dimension;
GhostType ghost_type;
ElementKind element_kind;
};
/* -------------------------------------------------------------------------- */
class MeshElementTypeMapArrayInitializer
: public ElementTypeMapArrayInitializer {
using CompFunc = ElementTypeMapArrayInitializer::CompFunc;
public:
MeshElementTypeMapArrayInitializer(
const Mesh & mesh, UInt nb_component = 1,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined,
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined,
bool with_nb_element = false, bool with_nb_nodes_per_element = false)
: MeshElementTypeMapArrayInitializer(
mesh,
- [nb_component](const ElementType &, const GhostType &) -> UInt {
+ [nb_component](ElementType /*unused*/,
+ GhostType /*unused*/) -> UInt {
return nb_component;
},
spatial_dimension, ghost_type, element_kind, with_nb_element,
with_nb_nodes_per_element) {}
MeshElementTypeMapArrayInitializer(
const Mesh & mesh, const CompFunc & comp_func,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined,
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined,
bool with_nb_element = false, bool with_nb_nodes_per_element = false)
: ElementTypeMapArrayInitializer(comp_func, spatial_dimension, ghost_type,
element_kind),
mesh(mesh), with_nb_element(with_nb_element),
with_nb_nodes_per_element(with_nb_nodes_per_element) {}
decltype(auto) elementTypes() const {
return mesh.elementTypes(this->spatial_dimension, this->ghost_type,
this->element_kind);
}
- virtual UInt size(const ElementType & type) const {
- if (with_nb_element)
+ virtual UInt size(ElementType type) const {
+ if (with_nb_element) {
return mesh.getNbElement(type, this->ghost_type);
+ }
return 0;
}
- UInt nbComponent(const ElementType & type) const override {
+ UInt nbComponent(ElementType type) const override {
UInt res = ElementTypeMapArrayInitializer::nbComponent(type);
- if (with_nb_nodes_per_element)
- return (res * mesh.getNbNodesPerElement(type));
+ if (with_nb_nodes_per_element) {
+ return (res * Mesh::getNbNodesPerElement(type));
+ }
return res;
}
bool isNodal() const override { return with_nb_nodes_per_element; }
protected:
const Mesh & mesh;
bool with_nb_element;
bool with_nb_nodes_per_element;
};
/* -------------------------------------------------------------------------- */
class FEEngineElementTypeMapArrayInitializer
: public MeshElementTypeMapArrayInitializer {
public:
FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine, UInt nb_component = 1,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine,
const ElementTypeMapArrayInitializer::CompFunc & nb_component,
UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & element_kind = _ek_not_defined);
+ GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
- UInt size(const ElementType & type) const override;
+ UInt size(ElementType type) const override;
using ElementTypesIteratorHelper =
ElementTypeMapArray<Real, ElementType>::ElementTypesIteratorHelper;
ElementTypesIteratorHelper elementTypes() const;
protected:
const FEEngine & fe_engine;
};
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
template <class Func>
void ElementTypeMapArray<T, SupportType>::initialize(const Func & f,
const T & default_value,
bool do_not_default) {
this->is_nodal = f.isNodal();
auto ghost_type = f.ghostType();
for (auto & type : f.elementTypes()) {
- if (not this->exists(type, ghost_type))
+ if (not this->exists(type, ghost_type)) {
if (do_not_default) {
auto & array = this->alloc(0, f.nbComponent(type), type, ghost_type);
array.resize(f.size(type));
} else {
this->alloc(f.size(type), f.nbComponent(type), type, ghost_type,
default_value);
}
- else {
+ } else {
auto & array = this->operator()(type, ghost_type);
- if (not do_not_default)
+ if (not do_not_default) {
array.resize(f.size(type), default_value);
- else
+ } else {
array.resize(f.size(type));
+ }
}
}
}
/* -------------------------------------------------------------------------- */
/**
* All parameters are named optionals
* \param _nb_component a functor giving the number of components per
* (ElementType, GhostType) pair or a scalar giving a unique number of
* components
* regardless of type
* \param _spatial_dimension a filter for the elements of a specific dimension
* \param _element_kind filter with element kind (_ek_regular, _ek_structural,
* ...)
* \param _with_nb_element allocate the arrays with the number of elements for
* each
* type in the mesh
* \param _with_nb_nodes_per_element multiply the number of components by the
* number of nodes per element
* \param _default_value default inital value
* \param _do_not_default do not initialize the allocated arrays
* \param _ghost_type filter a type of ghost
*/
template <typename T, typename SupportType>
template <typename... pack>
void ElementTypeMapArray<T, SupportType>::initialize(const Mesh & mesh,
pack &&... _pack) {
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _casper);
bool all_ghost_types = requested_ghost_type == _casper;
for (auto ghost_type : ghost_types) {
- if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types))
+ if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types)) {
continue;
+ }
auto functor = MeshElementTypeMapArrayInitializer(
mesh, OPTIONAL_NAMED_ARG(nb_component, 1),
OPTIONAL_NAMED_ARG(spatial_dimension, mesh.getSpatialDimension()),
ghost_type, OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined),
OPTIONAL_NAMED_ARG(with_nb_element, false),
OPTIONAL_NAMED_ARG(with_nb_nodes_per_element, false));
this->initialize(functor, OPTIONAL_NAMED_ARG(default_value, T()),
OPTIONAL_NAMED_ARG(do_not_default, false));
}
}
/* -------------------------------------------------------------------------- */
/**
* All parameters are named optionals
* \param _nb_component a functor giving the number of components per
* (ElementType, GhostType) pair or a scalar giving a unique number of
* components
* regardless of type
* \param _spatial_dimension a filter for the elements of a specific dimension
* \param _element_kind filter with element kind (_ek_regular, _ek_structural,
* ...)
* \param _default_value default inital value
* \param _do_not_default do not initialize the allocated arrays
* \param _ghost_type filter a specific ghost type
* \param _all_ghost_types get all ghost types
*/
template <typename T, typename SupportType>
template <typename... pack>
void ElementTypeMapArray<T, SupportType>::initialize(const FEEngine & fe_engine,
pack &&... _pack) {
bool all_ghost_types = OPTIONAL_NAMED_ARG(all_ghost_types, true);
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _not_ghost);
for (auto ghost_type : ghost_types) {
- if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types))
+ if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types)) {
continue;
+ }
auto functor = FEEngineElementTypeMapArrayInitializer(
fe_engine, OPTIONAL_NAMED_ARG(nb_component, 1),
OPTIONAL_NAMED_ARG(spatial_dimension, UInt(-2)), ghost_type,
OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined));
this->initialize(functor, OPTIONAL_NAMED_ARG(default_value, T()),
OPTIONAL_NAMED_ARG(do_not_default, false));
}
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
inline T & ElementTypeMapArray<T, SupportType>::
operator()(const Element & element, UInt component) {
return this->operator()(element.type, element.ghost_type)(element.element,
component);
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
inline const T & ElementTypeMapArray<T, SupportType>::
operator()(const Element & element, UInt component) const {
return this->operator()(element.type, element.ghost_type)(element.element,
component);
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
UInt ElementTypeMapArray<T, SupportType>::sizeImpl(
- UInt spatial_dimension, const GhostType & ghost_type,
- const ElementKind & kind) const {
+ UInt spatial_dimension, GhostType ghost_type,
+ ElementKind kind) const {
UInt size = 0;
for (auto && type : this->elementTypes(spatial_dimension, ghost_type, kind)) {
size += this->operator()(type, ghost_type).size();
}
return size;
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
template <typename... pack>
UInt ElementTypeMapArray<T, SupportType>::size(pack &&... _pack) const {
UInt size = 0;
bool all_ghost_types = OPTIONAL_NAMED_ARG(all_ghost_types, true);
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _not_ghost);
for (auto ghost_type : ghost_types) {
- if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types))
+ if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types)) {
continue;
+ }
size +=
sizeImpl(OPTIONAL_NAMED_ARG(spatial_dimension, _all_dimensions),
ghost_type, OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined));
}
return size;
}
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_TYPE_MAP_TMPL_HH__ */
+#endif /* AKANTU_ELEMENT_TYPE_MAP_TMPL_HH_ */
diff --git a/src/mesh/group_manager.cc b/src/mesh/group_manager.cc
index b6dfcfbe7..105b1f491 100644
--- a/src/mesh/group_manager.cc
+++ b/src/mesh/group_manager.cc
@@ -1,1034 +1,1036 @@
/**
* @file group_manager.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Tue Feb 20 2018
*
* @brief Stores information about ElementGroup and NodeGroup
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "group_manager.hh"
#include "aka_csr.hh"
#include "data_accessor.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iterator>
#include <list>
#include <numeric>
#include <queue>
#include <sstream>
#include <utility>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
GroupManager::GroupManager(Mesh & mesh, const ID & id, const MemoryID & mem_id)
: id(id), memory_id(mem_id), mesh(mesh) {
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
GroupManager::~GroupManager() = default;
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::createNodeGroup(const std::string & group_name,
bool replace_group) {
AKANTU_DEBUG_IN();
auto it = node_groups.find(group_name);
if (it != node_groups.end()) {
if (replace_group) {
it->second.reset();
} else {
AKANTU_EXCEPTION(
"Trying to create a node group that already exists:" << group_name);
}
}
std::stringstream sstr;
sstr << this->id << ":" << group_name << "_node_group";
auto && ptr =
std::make_unique<NodeGroup>(group_name, mesh, sstr.str(), memory_id);
auto & node_group = *ptr;
// \todo insert_or_assign in c++17
if (it != node_groups.end()) {
it->second = std::move(ptr);
} else {
node_groups[group_name] = std::move(ptr);
}
AKANTU_DEBUG_OUT();
return node_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
NodeGroup &
GroupManager::createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & source_node_group,
T & filter) {
AKANTU_DEBUG_IN();
NodeGroup & node_group = this->createNodeGroup(group_name);
node_group.append(source_node_group);
if (T::type == FilterFunctor::_node_filter_functor) {
node_group.applyNodeFilter(filter);
} else {
AKANTU_ERROR("ElementFilter cannot be applied to NodeGroup yet."
<< " Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
return node_group;
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
bool replace_group) {
AKANTU_DEBUG_IN();
auto it = element_groups.find(group_name);
if (it != element_groups.end()) {
if (replace_group) {
it->second.reset();
} else {
AKANTU_EXCEPTION("Trying to create a element group that already exists:"
<< group_name);
}
}
NodeGroup & new_node_group =
createNodeGroup(group_name + "_nodes", replace_group);
auto && ptr = std::make_unique<ElementGroup>(
group_name, mesh, new_node_group, dimension,
this->id + ":" + group_name + "_element_group", memory_id);
auto & element_group = *ptr;
if (it != element_groups.end()) {
it->second = std::move(ptr);
} else {
element_groups[group_name] = std::move(ptr);
}
AKANTU_DEBUG_OUT();
return element_group;
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyElementGroup(const std::string & group_name,
bool destroy_node_group) {
AKANTU_DEBUG_IN();
auto eit = element_groups.find(group_name);
if (eit != element_groups.end()) {
- if (destroy_node_group)
+ if (destroy_node_group) {
destroyNodeGroup(eit->second->getNodeGroup().getName());
+ }
element_groups.erase(eit);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyNodeGroup(const std::string & group_name) {
AKANTU_DEBUG_IN();
auto nit = node_groups.find(group_name);
if (nit != node_groups.end()) {
node_groups.erase(nit);
}
AKANTU_DEBUG_OUT();
}
-// /* --------------------------------------------------------------------------
-// */ void GroupManager::destroyAllElementGroups(bool destroy_node_groups) {
-// AKANTU_DEBUG_IN();
-
-// if (destroy_node_groups)
-// for (auto && data : element_groups) {
-// destroyNodeGroup(std::get<1>(data)->getNodeGroup().getName());
-// }
-
-// element_groups.clear();
-
-// AKANTU_DEBUG_OUT();
-// }
-
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
NodeGroup & node_group) {
AKANTU_DEBUG_IN();
- if (element_groups.find(group_name) != element_groups.end())
+ if (element_groups.find(group_name) != element_groups.end()) {
AKANTU_EXCEPTION(
"Trying to create a element group that already exists:" << group_name);
+ }
auto && ptr = std::make_unique<ElementGroup>(
group_name, mesh, node_group, dimension,
id + ":" + group_name + "_element_group", memory_id);
auto & element_group = *ptr;
element_groups[group_name] = std::move(ptr);
AKANTU_DEBUG_OUT();
return element_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementGroup & GroupManager::createFilteredElementGroup(
const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter) {
AKANTU_DEBUG_IN();
if (T::type == FilterFunctor::_node_filter_functor) {
auto & filtered_node_group = this->createFilteredNodeGroup(
group_name + "_nodes", node_group, filter);
AKANTU_DEBUG_OUT();
return this->createElementGroup(group_name, dimension, filtered_node_group);
- } else if (T::type == FilterFunctor::_element_filter_functor) {
+ }
+ if (T::type == FilterFunctor::_element_filter_functor) {
AKANTU_ERROR(
"Cannot handle an ElementFilter yet. Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
class ClusterSynchronizer : public DataAccessor<Element> {
using DistantIDs = std::set<std::pair<UInt, UInt>>;
public:
ClusterSynchronizer(GroupManager & group_manager, UInt element_dimension,
std::string cluster_name_prefix,
ElementTypeMapArray<UInt> & element_to_fragment,
const ElementSynchronizer & element_synchronizer,
UInt nb_cluster)
: group_manager(group_manager), element_dimension(element_dimension),
cluster_name_prefix(std::move(cluster_name_prefix)),
element_to_fragment(element_to_fragment),
element_synchronizer(element_synchronizer), nb_cluster(nb_cluster) {}
UInt synchronize() {
Communicator & comm = Communicator::getStaticCommunicator();
UInt rank = comm.whoAmI();
UInt nb_proc = comm.getNbProc();
/// find starting index to renumber local clusters
Array<UInt> nb_cluster_per_proc(nb_proc);
nb_cluster_per_proc(rank) = nb_cluster;
comm.allGather(nb_cluster_per_proc);
starting_index = std::accumulate(nb_cluster_per_proc.begin(),
- nb_cluster_per_proc.begin() + rank, 0);
+ nb_cluster_per_proc.begin() + rank, 0U);
UInt global_nb_fragment =
std::accumulate(nb_cluster_per_proc.begin() + rank,
nb_cluster_per_proc.end(), starting_index);
/// create the local to distant cluster pairs with neighbors
element_synchronizer.synchronizeOnce(*this,
SynchronizationTag::_gm_clusters);
/// count total number of pairs
Array<int> nb_pairs(nb_proc); // This is potentially a bug for more than
// 2**31 pairs, but due to a all gatherv after
// it must be int to match MPI interfaces
nb_pairs(rank) = distant_ids.size();
comm.allGather(nb_pairs);
UInt total_nb_pairs = std::accumulate(nb_pairs.begin(), nb_pairs.end(), 0);
/// generate pairs global array
UInt local_pair_index =
std::accumulate(nb_pairs.storage(), nb_pairs.storage() + rank, 0);
Array<UInt> total_pairs(total_nb_pairs, 2);
- for (auto & ids : distant_ids) {
+ for (const auto & ids : distant_ids) {
total_pairs(local_pair_index, 0) = ids.first;
total_pairs(local_pair_index, 1) = ids.second;
++local_pair_index;
}
/// communicate pairs to all processors
nb_pairs *= 2;
comm.allGatherV(total_pairs, nb_pairs);
/// renumber clusters
/// generate fragment list
std::vector<std::set<UInt>> global_clusters;
UInt total_nb_cluster = 0;
Array<bool> is_fragment_in_cluster(global_nb_fragment, 1, false);
std::queue<UInt> fragment_check_list;
- while (total_pairs.size() != 0) {
+ while (not total_pairs.empty()) {
/// create a new cluster
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster = global_clusters[total_nb_cluster - 1];
UInt first_fragment = total_pairs(0, 0);
UInt second_fragment = total_pairs(0, 1);
total_pairs.erase(0);
fragment_check_list.push(first_fragment);
fragment_check_list.push(second_fragment);
while (!fragment_check_list.empty()) {
UInt current_fragment = fragment_check_list.front();
UInt * total_pairs_end = total_pairs.storage() + total_pairs.size() * 2;
UInt * fragment_found =
std::find(total_pairs.storage(), total_pairs_end, current_fragment);
if (fragment_found != total_pairs_end) {
UInt position = fragment_found - total_pairs.storage();
UInt pair = position / 2;
UInt other_index = (position + 1) % 2;
fragment_check_list.push(total_pairs(pair, other_index));
total_pairs.erase(pair);
} else {
fragment_check_list.pop();
current_cluster.insert(current_fragment);
is_fragment_in_cluster(current_fragment) = true;
}
}
}
/// add to FragmentToCluster all local fragments
for (UInt c = 0; c < global_nb_fragment; ++c) {
if (!is_fragment_in_cluster(c)) {
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster =
global_clusters[total_nb_cluster - 1];
current_cluster.insert(c);
}
}
/// reorganize element groups to match global clusters
for (UInt c = 0; c < global_clusters.size(); ++c) {
/// create new element group corresponding to current cluster
std::stringstream sstr;
sstr << cluster_name_prefix << "_" << c;
ElementGroup & cluster =
group_manager.createElementGroup(sstr.str(), element_dimension, true);
auto it = global_clusters[c].begin();
auto end = global_clusters[c].end();
/// append to current element group all fragments that belong to
/// the same cluster if they exist
for (; it != end; ++it) {
Int local_index = *it - starting_index;
- if (local_index < 0 || local_index >= Int(nb_cluster))
+ if (local_index < 0 || local_index >= Int(nb_cluster)) {
continue;
+ }
std::stringstream tmp_sstr;
tmp_sstr << "tmp_" << cluster_name_prefix << "_" << local_index;
AKANTU_DEBUG_ASSERT(group_manager.elementGroupExists(tmp_sstr.str()),
"Temporary fragment \"" << tmp_sstr.str()
<< "\" not found");
cluster.append(group_manager.getElementGroup(tmp_sstr.str()));
group_manager.destroyElementGroup(tmp_sstr.str(), true);
}
}
return total_nb_cluster;
}
private:
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override {
- if (tag == SynchronizationTag::_gm_clusters)
+ if (tag == SynchronizationTag::_gm_clusters) {
return elements.size() * sizeof(UInt);
+ }
return 0;
}
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override {
- if (tag != SynchronizationTag::_gm_clusters)
+ if (tag != SynchronizationTag::_gm_clusters) {
return;
+ }
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
const Element & el = *el_it;
/// for each element pack its global cluster index
buffer << element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
}
}
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override {
- if (tag != SynchronizationTag::_gm_clusters)
+ if (tag != SynchronizationTag::_gm_clusters) {
return;
+ }
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
UInt distant_cluster;
buffer >> distant_cluster;
const Element & el = *el_it;
UInt local_cluster =
element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
distant_ids.insert(std::make_pair(local_cluster, distant_cluster));
}
}
private:
GroupManager & group_manager;
UInt element_dimension;
std::string cluster_name_prefix;
ElementTypeMapArray<UInt> & element_to_fragment;
const ElementSynchronizer & element_synchronizer;
UInt nb_cluster;
DistantIDs distant_ids;
UInt starting_index;
};
/* -------------------------------------------------------------------------- */
/// \todo this function doesn't work in 1D
UInt GroupManager::createBoundaryGroupFromGeometry() {
UInt spatial_dimension = mesh.getSpatialDimension();
return createClusters(spatial_dimension - 1, "boundary");
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::createClusters(
- UInt element_dimension, Mesh & mesh_facets, std::string cluster_name_prefix,
+ UInt element_dimension, Mesh & mesh_facets,
+ const std::string & cluster_name_prefix,
const GroupManager::ClusteringFilter & filter) {
- return createClusters(element_dimension, std::move(cluster_name_prefix),
- filter, mesh_facets);
+ return createClusters(element_dimension, cluster_name_prefix, filter,
+ mesh_facets);
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::createClusters(
- UInt element_dimension, std::string cluster_name_prefix,
+ UInt element_dimension, const std::string & cluster_name_prefix,
const GroupManager::ClusteringFilter & filter) {
MeshAccessor mesh_accessor(mesh);
auto mesh_facets = std::make_unique<Mesh>(mesh.getSpatialDimension(),
mesh_accessor.getNodesSharedPtr(),
"mesh_facets_for_clusters");
mesh_facets->defineMeshParent(mesh);
MeshUtils::buildAllFacets(mesh, *mesh_facets, element_dimension,
element_dimension - 1);
- return createClusters(element_dimension, std::move(cluster_name_prefix),
- filter, *mesh_facets);
+ return createClusters(element_dimension, cluster_name_prefix, filter,
+ *mesh_facets);
}
/* -------------------------------------------------------------------------- */
//// \todo if needed element list construction can be optimized by
//// templating the filter class
UInt GroupManager::createClusters(UInt element_dimension,
const std::string & cluster_name_prefix,
const GroupManager::ClusteringFilter & filter,
Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
UInt nb_proc = mesh.getCommunicator().getNbProc();
std::string tmp_cluster_name_prefix = cluster_name_prefix;
ElementTypeMapArray<UInt> * element_to_fragment = nullptr;
if (nb_proc > 1 && mesh.isDistributed()) {
element_to_fragment =
new ElementTypeMapArray<UInt>("element_to_fragment", id, memory_id);
element_to_fragment->initialize(
mesh, _nb_component = 1, _spatial_dimension = element_dimension,
_element_kind = _ek_not_defined, _with_nb_element = true);
// mesh.initElementTypeMapArray(*element_to_fragment, 1, element_dimension,
// false, _ek_not_defined, true);
tmp_cluster_name_prefix = "tmp_" + tmp_cluster_name_prefix;
}
ElementTypeMapArray<bool> seen_elements("seen_elements", id, memory_id);
seen_elements.initialize(mesh, _spatial_dimension = element_dimension,
_element_kind = _ek_not_defined,
_with_nb_element = true);
// mesh.initElementTypeMapArray(seen_elements, 1, element_dimension, false,
// _ek_not_defined, true);
for (auto ghost_type : ghost_types) {
Element el;
el.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(_spatial_dimension = element_dimension,
_ghost_type = ghost_type, _element_kind = _ek_not_defined)) {
el.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<bool> & seen_elements_array = seen_elements(type, ghost_type);
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
- if (!filter(el))
+ if (!filter(el)) {
seen_elements_array(e) = true;
+ }
}
}
}
Array<bool> checked_node(mesh.getNbNodes(), 1, false);
UInt nb_cluster = 0;
for (auto ghost_type : ghost_types) {
Element uns_el;
uns_el.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(_spatial_dimension = element_dimension,
_ghost_type = ghost_type, _element_kind = _ek_not_defined)) {
uns_el.type = type;
Array<bool> & seen_elements_vec =
seen_elements(uns_el.type, uns_el.ghost_type);
for (UInt e = 0; e < seen_elements_vec.size(); ++e) {
// skip elements that have been already seen
- if (seen_elements_vec(e) == true)
+ if (seen_elements_vec(e)) {
continue;
+ }
// set current element
uns_el.element = e;
seen_elements_vec(e) = true;
/// create a new cluster
std::stringstream sstr;
sstr << tmp_cluster_name_prefix << "_" << nb_cluster;
ElementGroup & cluster =
createElementGroup(sstr.str(), element_dimension, true);
++nb_cluster;
// point element are cluster by themself
if (element_dimension == 0) {
cluster.add(uns_el);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(uns_el.type);
Vector<UInt> connect =
mesh.getConnectivity(uns_el.type, uns_el.ghost_type)
.begin(nb_nodes_per_element)[uns_el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node);
checked_node(node) = true;
}
}
continue;
}
std::queue<Element> element_to_add;
element_to_add.push(uns_el);
/// keep looping until current cluster is complete (no more
/// connected elements)
while (!element_to_add.empty()) {
/// take first element and erase it in the queue
Element el = element_to_add.front();
element_to_add.pop();
/// if parallel, store cluster index per element
- if (nb_proc > 1 && mesh.isDistributed())
+ if (nb_proc > 1 && mesh.isDistributed()) {
(*element_to_fragment)(el.type, el.ghost_type)(el.element) =
nb_cluster - 1;
+ }
/// add current element to the cluster
cluster.add(el);
const Array<Element> & element_to_facet =
mesh_facets.getSubelementToElement(el.type, el.ghost_type);
UInt nb_facet_per_element = element_to_facet.getNbComponent();
for (UInt f = 0; f < nb_facet_per_element; ++f) {
const Element & facet = element_to_facet(el.element, f);
- if (facet == ElementNull)
+ if (facet == ElementNull) {
continue;
+ }
const std::vector<Element> & connected_elements =
mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
for (UInt elem = 0; elem < connected_elements.size(); ++elem) {
const Element & check_el = connected_elements[elem];
// check if this element has to be skipped
- if (check_el == ElementNull || check_el == el)
+ if (check_el == ElementNull || check_el == el) {
continue;
+ }
Array<bool> & seen_elements_vec_current =
seen_elements(check_el.type, check_el.ghost_type);
- if (seen_elements_vec_current(check_el.element) == false) {
+ if (not seen_elements_vec_current(check_el.element)) {
seen_elements_vec_current(check_el.element) = true;
element_to_add.push(check_el);
}
}
}
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
Vector<UInt> connect = mesh.getConnectivity(el.type, el.ghost_type)
.begin(nb_nodes_per_element)[el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node, false);
checked_node(node) = true;
}
}
}
}
}
}
if (nb_proc > 1 && mesh.isDistributed()) {
ClusterSynchronizer cluster_synchronizer(
*this, element_dimension, cluster_name_prefix, *element_to_fragment,
this->mesh.getElementSynchronizer(), nb_cluster);
nb_cluster = cluster_synchronizer.synchronize();
delete element_to_fragment;
}
- if (mesh.isDistributed())
+ if (mesh.isDistributed()) {
this->synchronizeGroupNames();
+ }
AKANTU_DEBUG_OUT();
return nb_cluster;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void GroupManager::createGroupsFromMeshData(const std::string & dataset_name) {
std::set<std::string> group_names;
const auto & datas = mesh.getData<T>(dataset_name);
std::map<std::string, UInt> group_dim;
for (auto ghost_type : ghost_types) {
for (auto type : datas.elementTypes(_ghost_type = ghost_type)) {
const Array<T> & dataset = datas(type, ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
"Not the same number of elements ("
<< type << ":" << ghost_type
<< ") in the map from MeshData ("
<< dataset.size() << ") " << dataset_name
<< " and in the mesh (" << nb_element << ")!");
for (UInt e(0); e < nb_element; ++e) {
std::stringstream sstr;
sstr << dataset(e);
std::string gname = sstr.str();
group_names.insert(gname);
auto it = group_dim.find(gname);
if (it == group_dim.end()) {
group_dim[gname] = mesh.getSpatialDimension(type);
} else {
it->second = std::max(it->second, mesh.getSpatialDimension(type));
}
}
}
}
auto git = group_names.begin();
auto gend = group_names.end();
- for (; git != gend; ++git)
+ for (; git != gend; ++git) {
createElementGroup(*git, group_dim[*git]);
+ }
- if (mesh.isDistributed())
+ if (mesh.isDistributed()) {
this->synchronizeGroupNames();
+ }
Element el;
for (auto ghost_type : ghost_types) {
el.ghost_type = ghost_type;
for (auto type : datas.elementTypes(_ghost_type = ghost_type)) {
el.type = type;
const Array<T> & dataset = datas(type, ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
"Not the same number of elements in the map from "
"MeshData and in the mesh!");
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(el.type);
Array<UInt>::const_iterator<Vector<UInt>> cit =
mesh.getConnectivity(type, ghost_type).begin(nb_nodes_per_element);
for (UInt e(0); e < nb_element; ++e, ++cit) {
el.element = e;
std::stringstream sstr;
sstr << dataset(e);
ElementGroup & group = getElementGroup(sstr.str());
group.add(el, false, false);
const Vector<UInt> & connect = *cit;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connect[n];
group.addNode(node, false);
}
}
}
}
git = group_names.begin();
for (; git != gend; ++git) {
getElementGroup(*git).optimize();
}
}
template void GroupManager::createGroupsFromMeshData<std::string>(
const std::string & dataset_name);
template void
GroupManager::createGroupsFromMeshData<UInt>(const std::string & dataset_name);
/* -------------------------------------------------------------------------- */
void GroupManager::createElementGroupFromNodeGroup(
const std::string & name, const std::string & node_group_name,
UInt dimension) {
NodeGroup & node_group = getNodeGroup(node_group_name);
ElementGroup & group = createElementGroup(name, dimension, node_group);
group.fillFromNodeGroup();
}
/* -------------------------------------------------------------------------- */
void GroupManager::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "GroupManager [" << std::endl;
std::set<std::string> node_group_seen;
for (auto & group : iterateElementGroups()) {
group.printself(stream, indent + 1);
node_group_seen.insert(group.getNodeGroup().getName());
}
for (auto & group : iterateNodeGroups()) {
- if (node_group_seen.find(group.getName()) == node_group_seen.end())
+ if (node_group_seen.find(group.getName()) == node_group_seen.end()) {
group.printself(stream, indent + 1);
+ }
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::getNbElementGroups(UInt dimension) const {
- if (dimension == _all_dimensions)
+ if (dimension == _all_dimensions) {
return element_groups.size();
+ }
- auto it = element_groups.begin();
- auto end = element_groups.end();
- UInt count = 0;
- for (; it != end; ++it)
- count += (it->second->getDimension() == dimension);
- return count;
+ return std::count_if(
+ element_groups.begin(), element_groups.end(),
+ [dimension](auto && eg) { return eg.second->getDimension() == dimension; });
}
/* -------------------------------------------------------------------------- */
void GroupManager::checkAndAddGroups(DynamicCommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
UInt nb_node_group;
buffer >> nb_node_group;
AKANTU_DEBUG_INFO("Received " << nb_node_group << " node group names");
for (UInt ng = 0; ng < nb_node_group; ++ng) {
std::string node_group_name;
buffer >> node_group_name;
if (node_groups.find(node_group_name) == node_groups.end()) {
this->createNodeGroup(node_group_name);
}
AKANTU_DEBUG_INFO("Received node goup name: " << node_group_name);
}
UInt nb_element_group;
buffer >> nb_element_group;
AKANTU_DEBUG_INFO("Received " << nb_element_group << " element group names");
for (UInt eg = 0; eg < nb_element_group; ++eg) {
std::string element_group_name;
buffer >> element_group_name;
std::string node_group_name;
buffer >> node_group_name;
UInt dim;
buffer >> dim;
AKANTU_DEBUG_INFO("Received element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with node group "
<< node_group_name);
NodeGroup & node_group = *node_groups[node_group_name];
if (element_groups.find(element_group_name) == element_groups.end()) {
this->createElementGroup(element_group_name, dim, node_group);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::fillBufferWithGroupNames(
DynamicCommunicationBuffer & comm_buffer) const {
AKANTU_DEBUG_IN();
// packing node group names;
UInt nb_groups = this->node_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " node group names");
auto nnames_it = node_groups.begin();
auto nnames_end = node_groups.end();
for (; nnames_it != nnames_end; ++nnames_it) {
std::string node_group_name = nnames_it->first;
comm_buffer << node_group_name;
AKANTU_DEBUG_INFO("Sending node goupe name: " << node_group_name);
}
// packing element group names with there associated node group name
nb_groups = this->element_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " element group names");
auto gnames_it = this->element_groups.begin();
auto gnames_end = this->element_groups.end();
for (; gnames_it != gnames_end; ++gnames_it) {
ElementGroup & element_group = *(gnames_it->second);
std::string element_group_name = gnames_it->first;
std::string node_group_name = element_group.getNodeGroup().getName();
UInt dim = element_group.getDimension();
comm_buffer << element_group_name;
comm_buffer << node_group_name;
comm_buffer << dim;
AKANTU_DEBUG_INFO("Sending element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with the node group "
<< node_group_name);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::synchronizeGroupNames() {
AKANTU_DEBUG_IN();
const Communicator & comm = mesh.getCommunicator();
Int nb_proc = comm.getNbProc();
Int my_rank = comm.whoAmI();
- if (nb_proc == 1)
+ if (nb_proc == 1) {
return;
+ }
if (my_rank == 0) {
for (Int p = 1; p < nb_proc; ++p) {
DynamicCommunicationBuffer recv_buffer;
- auto tag = Tag::genTag(p, 0, Tag::_ELEMENT_GROUP);
+ auto tag = Tag::genTag(p, 0, Tag::_element_group);
comm.receive(recv_buffer, p, tag);
AKANTU_DEBUG_INFO("Got " << printMemorySize<char>(recv_buffer.size())
<< " from proc " << p << " " << tag);
this->checkAndAddGroups(recv_buffer);
}
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
AKANTU_DEBUG_INFO("Initiating broadcast with "
<< printMemorySize<char>(comm_buffer.size()));
comm.broadcast(comm_buffer);
} else {
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
- auto tag = Tag::genTag(my_rank, 0, Tag::_ELEMENT_GROUP);
+ auto tag = Tag::genTag(my_rank, 0, Tag::_element_group);
AKANTU_DEBUG_INFO("Sending " << printMemorySize<char>(comm_buffer.size())
<< " to proc " << 0 << " " << tag);
comm.send(comm_buffer, 0, tag);
DynamicCommunicationBuffer recv_buffer;
comm.broadcast(recv_buffer);
AKANTU_DEBUG_INFO("Receiving broadcast with "
<< printMemorySize<char>(recv_buffer.size()));
this->checkAndAddGroups(recv_buffer);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
const ElementGroup &
GroupManager::getElementGroup(const std::string & name) const {
auto it = element_groups.find(name);
if (it == element_groups.end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::getElementGroup(const std::string & name) {
auto it = element_groups.find(name);
if (it == element_groups.end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
const NodeGroup & GroupManager::getNodeGroup(const std::string & name) const {
auto it = node_groups.find(name);
if (it == node_groups.end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::getNodeGroup(const std::string & name) {
auto it = node_groups.find(name);
if (it == node_groups.end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename GroupsType>
void GroupManager::renameGroup(GroupsType & groups, const std::string & name,
const std::string & new_name) {
auto it = groups.find(name);
if (it == groups.end()) {
AKANTU_EXCEPTION("There are no group named "
<< name << " associated to the group manager: " << id);
}
auto && group_ptr = std::move(it->second);
group_ptr->name = new_name;
groups.erase(it);
groups[new_name] = std::move(group_ptr);
}
/* -------------------------------------------------------------------------- */
void GroupManager::renameElementGroup(const std::string & name,
const std::string & new_name) {
renameGroup(element_groups, name, new_name);
}
/* -------------------------------------------------------------------------- */
void GroupManager::renameNodeGroup(const std::string & name,
const std::string & new_name) {
renameGroup(node_groups, name, new_name);
}
/* -------------------------------------------------------------------------- */
void GroupManager::copyElementGroup(const std::string & name,
const std::string & new_name) {
const auto & grp = getElementGroup(name);
auto & new_grp = createElementGroup(new_name, grp.getDimension());
new_grp.getElements().copy(grp.getElements());
}
/* -------------------------------------------------------------------------- */
void GroupManager::copyNodeGroup(const std::string & name,
const std::string & new_name) {
const auto & grp = getNodeGroup(name);
auto & new_grp = createNodeGroup(new_name);
new_grp.getNodes().copy(grp.getNodes());
}
} // namespace akantu
diff --git a/src/mesh/group_manager.hh b/src/mesh/group_manager.hh
index e20b746ba..43a5becc6 100644
--- a/src/mesh/group_manager.hh
+++ b/src/mesh/group_manager.hh
@@ -1,351 +1,351 @@
/**
* @file group_manager.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Wed Feb 07 2018
*
* @brief Stores information relevent to the notion of element and nodes
* groups.
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_GROUP_MANAGER_HH__
-#define __AKANTU_GROUP_MANAGER_HH__
+#ifndef AKANTU_GROUP_MANAGER_HH_
+#define AKANTU_GROUP_MANAGER_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_iterators.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementGroup;
class NodeGroup;
class Mesh;
class Element;
class ElementSynchronizer;
template <bool> class CommunicationBufferTemplated;
namespace dumpers {
class Field;
}
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
class GroupManager {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
using ElementGroups = std::map<std::string, std::unique_ptr<ElementGroup>>;
using NodeGroups = std::map<std::string, std::unique_ptr<NodeGroup>>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GroupManager(Mesh & mesh, const ID & id = "group_manager",
- const MemoryID & memory_id = 0);
+ const MemoryID & mem_id = 0);
virtual ~GroupManager();
/* ------------------------------------------------------------------------ */
/* Groups iterators */
/* ------------------------------------------------------------------------ */
public:
using node_group_iterator = NodeGroups::iterator;
using element_group_iterator = ElementGroups::iterator;
using const_node_group_iterator = NodeGroups::const_iterator;
using const_element_group_iterator = ElementGroups::const_iterator;
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(group_type, function, \
param_in, param_out) \
[[deprecated( \
"use iterate(Element|Node)Groups or " \
"(element|node)GroupExists")]] inline BOOST_PP_CAT(BOOST_PP_CAT(const_, \
group_type), \
_iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) const { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}; \
\
[[deprecated("use iterate(Element|Node)Groups or " \
"(element|node)GroupExists")]] inline BOOST_PP_CAT(group_type, \
_iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(group_type, function) \
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION( \
group_type, function, BOOST_PP_EMPTY(), BOOST_PP_EMPTY())
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(element_group, find,
const std::string & name, name);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(node_group, find,
const std::string & name, name);
public:
decltype(auto) iterateNodeGroups() {
return make_dereference_adaptor(make_values_adaptor(node_groups));
}
decltype(auto) iterateNodeGroups() const {
return make_dereference_adaptor(make_values_adaptor(node_groups));
}
decltype(auto) iterateElementGroups() {
return make_dereference_adaptor(make_values_adaptor(element_groups));
}
decltype(auto) iterateElementGroups() const {
return make_dereference_adaptor(make_values_adaptor(element_groups));
}
/* ------------------------------------------------------------------------ */
/* Clustering filter */
/* ------------------------------------------------------------------------ */
public:
class ClusteringFilter {
public:
- virtual bool operator()(const Element &) const { return true; }
+ virtual bool operator()(const Element & /*unused*/) const { return true; }
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create an empty node group
NodeGroup & createNodeGroup(const std::string & group_name,
bool replace_group = false);
/// create an element group and the associated node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension = _all_dimensions,
bool replace_group = false);
/* ------------------------------------------------------------------------ */
/// renames an element group
void renameElementGroup(const std::string & name,
const std::string & new_name);
/// renames a node group
void renameNodeGroup(const std::string & name, const std::string & new_name);
/// copy an existing element group
void copyElementGroup(const std::string & name, const std::string & new_name);
/// copy an existing node group
void copyNodeGroup(const std::string & name, const std::string & new_name);
/* ------------------------------------------------------------------------ */
/// create a node group from another node group but filtered
template <typename T>
NodeGroup & createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & node_group, T & filter);
/// create an element group from another element group but filtered
template <typename T>
ElementGroup &
createFilteredElementGroup(const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter);
/// destroy a node group
void destroyNodeGroup(const std::string & group_name);
/// destroy an element group and the associated node group
void destroyElementGroup(const std::string & group_name,
bool destroy_node_group = false);
// /// destroy all element groups and the associated node groups
// void destroyAllElementGroups(bool destroy_node_groups = false);
/// create a element group using an existing node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension, NodeGroup & node_group);
/// create groups based on values stored in a given mesh data
template <typename T>
void createGroupsFromMeshData(const std::string & dataset_name);
/// create boundaries group by a clustering algorithm \todo extend to parallel
UInt createBoundaryGroupFromGeometry();
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension, Mesh & mesh_facets,
- std::string cluster_name_prefix = "cluster",
+ const std::string & cluster_name_prefix = "cluster",
const ClusteringFilter & filter = ClusteringFilter());
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension,
- std::string cluster_name_prefix = "cluster",
+ const std::string & cluster_name_prefix = "cluster",
const ClusteringFilter & filter = ClusteringFilter());
private:
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension,
const std::string & cluster_name_prefix,
const ClusteringFilter & filter, Mesh & mesh_facets);
public:
/// Create an ElementGroup based on a NodeGroup
void createElementGroupFromNodeGroup(const std::string & name,
const std::string & node_group,
UInt dimension = _all_dimensions);
virtual void printself(std::ostream & stream, int indent = 0) const;
/// this function insure that the group names are present on all processors
/// /!\ it is a SMP call
void synchronizeGroupNames();
/// register an elemental field to the given group name (overloading for
/// ElementalPartionField)
template <typename T, template <bool> class dump_type>
std::shared_ptr<dumpers::Field> createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
- UInt spatial_dimension, const ElementKind & kind,
+ UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// ElementalField)
template <typename T, template <class> class ret_type,
template <class, template <class> class, bool> class dump_type>
std::shared_ptr<dumpers::Field> createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
- UInt spatial_dimension, const ElementKind & kind,
+ UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// MaterialInternalField)
template <typename T,
/// type of InternalMaterialField
template <typename, bool filtered> class dump_type>
std::shared_ptr<dumpers::Field>
createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name, UInt spatial_dimension,
- const ElementKind & kind,
+ ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem);
template <typename type, bool flag, template <class, bool> class ftype>
std::shared_ptr<dumpers::Field>
createNodalField(const ftype<type, flag> * field,
const std::string & group_name, UInt padding_size = 0);
template <typename type, bool flag, template <class, bool> class ftype>
std::shared_ptr<dumpers::Field>
createStridedNodalField(const ftype<type, flag> * field,
const std::string & group_name, UInt size,
UInt stride, UInt padding_size);
protected:
/// fill a buffer with all the group names
void fillBufferWithGroupNames(
CommunicationBufferTemplated<false> & comm_buffer) const;
/// take a buffer and create the missing groups localy
void checkAndAddGroups(CommunicationBufferTemplated<false> & buffer);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline std::shared_ptr<dumpers::Field>
createElementalField(const field_type & field, const std::string & group_name,
- UInt spatial_dimension, const ElementKind & kind,
+ UInt spatial_dimension, ElementKind kind,
const ElementTypeMap<UInt> & nb_data_per_elem);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline std::shared_ptr<dumpers::Field>
createElementalFilteredField(const field_type & field,
const std::string & group_name,
- UInt spatial_dimension, const ElementKind & kind,
+ UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem);
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
// AKANTU_GET_MACRO(ElementGroups, element_groups, const ElementGroups &);
const ElementGroup & getElementGroup(const std::string & name) const;
const NodeGroup & getNodeGroup(const std::string & name) const;
ElementGroup & getElementGroup(const std::string & name);
NodeGroup & getNodeGroup(const std::string & name);
UInt getNbElementGroups(UInt dimension = _all_dimensions) const;
UInt getNbNodeGroups() { return node_groups.size(); };
bool elementGroupExists(const std::string & name) {
return element_groups.find(name) != element_groups.end();
}
bool nodeGroupExists(const std::string & name) {
return node_groups.find(name) != node_groups.end();
}
private:
template <typename GroupsType>
void renameGroup(GroupsType & groups, const std::string & name,
const std::string & new_name);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id to create element and node groups
ID id;
/// memory_id to create element and node groups
MemoryID memory_id;
/// list of the node groups managed
NodeGroups node_groups;
/// list of the element groups managed
ElementGroups element_groups;
/// Mesh to which the element belongs
Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const GroupManager & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AKANTU_GROUP_MANAGER_HH__ */
+#endif /* AKANTU_GROUP_MANAGER_HH_ */
diff --git a/src/mesh/group_manager_inline_impl.hh b/src/mesh/group_manager_inline_impl.hh
index 499b12c5b..edb211784 100644
--- a/src/mesh/group_manager_inline_impl.hh
+++ b/src/mesh/group_manager_inline_impl.hh
@@ -1,184 +1,195 @@
/**
* @file group_manager_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Sun Dec 03 2017
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_field.hh"
#include "element_group.hh"
#include "element_type_map_filter.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_nodal_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, template <bool> class dump_type>
-std::shared_ptr<dumpers::Field> GroupManager::createElementalField(
- const ElementTypeMapArray<T> & field, const std::string & group_name,
- UInt spatial_dimension, const ElementKind & kind,
- ElementTypeMap<UInt> nb_data_per_elem) {
+std::shared_ptr<dumpers::Field>
+GroupManager::createElementalField(const ElementTypeMapArray<T> & field,
+ const std::string & group_name,
+ UInt spatial_dimension, ElementKind kind,
+ ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
- if (field_ptr == nullptr)
+ if (field_ptr == nullptr) {
return nullptr;
- if (group_name == "all")
+ }
+ if (group_name == "all") {
return this->createElementalField<dump_type<false>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
- else
- return this->createElementalFilteredField<dump_type<true>>(
- field, group_name, spatial_dimension, kind, nb_data_per_elem);
+ }
+ return this->createElementalFilteredField<dump_type<true>>(
+ field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <class> class T2,
template <class, template <class> class, bool> class dump_type>
-std::shared_ptr<dumpers::Field> GroupManager::createElementalField(
- const ElementTypeMapArray<T> & field, const std::string & group_name,
- UInt spatial_dimension, const ElementKind & kind,
- ElementTypeMap<UInt> nb_data_per_elem) {
+std::shared_ptr<dumpers::Field>
+GroupManager::createElementalField(const ElementTypeMapArray<T> & field,
+ const std::string & group_name,
+ UInt spatial_dimension, ElementKind kind,
+ ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
- if (field_ptr == nullptr)
+ if (field_ptr == nullptr) {
return nullptr;
- if (group_name == "all")
+ }
+ if (group_name == "all") {
return this->createElementalField<dump_type<T, T2, false>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
- else
- return this->createElementalFilteredField<dump_type<T, T2, true>>(
- field, group_name, spatial_dimension, kind, nb_data_per_elem);
+ }
+ return this->createElementalFilteredField<dump_type<T, T2, true>>(
+ field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename T2, bool filtered>
class dump_type> ///< type of InternalMaterialField
-std::shared_ptr<dumpers::Field> GroupManager::createElementalField(
- const ElementTypeMapArray<T> & field, const std::string & group_name,
- UInt spatial_dimension, const ElementKind & kind,
- ElementTypeMap<UInt> nb_data_per_elem) {
+std::shared_ptr<dumpers::Field>
+GroupManager::createElementalField(const ElementTypeMapArray<T> & field,
+ const std::string & group_name,
+ UInt spatial_dimension, ElementKind kind,
+ ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
- if (field_ptr == nullptr)
+ if (field_ptr == nullptr) {
return nullptr;
- if (group_name == "all")
+ }
+ if (group_name == "all") {
return this->createElementalField<dump_type<T, false>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
- else
- return this->createElementalFilteredField<dump_type<T, true>>(
- field, group_name, spatial_dimension, kind, nb_data_per_elem);
+ }
+ return this->createElementalFilteredField<dump_type<T, true>>(
+ field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename dump_type, typename field_type>
std::shared_ptr<dumpers::Field> GroupManager::createElementalField(
const field_type & field, const std::string & group_name,
- UInt spatial_dimension, const ElementKind & kind,
+ UInt spatial_dimension, ElementKind kind,
const ElementTypeMap<UInt> & nb_data_per_elem) {
const field_type * field_ptr = &field;
- if (field_ptr == nullptr)
+ if (field_ptr == nullptr) {
return nullptr;
- if (group_name != "all")
+ }
+ if (group_name != "all") {
throw;
+ }
auto dumper =
std::make_shared<dump_type>(field, spatial_dimension, _not_ghost, kind);
dumper->setNbDataPerElem(nb_data_per_elem);
return dumper;
}
/* -------------------------------------------------------------------------- */
template <typename dump_type, typename field_type>
std::shared_ptr<dumpers::Field> GroupManager::createElementalFilteredField(
const field_type & field, const std::string & group_name,
- UInt spatial_dimension, const ElementKind & kind,
+ UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const field_type * field_ptr = &field;
- if (field_ptr == nullptr)
+ if (field_ptr == nullptr) {
return nullptr;
- if (group_name == "all")
+ }
+ if (group_name == "all") {
throw;
+ }
using T = typename field_type::type;
ElementGroup & group = this->getElementGroup(group_name);
UInt dim = group.getDimension();
- if (dim != spatial_dimension)
+ if (dim != spatial_dimension) {
throw;
+ }
const ElementTypeMapArray<UInt> & elemental_filter = group.getElements();
auto * filtered = new ElementTypeMapArrayFilter<T>(field, elemental_filter,
nb_data_per_elem);
auto dumper = std::make_shared<dump_type>(*filtered, dim, _not_ghost, kind);
dumper->setNbDataPerElem(nb_data_per_elem);
return dumper;
}
/* -------------------------------------------------------------------------- */
template <typename type, bool flag, template <class, bool> class ftype>
std::shared_ptr<dumpers::Field>
GroupManager::createNodalField(const ftype<type, flag> * field,
const std::string & group_name,
UInt padding_size) {
return createStridedNodalField(field, group_name, 0, 0, padding_size);
}
/* -------------------------------------------------------------------------- */
template <typename type, bool flag, template <class, bool> class ftype>
std::shared_ptr<dumpers::Field>
GroupManager::createStridedNodalField(const ftype<type, flag> * field,
const std::string & group_name, UInt size,
UInt stride, UInt padding_size) {
- if (not field)
+ if (not field) {
return nullptr;
+ }
+
if (group_name == "all") {
using DumpType = typename dumpers::NodalField<type, false>;
auto dumper = std::make_shared<DumpType>(*field, size, stride);
dumper->setPadding(padding_size);
return dumper;
- } else {
- ElementGroup & group = this->getElementGroup(group_name);
- const Array<UInt> * nodal_filter = &(group.getNodeGroup().getNodes());
- using DumpType = typename dumpers::NodalField<type, true>;
- auto dumper =
- std::make_shared<DumpType>(*field, size, stride, nodal_filter);
- dumper->setPadding(padding_size);
- return dumper;
}
- return nullptr;
+
+ ElementGroup & group = this->getElementGroup(group_name);
+ const Array<UInt> * nodal_filter = &(group.getNodeGroup().getNodes());
+ using DumpType = typename dumpers::NodalField<type, true>;
+ auto dumper = std::make_shared<DumpType>(*field, size, stride, nodal_filter);
+ dumper->setPadding(padding_size);
+ return dumper;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif
diff --git a/src/mesh/mesh.cc b/src/mesh/mesh.cc
index 20288a86b..90ef2ef34 100644
--- a/src/mesh/mesh.cc
+++ b/src/mesh/mesh.cc
@@ -1,659 +1,662 @@
/**
* @file mesh.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief class handling meshes
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "group_manager_inline_impl.hh"
#include "mesh.hh"
#include "mesh_global_data_updater.hh"
#include "mesh_io.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "facet_synchronizer.hh"
#include "mesh_utils_distribution.hh"
#include "node_synchronizer.hh"
#include "periodic_node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_field.hh"
#include "dumper_internal_material_field.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <limits>
#include <sstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id,
Communicator & communicator)
: Memory(id, memory_id),
GroupManager(*this, id + ":group_manager", memory_id),
MeshData("mesh_data", id, memory_id),
connectivities("connectivities", id, memory_id),
ghosts_counters("ghosts_counters", id, memory_id),
normals("normals", id, memory_id), spatial_dimension(spatial_dimension),
size(spatial_dimension, 0.), bbox(spatial_dimension),
bbox_local(spatial_dimension), communicator(&communicator) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, Communicator & communicator, const ID & id,
const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id, communicator) {
AKANTU_DEBUG_IN();
this->nodes =
std::make_shared<Array<Real>>(0, spatial_dimension, id + ":coordinates");
this->nodes_flags = std::make_shared<Array<NodeFlag>>(0, 1, NodeFlag::_normal,
id + ":nodes_flags");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, Communicator::getStaticCommunicator(), id,
memory_id) {}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const std::shared_ptr<Array<Real>> & nodes,
const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id,
Communicator::getStaticCommunicator()) {
this->nodes = nodes;
this->nb_global_nodes = this->nodes->size();
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
-void Mesh::getBarycenters(Array<Real> & barycenter, const ElementType & type,
- const GhostType & ghost_type) const {
+void Mesh::getBarycenters(Array<Real> & barycenter, ElementType type,
+ GhostType ghost_type) const {
barycenter.resize(getNbElement(type, ghost_type));
for (auto && data : enumerate(make_view(barycenter, spatial_dimension))) {
getBarycenter(Element{type, UInt(std::get<0>(data)), ghost_type},
std::get<1>(data));
}
}
class FacetGlobalConnectivityAccessor : public DataAccessor<Element> {
public:
FacetGlobalConnectivityAccessor(Mesh & mesh)
: global_connectivity("global_connectivity",
"facet_connectivity_synchronizer") {
global_connectivity.initialize(
mesh, _spatial_dimension = _all_dimensions, _with_nb_element = true,
_with_nb_nodes_per_element = true, _element_kind = _ek_regular);
mesh.getGlobalConnectivity(global_connectivity);
}
UInt getNbData(const Array<Element> & elements,
- const SynchronizationTag & tag) const {
+ const SynchronizationTag & tag) const override {
UInt size = 0;
if (tag == SynchronizationTag::_smmc_facets_conn) {
UInt nb_nodes = Mesh::getNbNodesPerElementList(elements);
size += nb_nodes * sizeof(UInt);
}
return size;
}
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
- const SynchronizationTag & tag) const {
+ const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_smmc_facets_conn) {
for (const auto & element : elements) {
- auto & conns = global_connectivity(element.type, element.ghost_type);
+ const auto & conns = global_connectivity(element.type, element.ghost_type);
for (auto n : arange(conns.getNbComponent())) {
buffer << conns(element.element, n);
}
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
- const SynchronizationTag & tag) {
+ const SynchronizationTag & tag) override {
if (tag == SynchronizationTag::_smmc_facets_conn) {
for (const auto & element : elements) {
auto & conns = global_connectivity(element.type, element.ghost_type);
for (auto n : arange(conns.getNbComponent())) {
buffer >> conns(element.element, n);
}
}
}
}
AKANTU_GET_MACRO(GlobalConnectivity, (global_connectivity), decltype(auto));
protected:
ElementTypeMapArray<UInt> global_connectivity;
};
/* -------------------------------------------------------------------------- */
Mesh & Mesh::initMeshFacets(const ID & id) {
AKANTU_DEBUG_IN();
if (mesh_facets) {
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
mesh_facets = std::make_unique<Mesh>(spatial_dimension, this->nodes,
getID() + ":" + id, getMemoryID());
mesh_facets->mesh_parent = this;
mesh_facets->is_mesh_facets = true;
mesh_facets->nodes_flags = this->nodes_flags;
mesh_facets->nodes_global_ids = this->nodes_global_ids;
MeshUtils::buildAllFacets(*this, *mesh_facets, 0);
if (mesh.isDistributed()) {
mesh_facets->is_distributed = true;
mesh_facets->element_synchronizer = std::make_unique<FacetSynchronizer>(
*mesh_facets, mesh.getElementSynchronizer());
FacetGlobalConnectivityAccessor data_accessor(*mesh_facets);
/// communicate
mesh_facets->element_synchronizer->synchronizeOnce(
data_accessor, SynchronizationTag::_smmc_facets_conn);
/// flip facets
MeshUtils::flipFacets(*mesh_facets, data_accessor.getGlobalConnectivity(),
_ghost);
}
/// transfers the the mesh physical names to the mesh facets
if (not this->hasData("physical_names")) {
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
auto & mesh_phys_data = this->getData<std::string>("physical_names");
auto & phys_data = mesh_facets->getData<std::string>("physical_names");
phys_data.initialize(*mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
ElementTypeMapArray<Real> barycenters(getID(), "temporary_barycenters");
barycenters.initialize(*mesh_facets, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
for (auto && ghost_type : ghost_types) {
for (auto && type :
barycenters.elementTypes(spatial_dimension - 1, ghost_type)) {
mesh_facets->getBarycenters(barycenters(type, ghost_type), type,
ghost_type);
}
}
for_each_element(
mesh,
[&](auto && element) {
Vector<Real> barycenter(spatial_dimension);
mesh.getBarycenter(element, barycenter);
auto norm_barycenter = barycenter.norm();
auto tolerance = Math::getTolerance();
- if (norm_barycenter > tolerance)
+ if (norm_barycenter > tolerance) {
tolerance *= norm_barycenter;
+ }
const auto & element_to_facet = mesh_facets->getElementToSubelement(
element.type, element.ghost_type);
Vector<Real> barycenter_facet(spatial_dimension);
auto range = enumerate(make_view(
barycenters(element.type, element.ghost_type), spatial_dimension));
#ifndef AKANTU_NDEBUG
auto min_dist = std::numeric_limits<Real>::max();
#endif
// this is a spacial search coded the most inefficient way.
auto facet =
std::find_if(range.begin(), range.end(), [&](auto && data) {
auto facet = std::get<0>(data);
- if (element_to_facet(facet)[1] == ElementNull)
+ if (element_to_facet(facet)[1] == ElementNull) {
return false;
+ }
auto norm_distance = barycenter.distance(std::get<1>(data));
#ifndef AKANTU_NDEBUG
min_dist = std::min(min_dist, norm_distance);
#endif
return (norm_distance < tolerance);
});
if (facet == range.end()) {
AKANTU_DEBUG_INFO("The element "
<< element
<< " did not find its associated facet in the "
"mesh_facets! Try to decrease math tolerance. "
"The closest element was at a distance of "
<< min_dist);
return;
}
// set physical name
phys_data(Element{element.type, UInt(std::get<0>(*facet)),
element.ghost_type}) = mesh_phys_data(element);
},
_spatial_dimension = spatial_dimension - 1);
mesh_facets->createGroupsFromMeshData<std::string>("physical_names");
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
/* -------------------------------------------------------------------------- */
void Mesh::defineMeshParent(const Mesh & mesh) {
AKANTU_DEBUG_IN();
this->mesh_parent = &mesh;
this->is_mesh_facets = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::~Mesh() = default;
/* -------------------------------------------------------------------------- */
void Mesh::read(const std::string & filename, const MeshIOType & mesh_io_type) {
AKANTU_DEBUG_ASSERT(not is_distributed,
"You cannot read a mesh that is already distributed");
- MeshIO mesh_io;
- mesh_io.read(filename, *this, mesh_io_type);
+ MeshIO::read(filename, *this, mesh_io_type);
auto types =
this->elementTypes(spatial_dimension, _not_ghost, _ek_not_defined);
auto it = types.begin();
auto last = types.end();
if (it == last) {
AKANTU_DEBUG_WARNING(
"The mesh contained in the file "
<< filename << " does not seem to be of the good dimension."
<< " No element of dimension " << spatial_dimension << " were read.");
}
this->makeReady();
}
/* -------------------------------------------------------------------------- */
void Mesh::write(const std::string & filename,
const MeshIOType & mesh_io_type) {
- MeshIO mesh_io;
- mesh_io.write(filename, *this, mesh_io_type);
+ MeshIO::write(filename, *this, mesh_io_type);
}
/* -------------------------------------------------------------------------- */
void Mesh::makeReady() {
this->nb_global_nodes = this->nodes->size();
this->computeBoundingBox();
this->nodes_flags->resize(nodes->size(), NodeFlag::_normal);
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
}
/* -------------------------------------------------------------------------- */
void Mesh::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Mesh [" << std::endl;
stream << space << " + id : " << getID() << std::endl;
stream << space << " + spatial dimension : " << this->spatial_dimension
<< std::endl;
stream << space << " + nodes [" << std::endl;
nodes->printself(stream, indent + 2);
stream << space << " + connectivities [" << std::endl;
connectivities.printself(stream, indent + 2);
stream << space << " ]" << std::endl;
GroupManager::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void Mesh::computeBoundingBox() {
AKANTU_DEBUG_IN();
bbox_local.reset();
for (auto & pos : make_view(*nodes, spatial_dimension)) {
// if(!isPureGhostNode(i))
bbox_local += pos;
}
if (this->is_distributed) {
bbox = bbox_local.allSum(*communicator);
} else {
bbox = bbox_local;
}
size = bbox.size();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Mesh::initNormals() {
normals.initialize(*this, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_element_kind = _ek_not_defined);
}
/* -------------------------------------------------------------------------- */
void Mesh::getGlobalConnectivity(
ElementTypeMapArray<UInt> & global_connectivity) {
AKANTU_DEBUG_IN();
for (auto && ghost_type : ghost_types) {
for (auto type :
global_connectivity.elementTypes(_spatial_dimension = _all_dimensions,
_element_kind = _ek_not_defined, _ghost_type = ghost_type)) {
- if (not connectivities.exists(type, ghost_type))
+ if (not connectivities.exists(type, ghost_type)) {
continue;
+ }
auto & local_conn = connectivities(type, ghost_type);
auto & g_connectivity = global_connectivity(type, ghost_type);
UInt nb_nodes = local_conn.size() * local_conn.getNbComponent();
std::transform(local_conn.begin_reinterpret(nb_nodes),
local_conn.end_reinterpret(nb_nodes),
g_connectivity.begin_reinterpret(nb_nodes),
[&](UInt l) -> UInt { return this->getNodeGlobalId(l); });
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Mesh::getGroupDumper(const std::string & dumper_name,
const std::string & group_name) {
- if (group_name == "all")
+ if (group_name == "all") {
return this->getDumper(dumper_name);
- else
- return element_groups[group_name]->getDumper(dumper_name);
+ }
+ return element_groups[group_name]->getDumper(dumper_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementTypeMap<UInt> Mesh::getNbDataPerElem(ElementTypeMapArray<T> & arrays) {
ElementTypeMap<UInt> nb_data_per_elem;
for (auto type : arrays.elementTypes()) {
UInt nb_elements = this->getNbElement(type);
auto & array = arrays(type);
nb_data_per_elem(type) = array.getNbComponent() * array.size();
nb_data_per_elem(type) /= nb_elements;
}
return nb_data_per_elem;
}
/* -------------------------------------------------------------------------- */
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<Real> & array);
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<UInt> & array);
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
template <typename T>
std::shared_ptr<dumpers::Field>
Mesh::createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
- const ElementKind & element_kind) {
+ ElementKind element_kind) {
std::shared_ptr<dumpers::Field> field;
ElementTypeMapArray<T> * internal = nullptr;
try {
internal = &(this->getData<T>(field_id));
} catch (...) {
return nullptr;
}
ElementTypeMap<UInt> nb_data_per_elem = this->getNbDataPerElem(*internal);
field = this->createElementalField<T, dumpers::InternalMaterialField>(
*internal, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
return field;
}
template std::shared_ptr<dumpers::Field>
Mesh::createFieldFromAttachedData<Real>(const std::string & field_id,
const std::string & group_name,
- const ElementKind & element_kind);
+ ElementKind element_kind);
template std::shared_ptr<dumpers::Field>
Mesh::createFieldFromAttachedData<UInt>(const std::string & field_id,
const std::string & group_name,
- const ElementKind & element_kind);
+ ElementKind element_kind);
#endif
/* -------------------------------------------------------------------------- */
void Mesh::distributeImpl(
Communicator & communicator,
- std::function<Int(const Element &, const Element &)> edge_weight_function
- [[gnu::unused]],
- std::function<Int(const Element &)> vertex_weight_function
+ const std::function<Int(const Element &, const Element &)> &
+ edge_weight_function [[gnu::unused]],
+ const std::function<Int(const Element &)> & vertex_weight_function
[[gnu::unused]]) {
AKANTU_DEBUG_ASSERT(is_distributed == false,
"This mesh is already distribute");
this->communicator = &communicator;
this->element_synchronizer = std::make_unique<ElementSynchronizer>(
*this, this->getID() + ":element_synchronizer", this->getMemoryID(),
true);
this->node_synchronizer = std::make_unique<NodeSynchronizer>(
*this, this->getID() + ":node_synchronizer", this->getMemoryID(), true);
Int psize = this->communicator->getNbProc();
if (psize > 1) {
#ifdef AKANTU_USE_SCOTCH
Int prank = this->communicator->whoAmI();
if (prank == 0) {
MeshPartitionScotch partition(*this, spatial_dimension);
partition.partitionate(psize, edge_weight_function,
vertex_weight_function);
MeshUtilsDistribution::distributeMeshCentralized(*this, 0, partition);
} else {
MeshUtilsDistribution::distributeMeshCentralized(*this, 0);
}
#else
if (psize > 1) {
AKANTU_ERROR("Cannot distribute a mesh without a partitioning tool");
}
#endif
}
// if (psize > 1)
this->is_distributed = true;
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
void Mesh::getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements) {
- for (const auto & node : node_list)
- for (const auto & element : *nodes_to_elements[node])
+ for (const auto & node : node_list) {
+ for (const auto & element : *nodes_to_elements[node]) {
elements.push_back(element);
+ }
+ }
}
/* -------------------------------------------------------------------------- */
void Mesh::fillNodesToElements() {
Element e;
UInt nb_nodes = nodes->size();
for (UInt n = 0; n < nb_nodes; ++n) {
- if (this->nodes_to_elements[n])
+ if (this->nodes_to_elements[n]) {
this->nodes_to_elements[n]->clear();
- else
+ } else {
this->nodes_to_elements[n] = std::make_unique<std::set<Element>>();
+ }
}
for (auto ghost_type : ghost_types) {
e.ghost_type = ghost_type;
for (const auto & type :
elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
e.type = type;
UInt nb_element = this->getNbElement(type, ghost_type);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
connectivities(type, ghost_type)
.begin(Mesh::getNbNodesPerElement(type));
for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
e.element = el;
const Vector<UInt> & conn = *conn_it;
- for (UInt n = 0; n < conn.size(); ++n)
+ for (UInt n = 0; n < conn.size(); ++n) {
nodes_to_elements[conn(n)]->insert(e);
+ }
}
}
}
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt>
Mesh::updateGlobalData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event) {
- if (global_data_updater)
+ if (global_data_updater) {
return this->global_data_updater->updateData(nodes_event, elements_event);
- else {
- return std::make_tuple(nodes_event.getList().size(),
- elements_event.getList().size());
}
+ return std::make_tuple(nodes_event.getList().size(),
+ elements_event.getList().size());
}
/* -------------------------------------------------------------------------- */
void Mesh::registerGlobalDataUpdater(
std::unique_ptr<MeshGlobalDataUpdater> && global_data_updater) {
this->global_data_updater = std::move(global_data_updater);
}
/* -------------------------------------------------------------------------- */
void Mesh::eraseElements(const Array<Element> & elements) {
ElementTypeMap<UInt> last_element;
RemovedElementsEvent event(*this, "new_numbering", AKANTU_CURRENT_FUNCTION);
auto & remove_list = event.getList();
auto & new_numbering = event.getNewNumbering();
for (auto && el : elements) {
if (el.ghost_type != _not_ghost) {
auto & count = ghosts_counters(el);
--count;
if (count > 0) {
continue;
}
}
remove_list.push_back(el);
if (not new_numbering.exists(el.type, el.ghost_type)) {
auto nb_element = mesh.getNbElement(el.type, el.ghost_type);
auto & numbering =
new_numbering.alloc(nb_element, 1, el.type, el.ghost_type);
for (auto && pair : enumerate(numbering)) {
std::get<1>(pair) = std::get<0>(pair);
}
}
new_numbering(el) = UInt(-1);
}
auto find_last_not_deleted = [](auto && array, Int start) -> Int {
do {
--start;
} while (start >= 0 and array[start] == UInt(-1));
return start;
};
auto find_first_deleted = [](auto && array, Int start) -> Int {
auto begin = array.begin();
auto it = std::find_if(begin + start, array.end(),
[](auto & el) { return el == UInt(-1); });
return Int(it - begin);
};
for (auto ghost_type : ghost_types) {
for (auto type : new_numbering.elementTypes(_ghost_type = ghost_type)) {
auto & numbering = new_numbering(type, ghost_type);
- auto last_not_delete =
- find_last_not_deleted(numbering, numbering.size());
+ auto last_not_delete = find_last_not_deleted(numbering, numbering.size());
if (last_not_delete < 0) {
continue;
}
auto pos = find_first_deleted(numbering, 0);
while (pos < last_not_delete) {
std::swap(numbering[pos], numbering[last_not_delete]);
last_not_delete = find_last_not_deleted(numbering, last_not_delete);
pos = find_first_deleted(numbering, pos + 1);
}
}
}
this->sendEvent(event);
}
} // namespace akantu
diff --git a/src/mesh/mesh.hh b/src/mesh/mesh.hh
index 950c771ea..fb7f685be 100644
--- a/src/mesh/mesh.hh
+++ b/src/mesh/mesh.hh
@@ -1,696 +1,690 @@
/**
* @file mesh.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Feb 19 2018
*
* @brief the class representing the meshes
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_HH__
-#define __AKANTU_MESH_HH__
+#ifndef AKANTU_MESH_HH_
+#define AKANTU_MESH_HH_
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_bbox.hh"
#include "aka_event_handler_manager.hh"
#include "aka_memory.hh"
#include "communicator.hh"
#include "dumpable.hh"
#include "element.hh"
#include "element_class.hh"
#include "element_type_map.hh"
#include "group_manager.hh"
#include "mesh_data.hh"
#include "mesh_events.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
#include <set>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer;
class NodeSynchronizer;
class PeriodicNodeSynchronizer;
class MeshGlobalDataUpdater;
} // namespace akantu
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(communicator);
DECLARE_NAMED_ARGUMENT(edge_weight_function);
DECLARE_NAMED_ARGUMENT(vertex_weight_function);
} // namespace
/* -------------------------------------------------------------------------- */
/* Mesh */
/* -------------------------------------------------------------------------- */
/**
* @class Mesh mesh.hh
*
* This class contaisn the coordinates of the nodes in the Mesh.nodes
* akant::Array, and the connectivity. The connectivity are stored in by element
* types.
*
* In order to loop on all element you have to loop on all types like this :
* @code{.cpp}
for(auto & type : mesh.elementTypes()) {
UInt nb_element = mesh.getNbElement(type);
const Array<UInt> & conn = mesh.getConnectivity(type);
for(UInt e = 0; e < nb_element; ++e) {
...
}
}
or
for_each_element(mesh, [](Element & element) {
std::cout << element << std::endl
});
@endcode
*/
class Mesh : protected Memory,
public EventHandlerManager<MeshEventHandler>,
public GroupManager,
public MeshData,
public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
/// default constructor used for chaining, the last parameter is just to
/// differentiate constructors
Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id,
Communicator & communicator);
public:
/// constructor that create nodes coordinates array
Mesh(UInt spatial_dimension, const ID & id = "mesh",
const MemoryID & memory_id = 0);
/// mesh not distributed and not using the default communicator
Mesh(UInt spatial_dimension, Communicator & communicator,
const ID & id = "mesh", const MemoryID & memory_id = 0);
/**
* constructor that use an existing nodes coordinates
* array, by getting the vector of coordinates
*/
Mesh(UInt spatial_dimension, const std::shared_ptr<Array<Real>> & nodes,
const ID & id = "mesh", const MemoryID & memory_id = 0);
~Mesh() override;
/// read the mesh from a file
void read(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
/// write the mesh to a file
void write(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
protected:
void makeReady();
private:
/// initialize the connectivity to NULL and other stuff
void init();
/// function that computes the bounding box (fills xmin, xmax)
void computeBoundingBox();
/* ------------------------------------------------------------------------ */
/* Distributed memory methods and accessors */
/* ------------------------------------------------------------------------ */
public:
protected:
/// patitionate the mesh among the processors involved in their computation
virtual void distributeImpl(
Communicator & communicator,
- std::function<Int(const Element &, const Element &)> edge_weight_function,
- std::function<Int(const Element &)> vertex_weight_function);
+ const std::function<Int(const Element &, const Element &)> &
+ edge_weight_function,
+ const std::function<Int(const Element &)> & vertex_weight_function);
public:
/// with the arguments to pass to the partitionner
template <typename... pack>
std::enable_if_t<are_named_argument<pack...>::value>
distribute(pack &&... _pack) {
distributeImpl(
OPTIONAL_NAMED_ARG(communicator, Communicator::getStaticCommunicator()),
OPTIONAL_NAMED_ARG(edge_weight_function,
[](auto &&, auto &&) { return 1; }),
OPTIONAL_NAMED_ARG(vertex_weight_function, [](auto &&) { return 1; }));
}
/// defines is the mesh is distributed or not
inline bool isDistributed() const { return this->is_distributed; }
/* ------------------------------------------------------------------------ */
/* Periodicity methods and accessors */
/* ------------------------------------------------------------------------ */
public:
/// set the periodicity in a given direction
void makePeriodic(const SpatialDirection & direction);
void makePeriodic(const SpatialDirection & direction, const ID & list_1,
const ID & list_2);
protected:
void makePeriodic(const SpatialDirection & direction,
- const Array<UInt> & list_1, const Array<UInt> & list_2);
+ const Array<UInt> & list_left,
+ const Array<UInt> & list_right);
/// Removes the face that the mesh is periodic
void wipePeriodicInfo();
inline void addPeriodicSlave(UInt slave, UInt master);
template <typename T>
void synchronizePeriodicSlaveDataWithMaster(Array<T> & data);
// update the periodic synchronizer (creates it if it does not exists)
void updatePeriodicSynchronizer();
public:
/// defines if the mesh is periodic or not
- inline bool isPeriodic() const { return (this->is_periodic != 0); }
+ inline bool isPeriodic() const { return this->is_periodic; }
- inline bool isPeriodic(const SpatialDirection & direction) const {
- return ((this->is_periodic & (1 << direction)) != 0);
+ inline bool isPeriodic(const SpatialDirection & /*direction*/) const {
+ return this->is_periodic;
}
class PeriodicSlaves;
/// get the master node for a given slave nodes, except if node not a slave
inline UInt getPeriodicMaster(UInt slave) const;
/// get an iterable list of slaves for a given master node
inline decltype(auto) getPeriodicSlaves(UInt master) const;
/* ------------------------------------------------------------------------ */
/* General Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// extract coordinates of nodes from an element
template <typename T>
- inline void extractNodalValuesFromElement(const Array<T> & nodal_values,
- T * elemental_values,
- UInt * connectivity, UInt n_nodes,
- UInt nb_degree_of_freedom) const;
+ inline void
+ extractNodalValuesFromElement(const Array<T> & nodal_values, T * local_coord,
+ const UInt * connectivity, UInt n_nodes,
+ UInt nb_degree_of_freedom) const;
// /// extract coordinates of nodes from a reversed element
// inline void extractNodalCoordinatesFromPBCElement(Real * local_coords,
// UInt * connectivity,
// UInt n_nodes);
/// add a Array of connectivity for the given ElementType and GhostType .
- inline void addConnectivityType(const ElementType & type,
- const GhostType & ghost_type = _not_ghost);
+ inline void addConnectivityType(ElementType type,
+ GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
template <class Event> inline void sendEvent(Event & event) {
// if(event.getList().size() != 0)
EventHandlerManager<MeshEventHandler>::sendEvent<Event>(event);
}
/// prepare the event to remove the elements listed
void eraseElements(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
template <typename T>
inline void removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering);
/// initialize normals
void initNormals();
/// init facets' mesh
Mesh & initMeshFacets(const ID & id = "mesh_facets");
/// define parent mesh
void defineMeshParent(const Mesh & mesh);
/// get global connectivity array
void getGlobalConnectivity(ElementTypeMapArray<UInt> & global_connectivity);
public:
void getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements);
private:
/// fills the nodes_to_elements structure
void fillNodesToElements();
/// update the global ids, nodes type, ...
std::tuple<UInt, UInt> updateGlobalData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event);
void registerGlobalDataUpdater(
std::unique_ptr<MeshGlobalDataUpdater> && global_data_updater);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the id of the mesh
AKANTU_GET_MACRO(ID, Memory::id, const ID &);
/// get the id of the mesh
AKANTU_GET_MACRO(MemoryID, Memory::memory_id, const MemoryID &);
/// get the spatial dimension of the mesh = number of component of the
/// coordinates
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the nodes Array aka coordinates
AKANTU_GET_MACRO(Nodes, *nodes, const Array<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Nodes, *nodes, Array<Real> &);
/// get the normals for the elements
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Normals, normals, Real);
/// get the number of nodes
AKANTU_GET_MACRO(NbNodes, nodes->size(), UInt);
/// get the Array of global ids of the nodes (only used in parallel)
AKANTU_GET_MACRO(GlobalNodesIds, *nodes_global_ids, const Array<UInt> &);
// AKANTU_GET_MACRO_NOT_CONST(GlobalNodesIds, *nodes_global_ids, Array<UInt>
// &);
/// get the global id of a node
inline UInt getNodeGlobalId(UInt local_id) const;
/// get the global id of a node
inline UInt getNodeLocalId(UInt global_id) const;
/// get the global number of nodes
inline UInt getNbGlobalNodes() const;
/// get the nodes type Array
AKANTU_GET_MACRO(NodesFlags, *nodes_flags, const Array<NodeFlag> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(NodesFlags, *nodes_flags, Array<NodeFlag> &);
public:
inline NodeFlag getNodeFlag(UInt local_id) const;
inline Int getNodePrank(UInt local_id) const;
/// say if a node is a pure ghost node
inline bool isPureGhostNode(UInt n) const;
/// say if a node is pur local or master node
inline bool isLocalOrMasterNode(UInt n) const;
inline bool isLocalNode(UInt n) const;
inline bool isMasterNode(UInt n) const;
inline bool isSlaveNode(UInt n) const;
inline bool isPeriodicSlave(UInt n) const;
inline bool isPeriodicMaster(UInt n) const;
const Vector<Real> & getLowerBounds() const { return bbox.getLowerBounds(); }
const Vector<Real> & getUpperBounds() const { return bbox.getUpperBounds(); }
AKANTU_GET_MACRO(BBox, bbox, const BBox &);
const Vector<Real> & getLocalLowerBounds() const {
return bbox_local.getLowerBounds();
}
const Vector<Real> & getLocalUpperBounds() const {
return bbox_local.getUpperBounds();
}
AKANTU_GET_MACRO(LocalBBox, bbox_local, const BBox &);
/// get the connectivity Array for a given type
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO(Connectivities, connectivities,
const ElementTypeMapArray<UInt> &);
/// get the number of element of a type in the mesh
- inline UInt getNbElement(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ inline UInt getNbElement(ElementType type,
+ GhostType ghost_type = _not_ghost) const;
/// get the number of element for a given ghost_type and a given dimension
- inline UInt getNbElement(const UInt spatial_dimension = _all_dimensions,
- const GhostType & ghost_type = _not_ghost,
- const ElementKind & kind = _ek_not_defined) const;
+ inline UInt getNbElement(UInt spatial_dimension = _all_dimensions,
+ GhostType ghost_type = _not_ghost,
+ ElementKind kind = _ek_not_defined) const;
/// compute the barycenter of a given element
inline void getBarycenter(const Element & element,
Vector<Real> & barycenter) const;
- void getBarycenters(Array<Real> & barycenter, const ElementType & type,
- const GhostType & ghost_type) const;
+ void getBarycenters(Array<Real> & barycenter, ElementType type,
+ GhostType ghost_type) const;
/// get the element connected to a subelement (element of lower dimension)
const auto & getElementToSubelement() const;
/// get the element connected to a subelement
- const auto &
- getElementToSubelement(const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ const auto & getElementToSubelement(ElementType el_type,
+ GhostType ghost_type = _not_ghost) const;
/// get the element connected to a subelement
- auto & getElementToSubelement(const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost);
+ auto & getElementToSubelement(ElementType el_type,
+ GhostType ghost_type = _not_ghost);
/// get the elements connected to a subelement
const auto & getElementToSubelement(const Element & element) const;
/// get the subelement (element of lower dimension) connected to a element
const auto & getSubelementToElement() const;
/// get the subelement connected to an element
- const auto &
- getSubelementToElement(const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ const auto & getSubelementToElement(ElementType el_type,
+ GhostType ghost_type = _not_ghost) const;
/// get the subelement connected to an element
- auto & getSubelementToElement(const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost);
+ auto & getSubelementToElement(ElementType el_type,
+ GhostType ghost_type = _not_ghost);
/// get the subelement (element of lower dimension) connected to a element
VectorProxy<Element> getSubelementToElement(const Element & element) const;
/// get connectivity of a given element
inline VectorProxy<UInt> getConnectivity(const Element & element) const;
inline Vector<UInt>
getConnectivityWithPeriodicity(const Element & element) const;
protected:
inline auto & getElementToSubelement(const Element & element);
inline VectorProxy<Element> getSubelementToElement(const Element & element);
inline VectorProxy<UInt> getConnectivity(const Element & element);
public:
/// get a name field associated to the mesh
template <typename T>
- inline const Array<T> &
- getData(const ID & data_name, const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ inline const Array<T> & getData(const ID & data_name, ElementType el_type,
+ GhostType ghost_type = _not_ghost) const;
/// get a name field associated to the mesh
template <typename T>
- inline Array<T> & getData(const ID & data_name, const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost);
+ inline Array<T> & getData(const ID & data_name, ElementType el_type,
+ GhostType ghost_type = _not_ghost);
/// get a name field associated to the mesh
template <typename T>
inline const ElementTypeMapArray<T> & getData(const ID & data_name) const;
/// get a name field associated to the mesh
template <typename T>
inline ElementTypeMapArray<T> & getData(const ID & data_name);
template <typename T>
ElementTypeMap<UInt> getNbDataPerElem(ElementTypeMapArray<T> & array);
template <typename T>
std::shared_ptr<dumpers::Field>
createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
- const ElementKind & element_kind);
+ ElementKind element_kind);
/// templated getter returning the pointer to data in MeshData (modifiable)
template <typename T>
inline Array<T> &
- getDataPointer(const std::string & data_name, const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost,
- UInt nb_component = 1, bool size_to_nb_element = true,
+ getDataPointer(const std::string & data_name, ElementType el_type,
+ GhostType ghost_type = _not_ghost, UInt nb_component = 1,
+ bool size_to_nb_element = true,
bool resize_with_parent = false);
template <typename T>
- inline Array<T> & getDataPointer(const ID & data_name,
- const ElementType & el_type,
- const GhostType & ghost_type,
- UInt nb_component, bool size_to_nb_element,
+ inline Array<T> & getDataPointer(const ID & data_name, ElementType el_type,
+ GhostType ghost_type, UInt nb_component,
+ bool size_to_nb_element,
bool resize_with_parent, const T & defaul_);
/// Facets mesh accessor
inline const Mesh & getMeshFacets() const;
inline Mesh & getMeshFacets();
/// Parent mesh accessor
inline const Mesh & getMeshParent() const;
inline bool isMeshFacets() const { return this->is_mesh_facets; }
/// return the dumper from a group and and a dumper name
DumperIOHelper & getGroupDumper(const std::string & dumper_name,
const std::string & group_name);
/* ------------------------------------------------------------------------ */
/* Wrappers on ElementClass functions */
/* ------------------------------------------------------------------------ */
public:
/// get the number of nodes per element for a given element type
- static inline UInt getNbNodesPerElement(const ElementType & type);
+ static inline UInt getNbNodesPerElement(ElementType type);
/// get the number of nodes per element for a given element type considered as
/// a first order element
- static inline ElementType getP1ElementType(const ElementType & type);
+ static inline ElementType getP1ElementType(ElementType type);
/// get the kind of the element type
- static inline ElementKind getKind(const ElementType & type);
+ static inline ElementKind getKind(ElementType type);
/// get spatial dimension of a type of element
- static inline UInt getSpatialDimension(const ElementType & type);
+ static inline UInt getSpatialDimension(ElementType type);
/// get number of facets of a given element type
- static inline UInt getNbFacetsPerElement(const ElementType & type);
+ static inline UInt getNbFacetsPerElement(ElementType type);
/// get number of facets of a given element type
- static inline UInt getNbFacetsPerElement(const ElementType & type, UInt t);
+ static inline UInt getNbFacetsPerElement(ElementType type, UInt t);
/// get local connectivity of a facet for a given facet type
- static inline auto getFacetLocalConnectivity(const ElementType & type,
- UInt t = 0);
+ static inline auto getFacetLocalConnectivity(ElementType type, UInt t = 0);
/// get connectivity of facets for a given element
inline auto getFacetConnectivity(const Element & element, UInt t = 0) const;
/// get the number of type of the surface element associated to a given
/// element type
- static inline UInt getNbFacetTypes(const ElementType & type, UInt t = 0);
+ static inline UInt getNbFacetTypes(ElementType type, UInt t = 0);
/// get the type of the surface element associated to a given element
- static inline constexpr auto getFacetType(const ElementType & type,
- UInt t = 0);
+ static inline constexpr auto getFacetType(ElementType type, UInt t = 0);
/// get all the type of the surface element associated to a given element
- static inline constexpr auto getAllFacetTypes(const ElementType & type);
+ static inline constexpr auto getAllFacetTypes(ElementType type);
/// get the number of nodes in the given element list
static inline UInt getNbNodesPerElementList(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
using type_iterator [[deprecated]] =
ElementTypeMapArray<UInt, ElementType>::type_iterator;
using ElementTypesIteratorHelper =
ElementTypeMapArray<UInt, ElementType>::ElementTypesIteratorHelper;
template <typename... pack>
ElementTypesIteratorHelper elementTypes(pack &&... _pack) const;
[[deprecated("Use elementTypes instead")]] inline decltype(auto)
firstType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.elementTypes(dim, ghost_type, kind).begin();
}
[[deprecated("Use elementTypes instead")]] inline decltype(auto)
lastType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.elementTypes(dim, ghost_type, kind).end();
}
AKANTU_GET_MACRO(ElementSynchronizer, *element_synchronizer,
const ElementSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(ElementSynchronizer, *element_synchronizer,
ElementSynchronizer &);
AKANTU_GET_MACRO(NodeSynchronizer, *node_synchronizer,
const NodeSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(NodeSynchronizer, *node_synchronizer,
NodeSynchronizer &);
AKANTU_GET_MACRO(PeriodicNodeSynchronizer, *periodic_node_synchronizer,
const PeriodicNodeSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(PeriodicNodeSynchronizer,
*periodic_node_synchronizer,
PeriodicNodeSynchronizer &);
// AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, StaticCommunicator
// &);
AKANTU_GET_MACRO(Communicator, *communicator, const auto &);
AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, auto &);
AKANTU_GET_MACRO(PeriodicMasterSlaves, periodic_master_slave, const auto &);
/* ------------------------------------------------------------------------ */
/* Private methods for friends */
/* ------------------------------------------------------------------------ */
private:
friend class MeshAccessor;
friend class MeshUtils;
AKANTU_GET_MACRO(NodesPointer, *nodes, Array<Real> &);
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline Array<UInt> & getNodesGlobalIdsPointer();
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline Array<NodeFlag> & getNodesFlagsPointer();
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
inline Array<UInt> &
- getConnectivityPointer(const ElementType & type,
- const GhostType & ghost_type = _not_ghost);
+ getConnectivityPointer(ElementType type, GhostType ghost_type = _not_ghost);
/// get the ghost element counter
- inline Array<UInt> &
- getGhostsCounters(const ElementType & type,
- const GhostType & ghost_type = _ghost) {
+ inline Array<UInt> & getGhostsCounters(ElementType type,
+ GhostType ghost_type = _ghost) {
AKANTU_DEBUG_ASSERT(ghost_type != _not_ghost,
"No ghost counter for _not_ghost elements");
return ghosts_counters(type, ghost_type);
}
/// get a pointer to the element_to_subelement Array for the given type and
/// create it if necessary
inline Array<std::vector<Element>> &
- getElementToSubelementPointer(const ElementType & type,
- const GhostType & ghost_type = _not_ghost);
+ getElementToSubelementPointer(ElementType type,
+ GhostType ghost_type = _not_ghost);
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
inline Array<Element> &
- getSubelementToElementPointer(const ElementType & type,
- const GhostType & ghost_type = _not_ghost);
+ getSubelementToElementPointer(ElementType type,
+ GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// array of the nodes coordinates
std::shared_ptr<Array<Real>> nodes;
/// global node ids
std::shared_ptr<Array<UInt>> nodes_global_ids;
/// node flags (shared/periodic/...)
std::shared_ptr<Array<NodeFlag>> nodes_flags;
/// processor handling the node when not local or master
std::unordered_map<UInt, Int> nodes_prank;
/// global number of nodes;
UInt nb_global_nodes{0};
/// all class of elements present in this mesh (for heterogenous meshes)
ElementTypeMapArray<UInt> connectivities;
/// count the references on ghost elements
ElementTypeMapArray<UInt> ghosts_counters;
/// map to normals for all class of elements present in this mesh
ElementTypeMapArray<Real> normals;
/// the spatial dimension of this mesh
UInt spatial_dimension{0};
/// size covered by the mesh on each direction
Vector<Real> size;
/// global bounding box
BBox bbox;
/// local bounding box
BBox bbox_local;
/// Extra data loaded from the mesh file
// MeshData mesh_data;
/// facets' mesh
std::unique_ptr<Mesh> mesh_facets;
/// parent mesh (this is set for mesh_facets meshes)
const Mesh * mesh_parent{nullptr};
/// defines if current mesh is mesh_facets or not
bool is_mesh_facets{false};
/// defines if the mesh is centralized or distributed
bool is_distributed{false};
/// defines if the mesh is periodic
bool is_periodic{false};
/// Communicator on which mesh is distributed
Communicator * communicator;
/// Element synchronizer
std::unique_ptr<ElementSynchronizer> element_synchronizer;
/// Node synchronizer
std::unique_ptr<NodeSynchronizer> node_synchronizer;
/// Node synchronizer for periodic nodes
std::unique_ptr<PeriodicNodeSynchronizer> periodic_node_synchronizer;
using NodesToElements = std::vector<std::unique_ptr<std::set<Element>>>;
/// class to update global data using external knowledge
std::unique_ptr<MeshGlobalDataUpdater> global_data_updater;
/// This info is stored to simplify the dynamic changes
NodesToElements nodes_to_elements;
/// periodicity local info
std::unordered_map<UInt, UInt> periodic_slave_master;
std::unordered_multimap<UInt, UInt> periodic_master_slave;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Mesh & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
#include "element_type_map_tmpl.hh"
#include "mesh_inline_impl.hh"
-#endif /* __AKANTU_MESH_HH__ */
+#endif /* AKANTU_MESH_HH_ */
diff --git a/src/mesh/mesh_accessor.hh b/src/mesh/mesh_accessor.hh
index 0e6f7e67e..0b7c2fd37 100644
--- a/src/mesh/mesh_accessor.hh
+++ b/src/mesh/mesh_accessor.hh
@@ -1,168 +1,168 @@
/**
* @file mesh_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jun 30 2015
* @date last modification: Tue Sep 19 2017
*
* @brief this class allow to access some private member of mesh it is used for
* IO for examples
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_ACCESSOR_HH__
-#define __AKANTU_MESH_ACCESSOR_HH__
+#ifndef AKANTU_MESH_ACCESSOR_HH_
+#define AKANTU_MESH_ACCESSOR_HH_
namespace akantu {
class NodeSynchronizer;
class ElementSynchronizer;
class MeshGlobalDataUpdater;
} // namespace akantu
namespace akantu {
class MeshAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit MeshAccessor(Mesh & mesh) : _mesh(mesh) {}
virtual ~MeshAccessor() = default;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the global number of nodes
inline UInt getNbGlobalNodes() const { return this->_mesh.nb_global_nodes; }
/// set the global number of nodes
inline void setNbGlobalNodes(UInt nb_global_nodes) {
this->_mesh.nb_global_nodes = nb_global_nodes;
}
/// set the mesh as being distributed
inline void setDistributed() { this->_mesh.is_distributed = true; }
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline auto & getNodesGlobalIds() {
return this->_mesh.getNodesGlobalIdsPointer();
}
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline auto & getNodesFlags() { return this->_mesh.getNodesFlags(); }
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline void setNodePrank(UInt node, Int prank) {
this->_mesh.nodes_prank[node] = prank;
}
/// get a pointer to the coordinates Array
inline auto & getNodes() { return this->_mesh.getNodesPointer(); }
/// get a pointer to the coordinates Array
inline auto getNodesSharedPtr() { return this->_mesh.nodes; }
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
- inline auto & getConnectivity(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) {
+ inline auto & getConnectivity(ElementType type,
+ GhostType ghost_type = _not_ghost) {
return this->_mesh.getConnectivityPointer(type, ghost_type);
}
/// get the ghost element counter
- inline auto & getGhostsCounters(const ElementType & type,
- const GhostType & ghost_type = _ghost) {
+ inline auto & getGhostsCounters(ElementType type,
+ GhostType ghost_type = _ghost) {
return this->_mesh.getGhostsCounters(type, ghost_type);
}
/// get a pointer to the element_to_subelement Array for the given type and
/// create it if necessary
inline auto &
- getElementToSubelement(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) {
+ getElementToSubelement(ElementType type,
+ GhostType ghost_type = _not_ghost) {
return this->_mesh.getElementToSubelementPointer(type, ghost_type);
}
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
inline auto &
- getSubelementToElement(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) {
+ getSubelementToElement(ElementType type,
+ GhostType ghost_type = _not_ghost) {
return this->_mesh.getSubelementToElementPointer(type, ghost_type);
}
template <typename T>
inline auto &
- getData(const std::string & data_name, const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost, UInt nb_component = 1,
+ getData(const std::string & data_name, ElementType el_type,
+ GhostType ghost_type = _not_ghost, UInt nb_component = 1,
bool size_to_nb_element = true, bool resize_with_parent = false) {
return this->_mesh.getDataPointer<T>(data_name, el_type, ghost_type,
nb_component, size_to_nb_element,
resize_with_parent);
}
/// get the node synchonizer
auto & getNodeSynchronizer() { return *this->_mesh.node_synchronizer; }
/// get the element synchonizer
auto & getElementSynchronizer() { return *this->_mesh.element_synchronizer; }
decltype(auto) updateGlobalData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event) {
return this->_mesh.updateGlobalData(nodes_event, elements_event);
}
void registerGlobalDataUpdater(
std::unique_ptr<MeshGlobalDataUpdater> && global_data_updater) {
this->_mesh.registerGlobalDataUpdater(
std::forward<std::unique_ptr<MeshGlobalDataUpdater>>(
global_data_updater));
}
/* ------------------------------------------------------------------------ */
void makeReady() { this->_mesh.makeReady(); }
/* ------------------------------------------------------------------------ */
void addPeriodicSlave(UInt slave, UInt master) {
this->_mesh.addPeriodicSlave(slave, master);
}
void markMeshPeriodic() {
for (UInt s : arange(this->_mesh.spatial_dimension)) {
this->_mesh.is_periodic |= 1 << s;
}
}
void wipePeriodicInfo() { this->_mesh.wipePeriodicInfo(); }
private:
Mesh & _mesh;
};
} // namespace akantu
-#endif /* __AKANTU_MESH_ACCESSOR_HH__ */
+#endif /* AKANTU_MESH_ACCESSOR_HH_ */
diff --git a/src/mesh/mesh_data.hh b/src/mesh/mesh_data.hh
index 8efa83cda..2815aa9eb 100644
--- a/src/mesh/mesh_data.hh
+++ b/src/mesh/mesh_data.hh
@@ -1,192 +1,191 @@
/**
* @file mesh_data.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Mon Dec 18 2017
*
* @brief Stores generic data loaded from the mesh file
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_DATA_HH__
-#define __AKANTU_MESH_DATA_HH__
+#ifndef AKANTU_MESH_DATA_HH_
+#define AKANTU_MESH_DATA_HH_
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "element_type_map.hh"
#include <map>
#include <string>
/* -------------------------------------------------------------------------- */
namespace akantu {
#define AKANTU_MESH_DATA_TYPES \
((_int, Int))((_uint, UInt))((_real, Real))((_bool, bool))( \
(_element, Element))((_std_string, std::string))( \
(_std_vector_element, std::vector<Element>))
#define AKANTU_MESH_DATA_TUPLE_FIRST_ELEM(s, data, elem) \
BOOST_PP_TUPLE_ELEM(2, 0, elem)
enum class MeshDataTypeCode : int {
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_MESH_DATA_TUPLE_FIRST_ELEM, ,
AKANTU_MESH_DATA_TYPES)),
_unknown
};
enum class MeshDataType {
_nodal,
_elemental,
};
class MeshData {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
using TypeCode = MeshDataTypeCode;
using ElementalDataMap =
std::map<std::string, std::unique_ptr<ElementTypeMapBase>>;
using NodalDataMap = std::map<std::string, std::unique_ptr<ArrayBase>>;
using TypeCodeMap = std::map<std::string, TypeCode>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshData(const ID & id = "mesh_data", const ID & parent_id = "",
- const MemoryID & memory_id = 0);
+ const MemoryID & mem_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods and accessors */
/* ------------------------------------------------------------------------ */
public:
/// tells if the given array exists
template <typename T>
- bool hasData(const ID & data_name, const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ bool hasData(const ID & data_name, ElementType elem_type,
+ GhostType ghost_type = _not_ghost) const;
/// tells if the given data exists
bool hasData(const ID & data_name,
MeshDataType type = MeshDataType::_elemental) const;
bool hasData(MeshDataType type = MeshDataType::_elemental) const;
/// get the names of the data stored in elemental_data
- inline auto getTagNames(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ inline auto getTagNames(ElementType type,
+ GhostType ghost_type = _not_ghost) const;
/// get the names of the data stored in elemental_data
inline auto getTagNames() const;
/// get the type of the data stored in elemental_data
template <typename T> TypeCode getTypeCode() const;
inline TypeCode
getTypeCode(const ID & name,
MeshDataType type = MeshDataType::_elemental) const;
/// Get an existing elemental data array
template <typename T>
const Array<T> &
- getElementalDataArray(const ID & data_name, const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ getElementalDataArray(const ID & data_name, ElementType elem_type,
+ GhostType ghost_type = _not_ghost) const;
template <typename T>
Array<T> & getElementalDataArray(const ID & data_name,
- const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost);
+ ElementType elem_type,
+ GhostType ghost_type = _not_ghost);
/// Get an elemental data array, if it does not exist: allocate it
template <typename T>
- Array<T> &
- getElementalDataArrayAlloc(const ID & data_name, const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost,
- UInt nb_component = 1);
+ Array<T> & getElementalDataArrayAlloc(
+ const ID & data_name, ElementType elem_type,
+ GhostType ghost_type = _not_ghost, UInt nb_component = 1);
template <typename T>
inline UInt getNbComponentTemplated(const ID & name,
- const ElementType & el_type,
- const GhostType & ghost_type) const;
- inline UInt getNbComponent(const ID & name, const ElementType & el_type,
- const GhostType & ghost_type = _not_ghost) const;
+ ElementType el_type,
+ GhostType ghost_type) const;
+ inline UInt getNbComponent(const ID & name, ElementType el_type,
+ GhostType ghost_type = _not_ghost) const;
inline UInt getNbComponent(const ID & name) const;
/// Get an existing elemental data
template <typename T>
const ElementTypeMapArray<T> & getElementalData(const ID & name) const;
template <typename T>
ElementTypeMapArray<T> & getElementalData(const ID & name);
template <typename T>
Array<T> & getNodalData(const ID & name, UInt nb_components = 1);
template <typename T> const Array<T> & getNodalData(const ID & name) const;
private:
/// Register new elemental data (and alloc data) with check if the name is
/// new
template <typename T>
ElementTypeMapArray<T> & registerElementalData(const ID & name);
inline void registerElementalData(const ID & name, TypeCode type);
/// Register new nodal data (and alloc data) with check if the name is
/// new
template <typename T>
Array<T> & registerNodalData(const ID & name, UInt nb_components = 1);
inline void registerNodalData(const ID & name, UInt nb_components,
TypeCode type);
/// Register new elemental data (add alloc data)
template <typename T>
ElementTypeMapArray<T> & allocElementalData(const ID & name);
/// Register new nodal data (add alloc data)
template <typename T>
Array<T> & allocNodalData(const ID & name, UInt nb_components);
friend class SlaveNodeInfoPerProc;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
ID _id;
UInt _memory_id{0};
/// Map when elemental data is stored as ElementTypeMap
ElementalDataMap elemental_data;
/// Map when elemental data is stored as ElementTypeMap
NodalDataMap nodal_data;
/// Map when elementalType of the data stored in elemental_data
std::map<MeshDataType, TypeCodeMap> typecode_map{
{MeshDataType::_elemental, {}}, {MeshDataType::_nodal, {}}};
};
} // namespace akantu
#include "mesh_data_tmpl.hh"
#undef AKANTU_MESH_DATA_TUPLE_FIRST_ELEM
-#endif /* __AKANTU_MESH_DATA_HH__ */
+#endif /* AKANTU_MESH_DATA_HH_ */
diff --git a/src/mesh/mesh_data_tmpl.hh b/src/mesh/mesh_data_tmpl.hh
index 4639eca5b..b7a054373 100644
--- a/src/mesh/mesh_data_tmpl.hh
+++ b/src/mesh/mesh_data_tmpl.hh
@@ -1,409 +1,412 @@
/**
* @file mesh_data_tmpl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Tue Feb 20 2018
*
* @brief Stores generic data loaded from the mesh file
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_data.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_DATA_TMPL_HH__
-#define __AKANTU_MESH_DATA_TMPL_HH__
+#ifndef AKANTU_MESH_DATA_TMPL_HH_
+#define AKANTU_MESH_DATA_TMPL_HH_
namespace akantu {
#define AKANTU_MESH_DATA_OSTREAM(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
stream << BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 1, elem)); \
break; \
}
inline std::ostream & operator<<(std::ostream & stream,
const MeshDataTypeCode & type_code) {
switch (type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_OSTREAM, name,
AKANTU_MESH_DATA_TYPES)
default:
stream << "(unknown type)";
}
return stream;
}
#undef AKANTU_MESH_DATA_OSTREAM
#define MESH_DATA_GET_TYPE(r, data, type) \
template <> \
inline MeshDataTypeCode \
MeshData::getTypeCode<BOOST_PP_TUPLE_ELEM(2, 1, type)>() const { \
return MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, type); \
}
/* -------------------------------------------------------------------------- */
// get the type of the data stored in elemental_data
template <typename T> inline MeshDataTypeCode MeshData::getTypeCode() const {
AKANTU_ERROR("Type " << debug::demangle(typeid(T).name())
<< " not implemented by MeshData.");
}
/* -------------------------------------------------------------------------- */
BOOST_PP_SEQ_FOR_EACH(MESH_DATA_GET_TYPE, void, AKANTU_MESH_DATA_TYPES)
#undef MESH_DATA_GET_TYPE
inline MeshDataTypeCode MeshData::getTypeCode(const ID & name,
MeshDataType type) const {
auto it = typecode_map.at(type).find(name);
- if (it == typecode_map.at(type).end())
+ if (it == typecode_map.at(type).end()) {
AKANTU_EXCEPTION("No dataset named " << name << " found.");
+ }
return it->second;
}
/* -------------------------------------------------------------------------- */
// Register new elemental data templated (and alloc data) with check if the
// name is new
template <typename T>
ElementTypeMapArray<T> & MeshData::registerElementalData(const ID & name) {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
return allocElementalData<T>(name);
- } else {
- AKANTU_DEBUG_INFO("Data named " << name << " already registered.");
- return getElementalData<T>(name);
}
+ AKANTU_DEBUG_INFO("Data named " << name << " already registered.");
+ return getElementalData<T>(name);
}
/* -------------------------------------------------------------------------- */
// Register new elemental data of a given MeshDataTypeCode with check if the
// name is new
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
registerElementalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(name); \
break; \
}
inline void MeshData::registerElementalData(const ID & name,
MeshDataTypeCode type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, name,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Type " << type << "not implemented by MeshData.");
}
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
/// Register new elemental data (and alloc data)
template <typename T>
ElementTypeMapArray<T> & MeshData::allocElementalData(const ID & name) {
auto dataset =
std::make_unique<ElementTypeMapArray<T>>(name, _id, _memory_id);
auto * dataset_typed = dataset.get();
elemental_data[name] = std::move(dataset);
typecode_map[MeshDataType::_elemental][name] = getTypeCode<T>();
return *dataset_typed;
}
/* -------------------------------------------------------------------------- */
// Register new nodal data templated (and alloc data) with check if the
// name is new
template <typename T>
Array<T> & MeshData::registerNodalData(const ID & name, UInt nb_components) {
auto it = nodal_data.find(name);
if (it == nodal_data.end()) {
return allocNodalData<T>(name, nb_components);
- } else {
- AKANTU_DEBUG_INFO("Data named " << name << " already registered.");
- return getNodalData<T>(name);
}
+ AKANTU_DEBUG_INFO("Data named " << name << " already registered.");
+ return getNodalData<T>(name);
}
/* -------------------------------------------------------------------------- */
// Register new elemental data of a given MeshDataTypeCode with check if the
// name is new
#define AKANTU_MESH_NODAL_DATA_CASE_MACRO(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
registerNodalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(name, nb_components); \
break; \
}
inline void MeshData::registerNodalData(const ID & name, UInt nb_components,
MeshDataTypeCode type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_NODAL_DATA_CASE_MACRO, name,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Type " << type << "not implemented by MeshData.");
}
}
#undef AKANTU_MESH_NODAL_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
/// Register new elemental data (and alloc data)
template <typename T>
Array<T> & MeshData::allocNodalData(const ID & name, UInt nb_components) {
auto dataset =
std::make_unique<Array<T>>(0, nb_components, T(), _id + ":" + name);
auto * dataset_typed = dataset.get();
nodal_data[name] = std::move(dataset);
typecode_map[MeshDataType::_nodal][name] = getTypeCode<T>();
return *dataset_typed;
}
/* -------------------------------------------------------------------------- */
template <typename T>
const Array<T> & MeshData::getNodalData(const ID & name) const {
auto it = nodal_data.find(name);
- if (it == nodal_data.end())
+ if (it == nodal_data.end()) {
AKANTU_EXCEPTION("No nodal dataset named " << name << " found.");
+ }
return aka::as_type<Array<T>>(*(it->second.get()));
}
/* -------------------------------------------------------------------------- */
// Get an existing elemental data
template <typename T>
Array<T> & MeshData::getNodalData(const ID & name, UInt nb_components) {
auto it = nodal_data.find(name);
- if (it == nodal_data.end())
+ if (it == nodal_data.end()) {
return allocNodalData<T>(name, nb_components);
+ }
return aka::as_type<Array<T>>(*(it->second.get()));
}
/* -------------------------------------------------------------------------- */
template <typename T>
const ElementTypeMapArray<T> &
MeshData::getElementalData(const ID & name) const {
auto it = elemental_data.find(name);
- if (it == elemental_data.end())
+ if (it == elemental_data.end()) {
AKANTU_EXCEPTION("No dataset named " << name << " found.");
+ }
return aka::as_type<ElementTypeMapArray<T>>(*(it->second.get()));
}
/* -------------------------------------------------------------------------- */
// Get an existing elemental data
template <typename T>
ElementTypeMapArray<T> & MeshData::getElementalData(const ID & name) {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
return allocElementalData<T>(name);
}
return aka::as_type<ElementTypeMapArray<T>>(*(it->second.get()));
}
/* -------------------------------------------------------------------------- */
template <typename T>
-bool MeshData::hasData(const ID & name, const ElementType & elem_type,
- const GhostType & ghost_type) const {
+bool MeshData::hasData(const ID & name, ElementType elem_type,
+ GhostType ghost_type) const {
auto it = elemental_data.find(name);
- if (it == elemental_data.end())
+ if (it == elemental_data.end()) {
return false;
+ }
auto & elem_map = aka::as_type<ElementTypeMapArray<T>>(*(it->second));
return elem_map.exists(elem_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool MeshData::hasData(const ID & name, MeshDataType type) const {
if (type == MeshDataType::_elemental) {
auto it = elemental_data.find(name);
return (it != elemental_data.end());
}
if (type == MeshDataType::_nodal) {
auto it = nodal_data.find(name);
return (it != nodal_data.end());
}
return false;
}
/* -------------------------------------------------------------------------- */
inline bool MeshData::hasData(MeshDataType type) const {
switch (type) {
case MeshDataType::_elemental:
return (not elemental_data.empty());
case MeshDataType::_nodal:
return (not nodal_data.empty());
}
return false;
}
/* -------------------------------------------------------------------------- */
template <typename T>
const Array<T> &
-MeshData::getElementalDataArray(const ID & name, const ElementType & elem_type,
- const GhostType & ghost_type) const {
+MeshData::getElementalDataArray(const ID & name, ElementType elem_type,
+ GhostType ghost_type) const {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
AKANTU_EXCEPTION("Data named " << name
<< " not registered for type: " << elem_type
<< " - ghost_type:" << ghost_type << "!");
}
return aka::as_type<ElementTypeMapArray<T>>(*(it->second))(elem_type,
ghost_type);
}
template <typename T>
Array<T> & MeshData::getElementalDataArray(const ID & name,
- const ElementType & elem_type,
- const GhostType & ghost_type) {
+ ElementType elem_type,
+ GhostType ghost_type) {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
AKANTU_EXCEPTION("Data named " << name
<< " not registered for type: " << elem_type
<< " - ghost_type:" << ghost_type << "!");
}
return aka::as_type<ElementTypeMapArray<T>>(*(it->second.get()))(elem_type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
// Get an elemental data array, if it does not exist: allocate it
template <typename T>
Array<T> & MeshData::getElementalDataArrayAlloc(const ID & name,
- const ElementType & elem_type,
- const GhostType & ghost_type,
+ ElementType elem_type,
+ GhostType ghost_type,
UInt nb_component) {
auto it = elemental_data.find(name);
ElementTypeMapArray<T> * dataset;
if (it == elemental_data.end()) {
dataset = &allocElementalData<T>(name);
} else {
dataset = dynamic_cast<ElementTypeMapArray<T> *>(it->second.get());
}
AKANTU_DEBUG_ASSERT(
getTypeCode<T>() ==
typecode_map.at(MeshDataType::_elemental).find(name)->second,
"Function getElementalDataArrayAlloc called with the wrong type!");
if (!(dataset->exists(elem_type, ghost_type))) {
dataset->alloc(0, nb_component, elem_type, ghost_type);
}
return (*dataset)(elem_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
nb_comp = getNbComponentTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>( \
name, el_type, ghost_type); \
break; \
}
inline UInt MeshData::getNbComponent(const ID & name,
- const ElementType & el_type,
- const GhostType & ghost_type) const {
+ ElementType el_type,
+ GhostType ghost_type) const {
auto it = typecode_map.at(MeshDataType::_elemental).find(name);
UInt nb_comp(0);
if (it == typecode_map.at(MeshDataType::_elemental).end()) {
AKANTU_EXCEPTION("Could not determine the type held in dataset "
<< name << " for type: " << el_type
<< " - ghost_type:" << ghost_type << ".");
}
MeshDataTypeCode type = it->second;
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, name,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR(
"Could not call the correct instance of getNbComponentTemplated.");
break;
}
return nb_comp;
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
template <typename T>
inline UInt
-MeshData::getNbComponentTemplated(const ID & name, const ElementType & el_type,
- const GhostType & ghost_type) const {
+MeshData::getNbComponentTemplated(const ID & name, ElementType el_type,
+ GhostType ghost_type) const {
return getElementalDataArray<T>(name, el_type, ghost_type).getNbComponent();
}
/* -------------------------------------------------------------------------- */
inline UInt MeshData::getNbComponent(const ID & name) const {
auto it = nodal_data.find(name);
if (it == nodal_data.end()) {
AKANTU_EXCEPTION("No nodal dataset registered with the name" << name
<< ".");
}
return it->second->getNbComponent();
}
/* -------------------------------------------------------------------------- */
// get the names of the data stored in elemental_data
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
ElementTypeMapArray<BOOST_PP_TUPLE_ELEM(2, 1, elem)> * dataset; \
dataset = \
dynamic_cast<ElementTypeMapArray<BOOST_PP_TUPLE_ELEM(2, 1, elem)> *>( \
it->second.get()); \
exists = dataset->exists(el_type, ghost_type); \
break; \
}
-inline auto MeshData::getTagNames(const ElementType & el_type,
- const GhostType & ghost_type) const {
+inline auto MeshData::getTagNames(ElementType el_type,
+ GhostType ghost_type) const {
std::vector<std::string> tags;
bool exists(false);
auto it = elemental_data.begin();
auto it_end = elemental_data.end();
for (; it != it_end; ++it) {
MeshDataTypeCode type = getTypeCode(it->first);
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not determine the proper type to (dynamic-)cast.");
break;
}
if (exists) {
tags.push_back(it->first);
}
}
return tags;
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
inline auto MeshData::getTagNames() const {
std::vector<std::string> tags;
for (auto && data : nodal_data) {
tags.push_back(std::get<0>(data));
}
return tags;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_MESH_DATA_TMPL_HH__ */
+#endif /* AKANTU_MESH_DATA_TMPL_HH_ */
diff --git a/src/mesh/mesh_events.hh b/src/mesh/mesh_events.hh
index 980ceb7b9..97fbbe209 100644
--- a/src/mesh/mesh_events.hh
+++ b/src/mesh/mesh_events.hh
@@ -1,202 +1,202 @@
/**
* @file mesh_events.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 20 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Classes corresponding to mesh events type
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <utility>
#include "aka_array.hh"
#include "element.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_EVENTS_HH__
-#define __AKANTU_MESH_EVENTS_HH__
+#ifndef AKANTU_MESH_EVENTS_HH_
+#define AKANTU_MESH_EVENTS_HH_
namespace akantu {
/// akantu::MeshEvent is the base event for meshes
template <class Entity> class MeshEvent {
public:
MeshEvent(const std::string & origin = "") : origin_(origin) {}
virtual ~MeshEvent() = default;
/// Get the list of entity modified by the event nodes or elements
const Array<Entity> & getList() const { return list; }
/// Get the list of entity modified by the event nodes or elements
Array<Entity> & getList() { return list; }
std::string origin() const { return origin_; }
protected:
Array<Entity> list;
private:
std::string origin_;
};
class Mesh;
/// akantu::MeshEvent related to new nodes in the mesh
class NewNodesEvent : public MeshEvent<UInt> {
public:
NewNodesEvent(const std::string & origin = "") : MeshEvent(origin) {}
~NewNodesEvent() override = default;
};
/// akantu::MeshEvent related to nodes removed from the mesh
class RemovedNodesEvent : public MeshEvent<UInt> {
public:
inline RemovedNodesEvent(const Mesh & mesh, const std::string & origin = "");
~RemovedNodesEvent() override = default;
/// Get the new numbering following suppression of nodes from nodes arrays
AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering, Array<UInt> &);
/// Get the new numbering following suppression of nodes from nodes arrays
AKANTU_GET_MACRO(NewNumbering, new_numbering, const Array<UInt> &);
private:
Array<UInt> new_numbering;
};
/// akantu::MeshEvent related to new elements in the mesh
class NewElementsEvent : public MeshEvent<Element> {
public:
NewElementsEvent(const std::string & origin = "") : MeshEvent<Element>(origin) {}
~NewElementsEvent() override = default;
};
/// akantu::MeshEvent related to elements removed from the mesh
class RemovedElementsEvent : public MeshEvent<Element> {
public:
inline RemovedElementsEvent(const Mesh & mesh,
const ID & new_numbering_id = "new_numbering",
const std::string & origin = "");
~RemovedElementsEvent() override = default;
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO(NewNumbering, new_numbering,
const ElementTypeMapArray<UInt> &);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering,
ElementTypeMapArray<UInt> &);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(NewNumbering, new_numbering, UInt);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(NewNumbering, new_numbering, UInt);
protected:
ElementTypeMapArray<UInt> new_numbering;
};
/// akantu::MeshEvent for element that changed in some sort, can be seen as a
/// combination of removed and added elements
class ChangedElementsEvent : public RemovedElementsEvent {
public:
inline ChangedElementsEvent(
- const Mesh & mesh, ID new_numbering_id = "changed_event:new_numbering",
+ const Mesh & mesh, const ID & new_numbering_id = "changed_event:new_numbering",
const std::string & origin = "")
- : RemovedElementsEvent(mesh, std::move(new_numbering_id), origin) {}
+ : RemovedElementsEvent(mesh, new_numbering_id, origin) {}
~ChangedElementsEvent() override = default;
AKANTU_GET_MACRO(ListOld, list, const Array<Element> &);
AKANTU_GET_MACRO_NOT_CONST(ListOld, list, Array<Element> &);
AKANTU_GET_MACRO(ListNew, new_list, const Array<Element> &);
AKANTU_GET_MACRO_NOT_CONST(ListNew, new_list, Array<Element> &);
protected:
Array<Element> new_list;
};
/* -------------------------------------------------------------------------- */
class MeshEventHandler {
public:
virtual ~MeshEventHandler() = default;
/* ------------------------------------------------------------------------ */
/* Internal code */
/* ------------------------------------------------------------------------ */
private:
/// send a akantu::NewNodesEvent
inline void sendEvent(const NewNodesEvent & event) {
onNodesAdded(event.getList(), event);
}
/// send a akantu::RemovedNodesEvent
inline void sendEvent(const RemovedNodesEvent & event) {
onNodesRemoved(event.getList(), event.getNewNumbering(), event);
}
/// send a akantu::NewElementsEvent
inline void sendEvent(const NewElementsEvent & event) {
onElementsAdded(event.getList(), event);
}
/// send a akantu::RemovedElementsEvent
inline void sendEvent(const RemovedElementsEvent & event) {
onElementsRemoved(event.getList(), event.getNewNumbering(), event);
}
/// send a akantu::ChangedElementsEvent
inline void sendEvent(const ChangedElementsEvent & event) {
onElementsChanged(event.getListOld(), event.getListNew(),
event.getNewNumbering(), event);
}
template <class EventHandler> friend class EventHandlerManager;
/* ------------------------------------------------------------------------ */
/* Interface */
/* ------------------------------------------------------------------------ */
public:
/// function to implement to react on akantu::NewNodesEvent
virtual void onNodesAdded(const Array<UInt> & /*nodes_list*/,
const NewNodesEvent & /*event*/) {}
/// function to implement to react on akantu::RemovedNodesEvent
virtual void onNodesRemoved(const Array<UInt> & /*nodes_list*/,
const Array<UInt> & /*new_numbering*/,
const RemovedNodesEvent & /*event*/) {}
/// function to implement to react on akantu::NewElementsEvent
virtual void onElementsAdded(const Array<Element> & /*elements_list*/,
const NewElementsEvent & /*event*/) {}
/// function to implement to react on akantu::RemovedElementsEvent
virtual void
onElementsRemoved(const Array<Element> & /*elements_list*/,
const ElementTypeMapArray<UInt> & /*new_numbering*/,
const RemovedElementsEvent & /*event*/) {}
/// function to implement to react on akantu::ChangedElementsEvent
virtual void
onElementsChanged(const Array<Element> & /*old_elements_list*/,
const Array<Element> & /*new_elements_list*/,
const ElementTypeMapArray<UInt> & /*new_numbering*/,
const ChangedElementsEvent & /*event*/) {}
};
} // namespace akantu
-#endif /* __AKANTU_MESH_EVENTS_HH__ */
+#endif /* AKANTU_MESH_EVENTS_HH_ */
diff --git a/src/mesh/mesh_filter.hh b/src/mesh/mesh_filter.hh
index bcc77139c..387bfb57a 100644
--- a/src/mesh/mesh_filter.hh
+++ b/src/mesh/mesh_filter.hh
@@ -1,71 +1,71 @@
/**
* @file mesh_filter.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief the class representing the meshes
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_FILTER_HH__
-#define __AKANTU_MESH_FILTER_HH__
+#ifndef AKANTU_MESH_FILTER_HH_
+#define AKANTU_MESH_FILTER_HH_
/* -------------------------------------------------------------------------- */
#include "element.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Filter Functors */
/* -------------------------------------------------------------------------- */
/// struct for the possible filter functors
struct FilterFunctor {
enum Type { _node_filter_functor, _element_filter_functor };
};
/// class (functor) for the node filter
class NodeFilterFunctor : public FilterFunctor {
public:
bool operator()(__attribute__((unused)) UInt node) { AKANTU_TO_IMPLEMENT(); }
public:
static const Type type = _node_filter_functor;
};
/// class (functor) for the element filter
class ElementFilterFunctor : public FilterFunctor {
public:
bool operator()(__attribute__((unused)) const Element & element) {
AKANTU_TO_IMPLEMENT();
}
public:
static const Type type = _element_filter_functor;
};
} // namespace akantu
-#endif /* __AKANTU_MESH_FILTER_HH__ */
+#endif /* AKANTU_MESH_FILTER_HH_ */
diff --git a/src/mesh/mesh_global_data_updater.hh b/src/mesh/mesh_global_data_updater.hh
index c79c9fd5e..b4a01f896 100644
--- a/src/mesh/mesh_global_data_updater.hh
+++ b/src/mesh/mesh_global_data_updater.hh
@@ -1,50 +1,50 @@
/**
* @file mesh_global_data_updater.hh
*
* @author Nicolas Richart
*
* @date creation Sat Mar 03 2018
*
* @brief interface for the global data updater
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_GLOBAL_DATA_UPDATER_HH__
-#define __AKANTU_MESH_GLOBAL_DATA_UPDATER_HH__
+#ifndef AKANTU_MESH_GLOBAL_DATA_UPDATER_HH_
+#define AKANTU_MESH_GLOBAL_DATA_UPDATER_HH_
namespace akantu {
class NewNodesEvent;
class NewElementsEvent;
class MeshGlobalDataUpdater {
public:
virtual ~MeshGlobalDataUpdater() = default;
virtual std::tuple<UInt, UInt>
updateData(NewNodesEvent & /*nodes_event*/,
NewElementsEvent & /*elements_event*/) {
return std::make_tuple(0, 0);
}
};
} // namespace akantu
-#endif /* __AKANTU_MESH_GLOBAL_DATA_UPDATER_HH__ */
+#endif /* AKANTU_MESH_GLOBAL_DATA_UPDATER_HH_ */
diff --git a/src/mesh/mesh_inline_impl.hh b/src/mesh/mesh_inline_impl.hh
index dedf9803c..8c46563c1 100644
--- a/src/mesh/mesh_inline_impl.hh
+++ b/src/mesh/mesh_inline_impl.hh
@@ -1,766 +1,778 @@
/**
* @file mesh_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jul 15 2010
* @date last modification: Mon Dec 18 2017
*
* @brief Implementation of the inline functions of the mesh class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "element_class.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_INLINE_IMPL_HH__
-#define __AKANTU_MESH_INLINE_IMPL_HH__
+#ifndef AKANTU_MESH_INLINE_IMPL_HH_
+#define AKANTU_MESH_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
inline ElementKind Element::kind() const { return Mesh::getKind(type); }
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename... pack>
Mesh::ElementTypesIteratorHelper Mesh::elementTypes(pack &&... _pack) const {
return connectivities.elementTypes(_pack...);
}
/* -------------------------------------------------------------------------- */
inline RemovedNodesEvent::RemovedNodesEvent(const Mesh & mesh,
const std::string & origin)
: MeshEvent<UInt>(origin), new_numbering(mesh.getNbNodes(), 1, "new_numbering") {}
/* -------------------------------------------------------------------------- */
inline RemovedElementsEvent::RemovedElementsEvent(const Mesh & mesh,
const ID & new_numbering_id,
const std::string & origin)
: MeshEvent<Element>(origin),
new_numbering(new_numbering_id, mesh.getID(), mesh.getMemoryID()) {}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<NewElementsEvent>(NewElementsEvent & event) {
this->nodes_to_elements.resize(nodes->size());
for (const auto & elem : event.getList()) {
const Array<UInt> & conn = connectivities(elem.type, elem.ghost_type);
- UInt nb_nodes_per_elem = this->getNbNodesPerElement(elem.type);
+ UInt nb_nodes_per_elem = Mesh::getNbNodesPerElement(elem.type);
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = conn(elem.element, n);
- if (not nodes_to_elements[node])
+ if (not nodes_to_elements[node]) {
nodes_to_elements[node] = std::make_unique<std::set<Element>>();
+ }
nodes_to_elements[node]->insert(elem);
}
}
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <> inline void Mesh::sendEvent<NewNodesEvent>(NewNodesEvent & event) {
this->computeBoundingBox();
this->nodes_flags->resize(this->nodes->size(), NodeFlag::_normal);
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
Mesh::sendEvent<RemovedElementsEvent>(RemovedElementsEvent & event) {
this->connectivities.onElementsRemoved(event.getNewNumbering());
this->fillNodesToElements();
this->computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<RemovedNodesEvent>(RemovedNodesEvent & event) {
const auto & new_numbering = event.getNewNumbering();
this->removeNodesFromArray(*nodes, new_numbering);
- if (nodes_global_ids and not is_mesh_facets)
+ if (nodes_global_ids and not is_mesh_facets) {
this->removeNodesFromArray(*nodes_global_ids, new_numbering);
- if (not is_mesh_facets)
+ }
+ if (not is_mesh_facets) {
this->removeNodesFromArray(*nodes_flags, new_numbering);
+ }
if (not nodes_to_elements.empty()) {
std::vector<std::unique_ptr<std::set<Element>>> tmp(
nodes_to_elements.size());
auto it = nodes_to_elements.begin();
UInt new_nb_nodes = 0;
for (auto new_i : new_numbering) {
if (new_i != UInt(-1)) {
tmp[new_i] = std::move(*it);
++new_nb_nodes;
}
++it;
}
tmp.resize(new_nb_nodes);
std::move(tmp.begin(), tmp.end(), nodes_to_elements.begin());
}
computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering) {
Array<T> tmp(vect.size(), vect.getNbComponent());
UInt nb_component = vect.getNbComponent();
UInt new_nb_nodes = 0;
for (UInt i = 0; i < new_numbering.size(); ++i) {
UInt new_i = new_numbering(i);
if (new_i != UInt(-1)) {
T * to_copy = vect.storage() + i * nb_component;
std::uninitialized_copy(to_copy, to_copy + nb_component,
tmp.storage() + new_i * nb_component);
++new_nb_nodes;
}
}
tmp.resize(new_nb_nodes);
vect.copy(tmp);
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> & Mesh::getNodesGlobalIdsPointer() {
AKANTU_DEBUG_IN();
if (not nodes_global_ids) {
nodes_global_ids = std::make_shared<Array<UInt>>(
nodes->size(), 1, getID() + ":nodes_global_ids");
for (auto && global_ids : enumerate(*nodes_global_ids)) {
std::get<1>(global_ids) = std::get<0>(global_ids);
}
}
AKANTU_DEBUG_OUT();
return *nodes_global_ids;
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> &
-Mesh::getConnectivityPointer(const ElementType & type,
- const GhostType & ghost_type) {
- if (connectivities.exists(type, ghost_type))
+Mesh::getConnectivityPointer(ElementType type,
+ GhostType ghost_type) {
+ if (connectivities.exists(type, ghost_type)) {
return connectivities(type, ghost_type);
+ }
if (ghost_type != _not_ghost) {
ghosts_counters.alloc(0, 1, type, ghost_type, 1);
}
AKANTU_DEBUG_INFO("The connectivity vector for the type " << type
<< " created");
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
return connectivities.alloc(0, nb_nodes_per_element, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<std::vector<Element>> &
-Mesh::getElementToSubelementPointer(const ElementType & type,
- const GhostType & ghost_type) {
+Mesh::getElementToSubelementPointer(ElementType type,
+ GhostType ghost_type) {
return getDataPointer<std::vector<Element>>("element_to_subelement", type,
ghost_type, 1, true);
}
/* -------------------------------------------------------------------------- */
inline Array<Element> &
-Mesh::getSubelementToElementPointer(const ElementType & type,
- const GhostType & ghost_type) {
+Mesh::getSubelementToElementPointer(ElementType type,
+ GhostType ghost_type) {
auto & array = getDataPointer<Element>(
"subelement_to_element", type, ghost_type, getNbFacetsPerElement(type),
true, is_mesh_facets, ElementNull);
return array;
}
/* -------------------------------------------------------------------------- */
inline const auto & Mesh::getElementToSubelement() const {
return getData<std::vector<Element>>("element_to_subelement");
}
/* -------------------------------------------------------------------------- */
inline const auto &
-Mesh::getElementToSubelement(const ElementType & type,
- const GhostType & ghost_type) const {
+Mesh::getElementToSubelement(ElementType type,
+ GhostType ghost_type) const {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
-inline auto & Mesh::getElementToSubelement(const ElementType & type,
- const GhostType & ghost_type) {
+inline auto & Mesh::getElementToSubelement(ElementType type,
+ GhostType ghost_type) {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const auto &
Mesh::getElementToSubelement(const Element & element) const {
return getData<std::vector<Element>>("element_to_subelement")(element);
}
/* -------------------------------------------------------------------------- */
inline auto & Mesh::getElementToSubelement(const Element & element) {
return getData<std::vector<Element>>("element_to_subelement")(element);
}
/* -------------------------------------------------------------------------- */
inline const auto & Mesh::getSubelementToElement() const {
return getData<Element>("subelement_to_element");
}
/* -------------------------------------------------------------------------- */
inline const auto &
-Mesh::getSubelementToElement(const ElementType & type,
- const GhostType & ghost_type) const {
+Mesh::getSubelementToElement(ElementType type,
+ GhostType ghost_type) const {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
-inline auto & Mesh::getSubelementToElement(const ElementType & type,
- const GhostType & ghost_type) {
+inline auto & Mesh::getSubelementToElement(ElementType type,
+ GhostType ghost_type) {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<Element>
Mesh::getSubelementToElement(const Element & element) const {
const auto & sub_to_element =
this->getSubelementToElement(element.type, element.ghost_type);
auto it = sub_to_element.begin(sub_to_element.getNbComponent());
return it[element.element];
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<Element>
Mesh::getSubelementToElement(const Element & element) {
auto & sub_to_element =
this->getSubelementToElement(element.type, element.ghost_type);
auto it = sub_to_element.begin(sub_to_element.getNbComponent());
return it[element.element];
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> &
-Mesh::getDataPointer(const ID & data_name, const ElementType & el_type,
- const GhostType & ghost_type, UInt nb_component,
+Mesh::getDataPointer(const ID & data_name, ElementType el_type,
+ GhostType ghost_type, UInt nb_component,
bool size_to_nb_element, bool resize_with_parent) {
Array<T> & tmp = this->getElementalDataArrayAlloc<T>(
data_name, el_type, ghost_type, nb_component);
if (size_to_nb_element) {
- if (resize_with_parent)
+ if (resize_with_parent) {
tmp.resize(mesh_parent->getNbElement(el_type, ghost_type));
- else
+ } else {
tmp.resize(this->getNbElement(el_type, ghost_type));
+ }
} else {
tmp.resize(0);
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> &
-Mesh::getDataPointer(const ID & data_name, const ElementType & el_type,
- const GhostType & ghost_type, UInt nb_component,
+Mesh::getDataPointer(const ID & data_name, ElementType el_type,
+ GhostType ghost_type, UInt nb_component,
bool size_to_nb_element, bool resize_with_parent,
const T & defaul_) {
Array<T> & tmp = this->getElementalDataArrayAlloc<T>(
data_name, el_type, ghost_type, nb_component);
if (size_to_nb_element) {
- if (resize_with_parent)
+ if (resize_with_parent) {
tmp.resize(mesh_parent->getNbElement(el_type, ghost_type), defaul_);
- else
+ } else {
tmp.resize(this->getNbElement(el_type, ghost_type), defaul_);
+ }
} else {
tmp.resize(0);
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const Array<T> & Mesh::getData(const ID & data_name,
- const ElementType & el_type,
- const GhostType & ghost_type) const {
+ ElementType el_type,
+ GhostType ghost_type) const {
return this->getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> & Mesh::getData(const ID & data_name,
- const ElementType & el_type,
- const GhostType & ghost_type) {
+ ElementType el_type,
+ GhostType ghost_type) {
return this->getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const ElementTypeMapArray<T> &
Mesh::getData(const ID & data_name) const {
return this->getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> & Mesh::getData(const ID & data_name) {
return this->getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
-inline UInt Mesh::getNbElement(const ElementType & type,
- const GhostType & ghost_type) const {
+inline UInt Mesh::getNbElement(ElementType type,
+ GhostType ghost_type) const {
try {
const Array<UInt> & conn = connectivities(type, ghost_type);
return conn.size();
} catch (...) {
return 0;
}
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const UInt spatial_dimension,
- const GhostType & ghost_type,
- const ElementKind & kind) const {
+ GhostType ghost_type,
+ ElementKind kind) const {
AKANTU_DEBUG_ASSERT(spatial_dimension <= 3 || spatial_dimension == UInt(-1),
"spatial_dimension is " << spatial_dimension
<< " and is greater than 3 !");
UInt nb_element = 0;
- for (auto type : elementTypes(spatial_dimension, ghost_type, kind))
+ for (auto type : elementTypes(spatial_dimension, ghost_type, kind)) {
nb_element += getNbElement(type, ghost_type);
+ }
return nb_element;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(const Element & element,
Vector<Real> & barycenter) const {
Vector<UInt> conn = getConnectivity(element);
Matrix<Real> local_coord(spatial_dimension, conn.size());
auto node_begin = make_view(*nodes, spatial_dimension).begin();
for (auto && node : enumerate(conn)) {
local_coord(std::get<0>(node)) =
Vector<Real>(node_begin[std::get<1>(node)]);
}
Math::barycenter(local_coord.storage(), conn.size(), spatial_dimension,
barycenter.storage());
}
/* -------------------------------------------------------------------------- */
-inline UInt Mesh::getNbNodesPerElement(const ElementType & type) {
+inline UInt Mesh::getNbNodesPerElement(ElementType type) {
UInt nb_nodes_per_element = 0;
#define GET_NB_NODES_PER_ELEMENT(type) \
nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_NODES_PER_ELEMENT);
#undef GET_NB_NODES_PER_ELEMENT
return nb_nodes_per_element;
}
/* -------------------------------------------------------------------------- */
-inline ElementType Mesh::getP1ElementType(const ElementType & type) {
+inline ElementType Mesh::getP1ElementType(ElementType type) {
ElementType p1_type = _not_defined;
#define GET_P1_TYPE(type) p1_type = ElementClass<type>::getP1ElementType()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_P1_TYPE);
#undef GET_P1_TYPE
return p1_type;
}
/* -------------------------------------------------------------------------- */
-inline ElementKind Mesh::getKind(const ElementType & type) {
+inline ElementKind Mesh::getKind(ElementType type) {
ElementKind kind = _ek_not_defined;
#define GET_KIND(type) kind = ElementClass<type>::getKind()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_KIND);
#undef GET_KIND
return kind;
}
/* -------------------------------------------------------------------------- */
-inline UInt Mesh::getSpatialDimension(const ElementType & type) {
+inline UInt Mesh::getSpatialDimension(ElementType type) {
UInt spatial_dimension = 0;
#define GET_SPATIAL_DIMENSION(type) \
spatial_dimension = ElementClass<type>::getSpatialDimension()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SPATIAL_DIMENSION);
#undef GET_SPATIAL_DIMENSION
return spatial_dimension;
}
/* -------------------------------------------------------------------------- */
-inline UInt Mesh::getNbFacetTypes(const ElementType & type,
+inline UInt Mesh::getNbFacetTypes(ElementType type,
__attribute__((unused)) UInt t) {
UInt nb = 0;
#define GET_NB_FACET_TYPE(type) nb = ElementClass<type>::getNbFacetTypes()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET_TYPE);
#undef GET_NB_FACET_TYPE
return nb;
}
/* -------------------------------------------------------------------------- */
-inline constexpr auto Mesh::getFacetType(const ElementType & type, UInt t) {
+inline constexpr auto Mesh::getFacetType(ElementType type, UInt t) {
#define GET_FACET_TYPE(type) return ElementClass<type>::getFacetType(t);
AKANTU_BOOST_ALL_ELEMENT_SWITCH_NO_DEFAULT(GET_FACET_TYPE);
#undef GET_FACET_TYPE
return _not_defined;
}
/* -------------------------------------------------------------------------- */
-inline constexpr auto Mesh::getAllFacetTypes(const ElementType & type) {
+inline constexpr auto Mesh::getAllFacetTypes(ElementType type) {
#define GET_FACET_TYPE(type) return ElementClass<type>::getFacetTypes();
AKANTU_BOOST_ALL_ELEMENT_SWITCH_NO_DEFAULT(GET_FACET_TYPE);
#undef GET_FACET_TYPE
return ElementClass<_not_defined>::getFacetTypes();
}
/* -------------------------------------------------------------------------- */
-inline UInt Mesh::getNbFacetsPerElement(const ElementType & type) {
+inline UInt Mesh::getNbFacetsPerElement(ElementType type) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) n_facet = ElementClass<type>::getNbFacetsPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
-inline UInt Mesh::getNbFacetsPerElement(const ElementType & type, UInt t) {
+inline UInt Mesh::getNbFacetsPerElement(ElementType type, UInt t) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) \
n_facet = ElementClass<type>::getNbFacetsPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
-inline auto Mesh::getFacetLocalConnectivity(const ElementType & type, UInt t) {
+inline auto Mesh::getFacetLocalConnectivity(ElementType type, UInt t) {
AKANTU_DEBUG_IN();
#define GET_FACET_CON(type) \
AKANTU_DEBUG_OUT(); \
return ElementClass<type>::getFacetLocalConnectivityPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_CON);
#undef GET_FACET_CON
AKANTU_DEBUG_OUT();
return ElementClass<_not_defined>::getFacetLocalConnectivityPerElement(0);
// This avoid a compilation warning but will certainly
// also cause a segfault if reached
}
/* -------------------------------------------------------------------------- */
inline auto Mesh::getFacetConnectivity(const Element & element, UInt t) const {
AKANTU_DEBUG_IN();
Matrix<const UInt> local_facets(getFacetLocalConnectivity(element.type, t));
Matrix<UInt> facets(local_facets.rows(), local_facets.cols());
const Array<UInt> & conn = connectivities(element.type, element.ghost_type);
for (UInt f = 0; f < facets.rows(); ++f) {
for (UInt n = 0; n < facets.cols(); ++n) {
facets(f, n) = conn(element.element, local_facets(f, n));
}
}
AKANTU_DEBUG_OUT();
return facets;
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<UInt> Mesh::getConnectivity(const Element & element) const {
const auto & conn = connectivities(element.type, element.ghost_type);
auto it = conn.begin(conn.getNbComponent());
return it[element.element];
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<UInt> Mesh::getConnectivity(const Element & element) {
auto & conn = connectivities(element.type, element.ghost_type);
auto it = conn.begin(conn.getNbComponent());
return it[element.element];
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::extractNodalValuesFromElement(
- const Array<T> & nodal_values, T * local_coord, UInt * connectivity,
+ const Array<T> & nodal_values, T * local_coord, const UInt * connectivity,
UInt n_nodes, UInt nb_degree_of_freedom) const {
for (UInt n = 0; n < n_nodes; ++n) {
memcpy(local_coord + n * nb_degree_of_freedom,
nodal_values.storage() + connectivity[n] * nb_degree_of_freedom,
nb_degree_of_freedom * sizeof(T));
}
}
/* -------------------------------------------------------------------------- */
-inline void Mesh::addConnectivityType(const ElementType & type,
- const GhostType & ghost_type) {
+inline void Mesh::addConnectivityType(ElementType type,
+ GhostType ghost_type) {
getConnectivityPointer(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPureGhostNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_shared_mask) == NodeFlag::_pure_ghost;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalOrMasterNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_local_master_mask) == NodeFlag::_normal;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_shared_mask) == NodeFlag::_normal;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isMasterNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_shared_mask) == NodeFlag::_master;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isSlaveNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_shared_mask) == NodeFlag::_slave;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPeriodicSlave(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_periodic_mask) ==
NodeFlag::_periodic_slave;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPeriodicMaster(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_periodic_mask) ==
NodeFlag::_periodic_master;
}
/* -------------------------------------------------------------------------- */
inline NodeFlag Mesh::getNodeFlag(UInt local_id) const {
return (*nodes_flags)(local_id);
}
/* -------------------------------------------------------------------------- */
inline Int Mesh::getNodePrank(UInt local_id) const {
auto it = nodes_prank.find(local_id);
return it == nodes_prank.end() ? -1 : it->second;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeGlobalId(UInt local_id) const {
return nodes_global_ids ? (*nodes_global_ids)(local_id) : local_id;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeLocalId(UInt global_id) const {
- if (nodes_global_ids == nullptr)
+ if (nodes_global_ids == nullptr) {
return global_id;
+ }
return nodes_global_ids->find(global_id);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbGlobalNodes() const {
return nodes_global_ids ? nb_global_nodes : nodes->size();
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElementList(const Array<Element> & elements) {
UInt nb_nodes_per_element = 0;
UInt nb_nodes = 0;
ElementType current_element_type = _not_defined;
for (const auto & el : elements) {
if (el.type != current_element_type) {
current_element_type = el.type;
nb_nodes_per_element = Mesh::getNbNodesPerElement(current_element_type);
}
nb_nodes += nb_nodes_per_element;
}
return nb_nodes;
}
/* -------------------------------------------------------------------------- */
inline Mesh & Mesh::getMeshFacets() {
- if (!this->mesh_facets)
+ if (this->mesh_facets == nullptr) {
AKANTU_SILENT_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
+ }
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshFacets() const {
- if (!this->mesh_facets)
+ if (this->mesh_facets == nullptr) {
AKANTU_SILENT_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
+ }
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshParent() const {
- if (!this->mesh_parent)
+ if (this->mesh_parent == nullptr) {
AKANTU_SILENT_EXCEPTION(
"No parent mesh is defined! This is only valid in a mesh_facets");
+ }
return *this->mesh_parent;
}
/* -------------------------------------------------------------------------- */
void Mesh::addPeriodicSlave(UInt slave, UInt master) {
- if (master == slave)
+ if (master == slave) {
return;
+ }
// if pair already registered
auto master_slaves = periodic_master_slave.equal_range(master);
auto slave_it =
std::find_if(master_slaves.first, master_slaves.second,
[&](auto & pair) { return pair.second == slave; });
if (slave_it == master_slaves.second) {
// no duplicates
periodic_master_slave.insert(std::make_pair(master, slave));
AKANTU_DEBUG_INFO("adding periodic slave, slave gid:"
<< getNodeGlobalId(slave) << " [lid: " << slave << "]"
<< ", master gid:" << getNodeGlobalId(master)
<< " [lid: " << master << "]");
// std::cout << "adding periodic slave, slave gid:" <<
// getNodeGlobalId(slave)
// << " [lid: " << slave << "]"
// << ", master gid:" << getNodeGlobalId(master)
// << " [lid: " << master << "]" << std::endl;
}
periodic_slave_master[slave] = master;
auto set_flag = [&](auto node, auto flag) {
(*nodes_flags)[node] &= ~NodeFlag::_periodic_mask; // clean periodic flags
(*nodes_flags)[node] |= flag;
};
set_flag(slave, NodeFlag::_periodic_slave);
set_flag(master, NodeFlag::_periodic_master);
}
/* -------------------------------------------------------------------------- */
UInt Mesh::getPeriodicMaster(UInt slave) const {
return periodic_slave_master.at(slave);
}
/* -------------------------------------------------------------------------- */
class Mesh::PeriodicSlaves {
using internal_iterator = std::unordered_multimap<UInt, UInt>::const_iterator;
std::pair<internal_iterator, internal_iterator> pair;
public:
PeriodicSlaves(const Mesh & mesh, UInt master)
: pair(mesh.getPeriodicMasterSlaves().equal_range(master)) {}
PeriodicSlaves(const PeriodicSlaves & other) = default;
PeriodicSlaves(PeriodicSlaves && other) = default;
PeriodicSlaves & operator=(const PeriodicSlaves & other) = default;
class const_iterator {
internal_iterator it;
public:
- const_iterator(internal_iterator it) : it(std::move(it)) {}
+ const_iterator(internal_iterator it) : it(it) {}
const_iterator operator++() {
++it;
return *this;
}
bool operator!=(const const_iterator & other) { return other.it != it; }
auto operator*() { return it->second; }
};
- auto begin() { return const_iterator(pair.first); }
- auto end() { return const_iterator(pair.second); }
+ auto begin() const { return const_iterator(pair.first); }
+ auto end() const { return const_iterator(pair.second); }
};
/* -------------------------------------------------------------------------- */
inline decltype(auto) Mesh::getPeriodicSlaves(UInt master) const {
return PeriodicSlaves(*this, master);
}
/* -------------------------------------------------------------------------- */
inline Vector<UInt>
Mesh::getConnectivityWithPeriodicity(const Element & element) const {
Vector<UInt> conn = getConnectivity(element);
if (not isPeriodic()) {
return conn;
}
for (auto && node : conn) {
if (isPeriodicSlave(node)) {
node = getPeriodicMaster(node);
}
}
return conn;
}
} // namespace akantu
-#endif /* __AKANTU_MESH_INLINE_IMPL_HH__ */
+#endif /* AKANTU_MESH_INLINE_IMPL_HH_ */
diff --git a/src/mesh/mesh_iterators.hh b/src/mesh/mesh_iterators.hh
index c8f3ed665..a10877ba8 100644
--- a/src/mesh/mesh_iterators.hh
+++ b/src/mesh/mesh_iterators.hh
@@ -1,227 +1,228 @@
/**
* @file mesh_iterators.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 16 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Set of helper classes to have fun with range based for
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "aka_static_if.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_ITERATORS_HH__
-#define __AKANTU_MESH_ITERATORS_HH__
+#ifndef AKANTU_MESH_ITERATORS_HH_
+#define AKANTU_MESH_ITERATORS_HH_
namespace akantu {
class MeshElementsByTypes {
using elements_iterator = Array<Element>::scalar_iterator;
public:
explicit MeshElementsByTypes(const Array<Element> & elements) {
this->elements.copy(elements);
std::sort(this->elements.begin(), this->elements.end());
}
/* ------------------------------------------------------------------------ */
class MeshElementsRange {
public:
MeshElementsRange() = default;
MeshElementsRange(const elements_iterator & begin,
const elements_iterator & end)
: type((*begin).type), ghost_type((*begin).ghost_type), begin(begin),
end(end) {}
- AKANTU_GET_MACRO(Type, type, const ElementType &);
- AKANTU_GET_MACRO(GhostType, ghost_type, const GhostType &);
+ AKANTU_GET_MACRO(Type, type, ElementType);
+ AKANTU_GET_MACRO(GhostType, ghost_type, GhostType);
const Array<UInt> & getElements() {
elements.resize(end - begin);
auto el_it = elements.begin();
for (auto it = begin; it != end; ++it, ++el_it) {
*el_it = it->element;
}
return elements;
}
private:
ElementType type{_not_defined};
GhostType ghost_type{_casper};
elements_iterator begin;
elements_iterator end;
Array<UInt> elements;
};
/* ------------------------------------------------------------------------ */
class iterator {
struct element_comparator {
bool operator()(const Element & lhs, const Element & rhs) const {
return ((rhs == ElementNull) || std::tie(lhs.ghost_type, lhs.type) <
std::tie(rhs.ghost_type, rhs.type));
}
};
public:
iterator(const iterator &) = default;
iterator(const elements_iterator & first, const elements_iterator & last)
: range(std::equal_range(first, last, *first, element_comparator())),
first(first), last(last) {}
decltype(auto) operator*() const {
return MeshElementsRange(range.first, range.second);
}
iterator operator++() {
first = range.second;
range = std::equal_range(first, last, *first, element_comparator());
return *this;
}
bool operator==(const iterator & other) const {
return (first == other.first and last == other.last);
}
bool operator!=(const iterator & other) const {
return (not operator==(other));
}
private:
std::pair<elements_iterator, elements_iterator> range;
elements_iterator first;
elements_iterator last;
};
iterator begin() { return iterator(elements.begin(), elements.end()); }
iterator end() { return iterator(elements.end(), elements.end()); }
private:
Array<Element> elements;
};
/* -------------------------------------------------------------------------- */
namespace mesh_iterators {
namespace details {
template <class internal_iterator> class delegated_iterator {
public:
using value_type = std::remove_pointer_t<
typename internal_iterator::value_type::second_type>;
using difference_type = std::ptrdiff_t;
using pointer = value_type *;
using reference = value_type &;
using iterator_category = std::input_iterator_tag;
explicit delegated_iterator(internal_iterator it) : it(std::move(it)) {}
decltype(auto) operator*() {
return std::forward<decltype(*(it->second))>(*(it->second));
}
delegated_iterator operator++() {
++it;
return *this;
}
bool operator==(const delegated_iterator & other) const {
return other.it == it;
}
bool operator!=(const delegated_iterator & other) const {
return other.it != it;
}
private:
internal_iterator it;
};
} // namespace details
} // namespace mesh_iterators
/* -------------------------------------------------------------------------- */
template <class Func>
void for_each_element(UInt nb_elements, const Array<UInt> & filter_elements,
Func && function) {
if (filter_elements != empty_filter) {
std::for_each(filter_elements.begin(), filter_elements.end(),
std::forward<Func>(function));
} else {
auto && range = arange(nb_elements);
std::for_each(range.begin(), range.end(), std::forward<Func>(function));
}
}
namespace {
DECLARE_NAMED_ARGUMENT(element_filter);
}
/* -------------------------------------------------------------------------- */
template <class Func, typename... pack>
void for_each_element(const Mesh & mesh, Func && function, pack &&... _pack) {
auto requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _casper);
const ElementTypeMapArray<UInt> * filter =
OPTIONAL_NAMED_ARG(element_filter, nullptr);
bool all_ghost_types = requested_ghost_type == _casper;
auto spatial_dimension =
OPTIONAL_NAMED_ARG(spatial_dimension, mesh.getSpatialDimension());
auto element_kind = OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined);
for (auto ghost_type : ghost_types) {
- if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types))
+ if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types)) {
continue;
+ }
auto element_types =
mesh.elementTypes(spatial_dimension, ghost_type, element_kind);
if (filter) {
element_types =
filter->elementTypes(spatial_dimension, ghost_type, element_kind);
}
for (auto type : element_types) {
const Array<UInt> * filter_array;
if (filter) {
filter_array = &((*filter)(type, ghost_type));
} else {
filter_array = &empty_filter;
}
auto nb_elements = mesh.getNbElement(type, ghost_type);
for_each_element(nb_elements, *filter_array, [&](auto && el) {
auto element = Element{type, el, ghost_type};
std::forward<Func>(function)(element);
});
}
}
}
} // namespace akantu
-#endif /* __AKANTU_MESH_ITERATORS_HH__ */
+#endif /* AKANTU_MESH_ITERATORS_HH_ */
diff --git a/src/mesh/mesh_periodic.cc b/src/mesh/mesh_periodic.cc
index 1ff73618b..01d226553 100644
--- a/src/mesh/mesh_periodic.cc
+++ b/src/mesh/mesh_periodic.cc
@@ -1,461 +1,463 @@
/**
* @file mesh_periodic.cc
*
* @author Nicolas Richart
*
* @date creation Sat Feb 10 2018
*
* @brief Implementation of the perdiodicity capabilities in the mesh
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_tag.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "periodic_node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void Mesh::makePeriodic(const SpatialDirection & direction) {
Array<UInt> list_1;
Array<UInt> list_2;
Real tolerance = 1e-10;
auto lower_bound = this->getLowerBounds();
auto upper_bound = this->getUpperBounds();
auto length = upper_bound(direction) - lower_bound(direction);
const auto & positions = *nodes;
for (auto && data : enumerate(make_view(positions, spatial_dimension))) {
UInt node = std::get<0>(data);
const auto & pos = std::get<1>(data);
if (std::abs((pos(direction) - lower_bound(direction)) / length) <
tolerance) {
list_1.push_back(node);
}
if (std::abs((pos(direction) - upper_bound(direction)) / length) <
tolerance) {
list_2.push_back(node);
}
}
this->makePeriodic(direction, list_1, list_2);
}
/* -------------------------------------------------------------------------- */
void Mesh::makePeriodic(const SpatialDirection & direction, const ID & list_1,
const ID & list_2) {
const auto & list_nodes_1 =
mesh.getElementGroup(list_1).getNodeGroup().getNodes();
const auto & list_nodes_2 =
mesh.getElementGroup(list_2).getNodeGroup().getNodes();
this->makePeriodic(direction, list_nodes_1, list_nodes_2);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace {
struct NodeInfo {
- NodeInfo() {}
+ NodeInfo() = default;
NodeInfo(UInt spatial_dimension) : position(spatial_dimension) {}
NodeInfo(UInt node, const Vector<Real> & position,
const SpatialDirection & direction)
: node(node), position(position) {
this->direction_position = position(direction);
this->position(direction) = 0.;
}
NodeInfo(const NodeInfo & other) = default;
- NodeInfo( NodeInfo && other) noexcept = default;
+ NodeInfo(NodeInfo && other) noexcept = default;
NodeInfo & operator=(const NodeInfo & other) = default;
- NodeInfo & operator=(NodeInfo && other) noexcept = default;
-
+ NodeInfo & operator=(NodeInfo && other) = default;
+
UInt node{0};
Vector<Real> position;
Real direction_position{0.};
};
} // namespace
/* -------------------------------------------------------------------------- */
// left is for lower values on direction and right for highest values
void Mesh::makePeriodic(const SpatialDirection & direction,
const Array<UInt> & list_left,
const Array<UInt> & list_right) {
Real tolerance = 1e-10;
const auto & positions = *nodes;
auto lower_bound = this->getLowerBounds();
auto upper_bound = this->getUpperBounds();
auto length = upper_bound(direction) - lower_bound(direction);
lower_bound(direction) = 0;
upper_bound(direction) = 0;
auto prank = communicator->whoAmI();
std::vector<NodeInfo> nodes_left(list_left.size());
std::vector<NodeInfo> nodes_right(list_right.size());
BBox bbox(spatial_dimension);
auto to_position = [&](UInt node) {
Vector<Real> pos(spatial_dimension);
for (UInt s : arange(spatial_dimension)) {
pos(s) = positions(node, s);
}
auto && info = NodeInfo(node, pos, direction);
bbox += info.position;
return std::move(info);
};
std::transform(list_left.begin(), list_left.end(), nodes_left.begin(),
to_position);
BBox bbox_left = bbox;
bbox.reset();
std::transform(list_right.begin(), list_right.end(), nodes_right.begin(),
to_position);
BBox bbox_right = bbox;
std::vector<UInt> new_nodes;
if (is_distributed) {
NewNodesEvent event(AKANTU_CURRENT_FUNCTION);
/* ---------------------------------------------------------------------- */
// function to send nodes in bboxes intersections
auto extract_and_send_nodes = [&](const auto & bbox, const auto & node_list,
auto & buffers, auto proc, auto cnt) {
// buffers.resize(buffers.size() + 1);
buffers.push_back(std::make_unique<DynamicCommunicationBuffer>());
auto & buffer = *buffers.back();
// std::cout << "Sending to " << proc << std::endl;
for (auto & info : node_list) {
if (bbox.contains(info.position) and isLocalOrMasterNode(info.node)) {
Vector<Real> pos = info.position;
pos(direction) = info.direction_position;
NodeFlag flag = (*nodes_flags)(info.node) & NodeFlag::_periodic_mask;
UInt gnode = getNodeGlobalId(info.node);
buffer << gnode;
buffer << pos;
buffer << flag;
// std::cout << " - node " << getNodeGlobalId(info.node);
// if is slave sends master info
if (flag == NodeFlag::_periodic_slave) {
UInt master = getNodeGlobalId(periodic_slave_master[info.node]);
// std::cout << " slave of " << master << std::endl;
buffer << master;
}
// if is master sends list of slaves
if (flag == NodeFlag::_periodic_master) {
UInt nb_slaves = periodic_master_slave.count(info.node);
buffer << nb_slaves;
// std::cout << " master of " << nb_slaves << " nodes : [";
auto slaves = periodic_master_slave.equal_range(info.node);
for (auto it = slaves.first; it != slaves.second; ++it) {
UInt gslave = getNodeGlobalId(it->second);
// std::cout << (it == slaves.first ? "" : ", ") << gslave;
buffer << gslave;
}
// std::cout << "]";
}
// std::cout << std::endl;
}
}
- auto tag = Tag::genTag(prank, 10 * direction + cnt, Tag::_PERIODIC_NODES);
+ auto tag = Tag::genTag(prank, 10 * direction + cnt, Tag::_periodic_nodes);
// std::cout << "SBuffer size " << buffer.size() << " " << tag <<
// std::endl;
return communicator->asyncSend(buffer, proc, tag);
};
/* ---------------------------------------------------------------------- */
// function to receive nodes in bboxes intersections
auto recv_and_extract_nodes = [&](auto & node_list, const auto proc,
auto cnt) {
DynamicCommunicationBuffer buffer;
- auto tag = Tag::genTag(proc, 10 * direction + cnt, Tag::_PERIODIC_NODES);
+ auto tag = Tag::genTag(proc, 10 * direction + cnt, Tag::_periodic_nodes);
communicator->receive(buffer, proc, tag);
// std::cout << "RBuffer size " << buffer.size() << " " << tag <<
// std::endl; std::cout << "Receiving from " << proc << std::endl;
while (not buffer.empty()) {
Vector<Real> pos(spatial_dimension);
UInt global_node;
NodeFlag flag;
buffer >> global_node;
buffer >> pos;
buffer >> flag;
// std::cout << " - node " << global_node;
auto local_node = getNodeLocalId(global_node);
// get the master info of is slave
if (flag == NodeFlag::_periodic_slave) {
UInt master_node;
buffer >> master_node;
// std::cout << " slave of " << master_node << std::endl;
// auto local_master_node = getNodeLocalId(master_node);
// AKANTU_DEBUG_ASSERT(local_master_node != UInt(-1),
//"Should I know the master node " << master_node);
}
// get the list of slaves if is master
if ((flag & NodeFlag::_periodic_mask) == NodeFlag::_periodic_master) {
UInt nb_slaves;
buffer >> nb_slaves;
// std::cout << " master of " << nb_slaves << " nodes : [";
for (auto ns [[gnu::unused]] : arange(nb_slaves)) {
UInt gslave_node;
buffer >> gslave_node;
// std::cout << (ns == 0 ? "" : ", ") << gslave_node;
// auto lslave_node = getNodeLocalId(gslave_node);
// AKANTU_DEBUG_ASSERT(lslave_node != UInt(-1),
// "Should I know the slave node " <<
// gslave_node);
}
// std::cout << "]";
}
// std::cout << std::endl;
- if (local_node != UInt(-1))
+ if (local_node != UInt(-1)) {
continue;
+ }
local_node = nodes->size();
NodeInfo info(local_node, pos, direction);
nodes->push_back(pos);
nodes_global_ids->push_back(global_node);
nodes_flags->push_back(flag | NodeFlag::_pure_ghost);
new_nodes.push_back(info.node);
node_list.push_back(info);
nodes_prank[info.node] = proc;
event.getList().push_back(local_node);
}
};
/* ---------------------------------------------------------------------- */
auto && intersections_with_right =
bbox_left.intersection(bbox_right, *communicator);
auto && intersections_with_left =
bbox_right.intersection(bbox_left, *communicator);
std::vector<CommunicationRequest> send_requests;
std::vector<std::unique_ptr<DynamicCommunicationBuffer>> send_buffers;
// sending nodes in the common zones
auto send_intersections = [&](auto & intersections, auto send_count) {
for (auto && data : intersections) {
auto proc = std::get<0>(data);
// Send local nodes if intersects with remote
const auto & intersection_with_proc = std::get<1>(data);
if (intersection_with_proc) {
send_requests.push_back(
extract_and_send_nodes(intersection_with_proc, nodes_right,
send_buffers, proc, send_count));
}
send_count += 2;
}
};
auto recv_intersections = [&](auto & intersections, auto recv_count) {
for (auto && data : intersections) {
auto proc = std::get<0>(data);
// receive remote nodes if intersects with local
const auto & intersection_with_proc = std::get<1>(data);
if (intersection_with_proc) {
recv_and_extract_nodes(nodes_right, proc, recv_count);
}
recv_count += 2;
}
};
send_intersections(intersections_with_left, 0);
send_intersections(intersections_with_right, 1);
recv_intersections(intersections_with_right, 0);
recv_intersections(intersections_with_right, 1);
- communicator->waitAll(send_requests);
- communicator->freeCommunicationRequest(send_requests);
+ Communicator::waitAll(send_requests);
+ Communicator::freeCommunicationRequest(send_requests);
this->sendEvent(event);
} // end distributed work
auto to_sort = [&](auto && info1, auto && info2) -> bool {
return info1.position < info2.position;
};
// sort nodes based on their distance to lower corner
std::sort(nodes_left.begin(), nodes_left.end(), to_sort);
std::sort(nodes_right.begin(), nodes_right.end(), to_sort);
// function to change the master of nodes
auto updating_master = [&](auto & old_master, auto & new_master) {
- if (old_master == new_master)
+ if (old_master == new_master) {
return;
+ }
auto slaves = periodic_master_slave.equal_range(old_master);
AKANTU_DEBUG_ASSERT(
isPeriodicMaster(
old_master), // slaves.first != periodic_master_slave.end(),
"Cannot update master " << old_master << ", its not a master node!");
decltype(periodic_master_slave) tmp_master_slave;
for (auto it = slaves.first; it != slaves.second; ++it) {
auto slave = it->second;
tmp_master_slave.insert(std::make_pair(new_master, slave));
periodic_slave_master[slave] = new_master;
}
periodic_master_slave.erase(old_master);
(*nodes_flags)[old_master] &= ~NodeFlag::_periodic_master;
addPeriodicSlave(old_master, new_master);
for (auto && data : tmp_master_slave) {
addPeriodicSlave(data.second, data.first);
}
};
// handling 2 nodes that are periodic
auto match_found = [&](auto & info1, auto & info2) {
const auto & node1 = info1.node;
const auto & node2 = info2.node;
auto master = node1;
bool node1_side_master = false;
if (isPeriodicMaster(node1)) {
node1_side_master = true;
} else if (isPeriodicSlave(node1)) {
node1_side_master = true;
master = periodic_slave_master[node1];
}
auto node2_master = node2;
if (isPeriodicSlave(node2)) {
node2_master = periodic_slave_master[node2];
}
if (node1_side_master) {
if (isPeriodicSlave(node2)) {
updating_master(node2_master, master);
return;
}
if (isPeriodicMaster(node2)) {
updating_master(node2, master);
return;
}
addPeriodicSlave(node2, master);
} else {
if (isPeriodicSlave(node2)) {
addPeriodicSlave(node1, node2_master);
return;
}
if (isPeriodicMaster(node2)) {
addPeriodicSlave(node1, node2);
return;
}
addPeriodicSlave(node2, node1);
}
};
// matching the nodes from 2 lists
auto match_pairs = [&](auto & nodes_1, auto & nodes_2) {
// Guillaume to Nico: It seems that the list of nodes is not sorted
// as it was: therefore the loop cannot be truncated anymore.
// Otherwise many pairs are missing.
// I replaced (temporarily?) for the N^2 loop so as not to miss
// any pbc pair.
//
// auto it = nodes_2.begin();
// for every nodes in 1st list
for (auto && info1 : nodes_1) {
auto & pos1 = info1.position;
// auto it_cur = it;
// try to find a match in 2nd list
for (auto && info2 : nodes_2) {
// auto & info2 = *it_cur;
auto & pos2 = info2.position;
auto dist = pos1.distance(pos2) / length;
if (dist < tolerance) {
// handles the found matches
match_found(info1, info2);
// it = it_cur;
break;
}
}
}
};
match_pairs(nodes_left, nodes_right);
// match_pairs(nodes_right, nodes_left);
this->updatePeriodicSynchronizer();
this->is_periodic = true;
}
/* -------------------------------------------------------------------------- */
void Mesh::wipePeriodicInfo() {
this->is_periodic = false;
this->periodic_slave_master.clear();
this->periodic_master_slave.clear();
for (auto && flags : *nodes_flags) {
flags &= ~NodeFlag::_periodic_mask;
}
}
/* -------------------------------------------------------------------------- */
void Mesh::updatePeriodicSynchronizer() {
if (not this->periodic_node_synchronizer) {
this->periodic_node_synchronizer =
std::make_unique<PeriodicNodeSynchronizer>(
*this, this->getID() + ":periodic_synchronizer",
this->getMemoryID(), false);
}
this->periodic_node_synchronizer->update();
}
} // namespace akantu
diff --git a/src/mesh/node_group.cc b/src/mesh/node_group.cc
index fcee8eb21..5b081ba47 100644
--- a/src/mesh/node_group.cc
+++ b/src/mesh/node_group.cc
@@ -1,95 +1,96 @@
/**
* @file node_group.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Feb 01 2018
*
* @brief Implementation of the node group
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_group.hh"
#include "dumpable.hh"
#include "dumpable_inline_impl.hh"
#include "mesh.hh"
#if defined(AKANTU_USE_IOHELPER)
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeGroup::NodeGroup(const std::string & name, const Mesh & mesh,
const std::string & id, const MemoryID & memory_id)
: Memory(id, memory_id), name(name),
node_group(alloc<UInt>(std::string(this->id + ":nodes"), 0, 1)) {
#if defined(AKANTU_USE_IOHELPER)
this->registerDumper<DumperParaview>("paraview_" + name, name, true);
auto field = std::make_shared<dumpers::NodalField<Real, true>>(
mesh.getNodes(), 0, 0, &this->getNodes());
this->getDumper().registerField("positions", field);
#endif
}
/* -------------------------------------------------------------------------- */
NodeGroup::~NodeGroup() = default;
/* -------------------------------------------------------------------------- */
-void NodeGroup::empty() { node_group.resize(0); }
-
+void NodeGroup::clear() { node_group.resize(0); }
+/* -------------------------------------------------------------------------- */
+//bool NodeGroup::empty() { return node_group.empty(); }
/* -------------------------------------------------------------------------- */
void NodeGroup::optimize() {
std::sort(node_group.begin(), node_group.end());
Array<UInt>::iterator<> end =
std::unique(node_group.begin(), node_group.end());
node_group.resize(end - node_group.begin());
}
/* -------------------------------------------------------------------------- */
void NodeGroup::append(const NodeGroup & other_group) {
AKANTU_DEBUG_IN();
UInt nb_nodes = node_group.size();
/// append new nodes to current list
node_group.resize(nb_nodes + other_group.node_group.size());
std::copy(other_group.node_group.begin(), other_group.node_group.end(),
node_group.begin() + nb_nodes);
optimize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeGroup::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "NodeGroup [" << std::endl;
stream << space << " + name: " << name << std::endl;
node_group.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/mesh/node_group.hh b/src/mesh/node_group.hh
index 4afcc094a..1c5c320ee 100644
--- a/src/mesh/node_group.hh
+++ b/src/mesh/node_group.hh
@@ -1,130 +1,134 @@
/**
* @file node_group.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Node group definition
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_memory.hh"
#include "dumpable.hh"
#include "mesh_filter.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NODE_GROUP_HH__
-#define __AKANTU_NODE_GROUP_HH__
+#ifndef AKANTU_NODE_GROUP_HH_
+#define AKANTU_NODE_GROUP_HH_
namespace akantu {
class NodeGroup : public Memory, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NodeGroup(const std::string & name, const Mesh & mesh,
const std::string & id = "node_group",
const MemoryID & memory_id = 0);
~NodeGroup() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
using const_node_iterator = Array<UInt>::const_iterator<UInt>;
/// empty the node group
- void empty();
+ void clear();
+
+ /// returns treu if the group is empty \warning this changed beahavior if you
+ /// want to empty the group use clear
+ bool empty() const __attribute__((warn_unused_result));
/// iterator to the beginning of the node group
inline const_node_iterator begin() const;
/// iterator to the end of the node group
inline const_node_iterator end() const;
/// add a node and give the local position through an iterator
inline const_node_iterator add(UInt node, bool check_for_duplicate = true);
/// remove a node
inline void remove(UInt node);
inline decltype(auto) find(UInt node) const { return node_group.find(node); }
/// remove duplicated nodes
void optimize();
/// append a group to current one
void append(const NodeGroup & other_group);
/// apply a filter on current node group
template <typename T> void applyNodeFilter(T & filter);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(Nodes, node_group, Array<UInt> &);
AKANTU_GET_MACRO(Nodes, node_group, const Array<UInt> &);
AKANTU_GET_MACRO(Name, name, const std::string &);
/// give the number of nodes in the current group
inline UInt size() const;
// UInt * storage() { return node_group.storage(); };
friend class GroupManager;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// name of the group
std::string name;
/// list of nodes in the group
Array<UInt> & node_group;
/// reference to the mesh in question
// const Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NodeGroup & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "node_group_inline_impl.hh"
-#endif /* __AKANTU_NODE_GROUP_HH__ */
+#endif /* AKANTU_NODE_GROUP_HH_ */
diff --git a/src/mesh/node_group_inline_impl.hh b/src/mesh/node_group_inline_impl.hh
index e127ef23e..c42d080dd 100644
--- a/src/mesh/node_group_inline_impl.hh
+++ b/src/mesh/node_group_inline_impl.hh
@@ -1,97 +1,97 @@
/**
* @file node_group_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Aug 13 2017
*
* @brief Node group inline function definitions
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::begin() const {
return node_group.begin();
}
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::end() const {
return node_group.end();
}
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::add(UInt node,
bool check_for_duplicate) {
if (check_for_duplicate) {
const_node_iterator it = std::find(begin(), end(), node);
if (it == node_group.end()) {
node_group.push_back(node);
return (node_group.end() - 1);
}
return it;
- } else {
- node_group.push_back(node);
- return (node_group.end() - 1);
}
+
+ node_group.push_back(node);
+ return (node_group.end() - 1);
}
/* -------------------------------------------------------------------------- */
inline void NodeGroup::remove(UInt node) {
Array<UInt>::iterator<> it = this->node_group.begin();
Array<UInt>::iterator<> end = this->node_group.end();
AKANTU_DEBUG_ASSERT(it != end, "The node group is empty!!");
for (; it != node_group.end(); ++it) {
if (*it == node) {
it = node_group.erase(it);
}
}
AKANTU_DEBUG_ASSERT(it != end, "The node was not found!");
}
/* -------------------------------------------------------------------------- */
inline UInt NodeGroup::size() const { return node_group.size(); }
/* -------------------------------------------------------------------------- */
struct FilterFunctor;
template <typename T> void NodeGroup::applyNodeFilter(T & filter) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(T::type == FilterFunctor::_node_filter_functor,
"NodeFilter can only apply node filter functor");
Array<UInt>::iterator<> it = this->node_group.begin();
for (; it != node_group.end(); ++it) {
/// filter == true -> keep node
if (!filter(*it)) {
it = node_group.erase(it);
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.cc b/src/mesh_utils/cohesive_element_inserter.cc
index 1575ed10e..b0ab5e2f5 100644
--- a/src/mesh_utils/cohesive_element_inserter.cc
+++ b/src/mesh_utils/cohesive_element_inserter.cc
@@ -1,307 +1,316 @@
/**
* @file cohesive_element_inserter.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
* @date last modification: Mon Feb 19 2018
*
* @brief Cohesive element inserter functions
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "global_ids_updater.hh"
#include "mesh_accessor.hh"
#include "mesh_iterators.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <limits>
/* -------------------------------------------------------------------------- */
namespace akantu {
CohesiveElementInserter::CohesiveElementInserter(Mesh & mesh, const ID & id)
: Parsable(ParserType::_cohesive_inserter), id(id), mesh(mesh),
mesh_facets(mesh.initMeshFacets()),
insertion_facets("insertion_facets", id),
insertion_limits(mesh.getSpatialDimension(), 2),
check_facets("check_facets", id) {
this->registerParam("cohesive_surfaces", physical_surfaces, _pat_parsable,
"List of groups to consider for insertion");
this->registerParam("cohesive_zones", physical_zones, _pat_parsable,
"List of groups to consider for insertion");
this->registerParam("bounding_box", insertion_limits, _pat_parsable,
"Global limit for insertion");
UInt spatial_dimension = mesh.getSpatialDimension();
MeshUtils::resetFacetToDouble(mesh_facets);
/// init insertion limits
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
insertion_limits(dim, 0) = std::numeric_limits<Real>::max() * Real(-1.);
insertion_limits(dim, 1) = std::numeric_limits<Real>::max();
}
insertion_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = false);
}
/* -------------------------------------------------------------------------- */
CohesiveElementInserter::~CohesiveElementInserter() = default;
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::parseSection(const ParserSection & section) {
Parsable::parseSection(section);
- if (is_extrinsic)
+ if (is_extrinsic) {
limitCheckFacets(this->check_facets);
+ }
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::limitCheckFacets() {
limitCheckFacets(this->check_facets);
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::setLimit(SpatialDirection axis, Real first_limit,
Real second_limit) {
AKANTU_DEBUG_ASSERT(
axis < mesh.getSpatialDimension(),
"You are trying to limit insertion in a direction that doesn't exist");
insertion_limits(axis, 0) = std::min(first_limit, second_limit);
insertion_limits(axis, 1) = std::max(first_limit, second_limit);
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertIntrinsicElements() {
limitCheckFacets(insertion_facets);
return insertElements();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::limitCheckFacets(
ElementTypeMapArray<bool> & check_facets) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
check_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = true);
check_facets.set(true);
// remove the pure ghost elements
for_each_element(
mesh_facets,
[&](auto && facet) {
const auto & element_to_facet = mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
auto & left = element_to_facet[0];
auto & right = element_to_facet[1];
if (right == ElementNull ||
(left.ghost_type == _ghost && right.ghost_type == _ghost)) {
check_facets(facet) = false;
return;
}
#ifndef AKANTU_NDEBUG
if (left == ElementNull) {
AKANTU_DEBUG_WARNING("By convention element should not have "
"ElementNull on there first side: "
<< facet);
}
#endif
if (left.kind() == _ek_cohesive or right.kind() == _ek_cohesive) {
check_facets(facet) = false;
}
},
_spatial_dimension = spatial_dimension - 1);
auto tolerance = Math::getTolerance();
Vector<Real> bary_facet(spatial_dimension);
// set the limits to the bounding box
for_each_element(
mesh_facets,
[&](auto && facet) {
auto & need_check = check_facets(facet);
- if (not need_check)
+ if (not need_check) {
return;
+ }
mesh_facets.getBarycenter(facet, bary_facet);
UInt coord_in_limit = 0;
while (coord_in_limit < spatial_dimension and
bary_facet(coord_in_limit) >
(insertion_limits(coord_in_limit, 0) - tolerance) and
bary_facet(coord_in_limit) <
- (insertion_limits(coord_in_limit, 1) + tolerance))
+ (insertion_limits(coord_in_limit, 1) + tolerance)) {
++coord_in_limit;
+ }
- if (coord_in_limit != spatial_dimension)
+ if (coord_in_limit != spatial_dimension) {
need_check = false;
+ }
},
_spatial_dimension = spatial_dimension - 1);
// remove the physical zones
- if(mesh.hasData("physical_names") and physical_zones.size() > 0) {
+ if(mesh.hasData("physical_names") and not physical_zones.empty()) {
auto && physical_names = mesh.getData<std::string>("physical_names");
for_each_element(
mesh_facets,
[&](auto && facet) {
const auto & element_to_facet = mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
auto count = 0;
for(auto i : arange(2)) {
const auto & element = element_to_facet[i];
- if(element == ElementNull)
+ if (element == ElementNull) {
continue;
+ }
const auto & name = physical_names(element);
count += find(physical_zones.begin(),
physical_zones.end(), name) != physical_zones.end();
}
- if(count != 2)
+ if (count != 2) {
check_facets(facet) = false;
+ }
},
_spatial_dimension = spatial_dimension - 1);
}
- if (physical_surfaces.size() == 0) {
+ if (physical_surfaces.empty()) {
AKANTU_DEBUG_OUT();
return;
}
if (not mesh_facets.hasData("physical_names")) {
AKANTU_DEBUG_ASSERT(
- physical_surfaces.size() == 0,
+ physical_surfaces.empty(),
"No physical names in the mesh but insertion limited to a group");
AKANTU_DEBUG_OUT();
return;
}
const auto & physical_ids =
mesh_facets.getData<std::string>("physical_names");
// set the limits to the physical surfaces
for_each_element(mesh_facets,
[&](auto && facet) {
auto & need_check = check_facets(facet);
- if (not need_check)
+ if (not need_check) {
return;
+ }
const auto & physical_id = physical_ids(facet);
auto it = find(physical_surfaces.begin(),
physical_surfaces.end(), physical_id);
need_check = (it != physical_surfaces.end());
},
_spatial_dimension = spatial_dimension - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertElements(bool only_double_facets) {
CohesiveNewNodesEvent node_event(AKANTU_CURRENT_FUNCTION);
NewElementsEvent element_event(AKANTU_CURRENT_FUNCTION);
Array<UInt> new_pairs(0, 2);
if (mesh_facets.isDistributed()) {
mesh_facets.getElementSynchronizer().synchronizeOnce(
*this, SynchronizationTag::_ce_groups);
}
UInt nb_new_elements = MeshUtils::insertCohesiveElements(
mesh, mesh_facets, insertion_facets, new_pairs, element_event.getList(),
only_double_facets);
UInt nb_new_nodes = new_pairs.size();
node_event.getList().reserve(nb_new_nodes);
node_event.getOldNodesList().reserve(nb_new_nodes);
for (UInt n = 0; n < nb_new_nodes; ++n) {
node_event.getList().push_back(new_pairs(n, 1));
node_event.getOldNodesList().push_back(new_pairs(n, 0));
}
if (nb_new_elements > 0) {
updateInsertionFacets();
}
MeshAccessor mesh_accessor(mesh);
std::tie(nb_new_nodes, nb_new_elements) =
mesh_accessor.updateGlobalData(node_event, element_event);
return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::updateInsertionFacets() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (auto && facet_gt : ghost_types) {
for (auto && facet_type :
mesh_facets.elementTypes(spatial_dimension - 1, facet_gt)) {
auto & ins_facets = insertion_facets(facet_type, facet_gt);
// this is the intrinsic case
- if (not is_extrinsic)
+ if (not is_extrinsic) {
continue;
+ }
auto & f_check = check_facets(facet_type, facet_gt);
for (auto && pair : zip(ins_facets, f_check)) {
bool & ins = std::get<0>(pair);
bool & check = std::get<1>(pair);
- if (ins)
+ if (ins) {
ins = check = false;
+ }
}
}
}
// resize for the newly added facets
insertion_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = false);
// resize for the newly added facets
if (is_extrinsic) {
check_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = false);
} else {
insertion_facets.set(false);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.hh b/src/mesh_utils/cohesive_element_inserter.hh
index 8707807e4..d29a1b757 100644
--- a/src/mesh_utils/cohesive_element_inserter.hh
+++ b/src/mesh_utils/cohesive_element_inserter.hh
@@ -1,173 +1,173 @@
/**
* @file cohesive_element_inserter.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
* @date last modification: Sun Feb 04 2018
*
* @brief Cohesive element inserter
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "mesh_utils.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
-#define __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
+#ifndef AKANTU_COHESIVE_ELEMENT_INSERTER_HH_
+#define AKANTU_COHESIVE_ELEMENT_INSERTER_HH_
namespace akantu {
class GlobalIdsUpdater;
class FacetSynchronizer;
class SolidMechanicsModeslCohesivel;
} // namespace akantu
namespace akantu {
class CohesiveElementInserter : public DataAccessor<Element>, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
CohesiveElementInserter(Mesh & mesh,
const ID & id = "cohesive_element_inserter");
~CohesiveElementInserter() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set range limitation for intrinsic cohesive element insertion
void setLimit(SpatialDirection axis, Real first_limit, Real second_limit);
/// insert intrinsic cohesive elements in a predefined range
auto insertIntrinsicElements() -> UInt;
/// insert extrinsic cohesive elements (returns the number of new
/// cohesive elements)
UInt insertElements(bool only_double_facets = false);
/// limit check facets to match given insertion limits
void limitCheckFacets();
protected:
void parseSection(const ParserSection & section) override;
protected:
/// internal version of limitCheckFacets
void limitCheckFacets(ElementTypeMapArray<bool> & check_facets);
/// update facet insertion arrays after facets doubling
void updateInsertionFacets();
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(InsertionFacetsByElement, insertion_facets,
ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO(InsertionFacetsByElement, insertion_facets,
const ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(InsertionFacets, insertion_facets, bool);
AKANTU_GET_MACRO(CheckFacets, check_facets,
const ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO(MeshFacets, mesh_facets, const Mesh &);
AKANTU_GET_MACRO_NOT_CONST(MeshFacets, mesh_facets, Mesh &);
AKANTU_SET_MACRO(IsExtrinsic, is_extrinsic, bool);
public:
friend class SolidMechanicsModelCohesive;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// object id
ID id;
/// main mesh where to insert cohesive elements
Mesh & mesh;
/// mesh containing facets
Mesh & mesh_facets;
/// list of facets where to insert elements
ElementTypeMapArray<bool> insertion_facets;
/// limits for element insertion
Matrix<Real> insertion_limits;
/// list of groups to consider for insertion, ignored if empty
std::set<ID> physical_surfaces;
/// list of groups in between which an inside which element are insterted
std::set<ID> physical_zones;
/// vector containing facets in which extrinsic cohesive elements can be
/// inserted
ElementTypeMapArray<bool> check_facets;
/// global connectivity ids updater
std::unique_ptr<GlobalIdsUpdater> global_ids_updater;
/// is this inserter used in extrinsic
bool is_extrinsic{false};
};
class CohesiveNewNodesEvent : public NewNodesEvent {
public:
CohesiveNewNodesEvent(const std::string & origin) : NewNodesEvent(origin) {}
~CohesiveNewNodesEvent() override = default;
AKANTU_GET_MACRO_NOT_CONST(OldNodesList, old_nodes, Array<UInt> &);
AKANTU_GET_MACRO(OldNodesList, old_nodes, const Array<UInt> &);
private:
Array<UInt> old_nodes;
};
} // namespace akantu
#include "cohesive_element_inserter_inline_impl.hh"
-#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__ */
+#endif /* AKANTU_COHESIVE_ELEMENT_INSERTER_HH_ */
diff --git a/src/mesh_utils/cohesive_element_inserter_inline_impl.hh b/src/mesh_utils/cohesive_element_inserter_inline_impl.hh
index 5ad62fc93..59540edb7 100644
--- a/src/mesh_utils/cohesive_element_inserter_inline_impl.hh
+++ b/src/mesh_utils/cohesive_element_inserter_inline_impl.hh
@@ -1,88 +1,88 @@
/**
* @file cohesive_element_inserter_inline_impl.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 05 2014
* @date last modification: Fri Dec 08 2017
*
* @brief Cohesive element inserter inline functions
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_HH__
-#define __AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_HH__
+#ifndef AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_HH_
+#define AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt
CohesiveElementInserter::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (tag == SynchronizationTag::_ce_groups) {
size = elements.size() * sizeof(bool);
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void
CohesiveElementInserter::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (tag == SynchronizationTag::_ce_groups) {
for (const auto & el : elements) {
const bool & data = insertion_facets(el);
buffer << data;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void
CohesiveElementInserter::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (tag == SynchronizationTag::_ce_groups) {
for (const auto & el : elements) {
bool & data = insertion_facets(el);
buffer >> data;
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_HH__ */
+#endif /* AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_HH_ */
diff --git a/src/mesh_utils/global_ids_updater.cc b/src/mesh_utils/global_ids_updater.cc
index 79a8ce52b..5820cb3ca 100644
--- a/src/mesh_utils/global_ids_updater.cc
+++ b/src/mesh_utils/global_ids_updater.cc
@@ -1,133 +1,138 @@
/**
* @file global_ids_updater.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Apr 13 2012
* @date last modification: Fri Dec 08 2017
*
* @brief Functions of the GlobalIdsUpdater
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "global_ids_updater.hh"
#include "element_synchronizer.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
UInt GlobalIdsUpdater::updateGlobalIDs(UInt local_nb_new_nodes) {
- if (mesh.getCommunicator().getNbProc() == 1)
+ if (mesh.getCommunicator().getNbProc() == 1) {
return local_nb_new_nodes;
+ }
UInt total_nb_new_nodes = this->updateGlobalIDsLocally(local_nb_new_nodes);
if (mesh.isDistributed()) {
this->synchronizeGlobalIDs();
}
return total_nb_new_nodes;
}
UInt GlobalIdsUpdater::updateGlobalIDsLocally(UInt local_nb_new_nodes) {
const auto & comm = mesh.getCommunicator();
Int nb_proc = comm.getNbProc();
- if (nb_proc == 1)
+ if (nb_proc == 1) {
return local_nb_new_nodes;
+ }
/// resize global ids array
MeshAccessor mesh_accessor(mesh);
auto && nodes_global_ids = mesh_accessor.getNodesGlobalIds();
UInt old_nb_nodes = mesh.getNbNodes() - local_nb_new_nodes;
nodes_global_ids.resize(mesh.getNbNodes(), -1);
/// compute the number of global nodes based on the number of old nodes
Vector<UInt> local_master_nodes(2, 0);
auto range_old = arange(old_nb_nodes);
local_master_nodes(0) =
aka::count_if(range_old.begin(), range_old.end(),
[&](auto && n) { return mesh.isLocalOrMasterNode(n); });
/// compute amount of local or master doubled nodes
auto range_new = arange(old_nb_nodes, mesh.getNbNodes());
local_master_nodes(1) =
aka::count_if(range_new.begin(), range_new.end(),
[&](auto && n) { return mesh.isLocalOrMasterNode(n); });
auto starting_index = local_master_nodes(1);
comm.allReduce(local_master_nodes);
UInt old_global_nodes = local_master_nodes(0);
UInt total_nb_new_nodes = local_master_nodes(1);
- if (total_nb_new_nodes == 0)
+ if (total_nb_new_nodes == 0) {
return 0;
+ }
/// set global ids of local and master nodes
comm.exclusiveScan(starting_index);
starting_index += old_global_nodes;
for (auto n : range_new) {
if (mesh.isLocalOrMasterNode(n)) {
nodes_global_ids(n) = starting_index;
++starting_index;
}
}
mesh_accessor.setNbGlobalNodes(old_global_nodes + total_nb_new_nodes);
return total_nb_new_nodes;
}
void GlobalIdsUpdater::synchronizeGlobalIDs() {
this->reduce = true;
this->synchronizer.slaveReductionOnce(*this,
SynchronizationTag::_giu_global_conn);
#ifndef AKANTU_NDEBUG
for (auto node : nodes_flags) {
auto node_flag = mesh.getNodeFlag(node.first);
- if (node_flag != NodeFlag::_pure_ghost)
+ if (node_flag != NodeFlag::_pure_ghost) {
continue;
- auto n = 0u;
+ }
+ auto n = 0U;
for (auto & pair : node.second) {
- if (std::get<1>(pair) == NodeFlag::_pure_ghost)
+ if (std::get<1>(pair) == NodeFlag::_pure_ghost) {
++n;
+ }
}
if (n == node.second.size()) {
AKANTU_DEBUG_WARNING(
"The node " << n << "is ghost on all the neighboring processors");
}
}
#endif
this->reduce = false;
this->synchronizer.synchronizeOnce(*this,
SynchronizationTag::_giu_global_conn);
}
} // namespace akantu
diff --git a/src/mesh_utils/global_ids_updater.hh b/src/mesh_utils/global_ids_updater.hh
index 2a7bee3ad..21ae2dea4 100644
--- a/src/mesh_utils/global_ids_updater.hh
+++ b/src/mesh_utils/global_ids_updater.hh
@@ -1,106 +1,106 @@
/**
* @file global_ids_updater.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Oct 02 2015
* @date last modification: Fri Dec 08 2017
*
* @brief Class that updates the global ids of new nodes that are
* inserted in the mesh. The functions in this class must be called
* after updating the node types
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_GLOBAL_IDS_UPDATER_HH__
-#define __AKANTU_GLOBAL_IDS_UPDATER_HH__
+#ifndef AKANTU_GLOBAL_IDS_UPDATER_HH_
+#define AKANTU_GLOBAL_IDS_UPDATER_HH_
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer;
} // namespace akantu
namespace akantu {
class GlobalIdsUpdater : public DataAccessor<Element> {
public:
GlobalIdsUpdater(Mesh & mesh, ElementSynchronizer & synchronizer)
: mesh(mesh), synchronizer(synchronizer) {}
/// function to update and synchronize the global connectivity of
/// new inserted nodes. It must be called after updating the node
/// types. (It calls in sequence the functions
/// updateGlobalIDsLocally and synchronizeGlobalIDs)
UInt updateGlobalIDs(UInt local_nb_new_nodes);
/// function to update the global connectivity (only locally) of new
/// inserted nodes. It must be called after updating the node types.
UInt updateGlobalIDsLocally(UInt local_nb_new_nodes);
/// function to synchronize the global connectivity of new inserted
/// nodes among the processors. It must be called after updating the
/// node types.
void synchronizeGlobalIDs();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
template <bool pack_mode>
inline void
packUnpackGlobalConnectivity(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
/// Reference to the mesh to update
Mesh & mesh;
/// distributed synchronizer to communicate the connectivity
ElementSynchronizer & synchronizer;
/// Tells if a reduction is taking place or not
bool reduce{false};
std::unordered_map<UInt, std::vector<std::pair<UInt, NodeFlag>>> nodes_flags;
};
} // namespace akantu
#include "global_ids_updater_inline_impl.hh"
-#endif /* __AKANTU_GLOBAL_IDS_UPDATER_HH__ */
+#endif /* AKANTU_GLOBAL_IDS_UPDATER_HH_ */
diff --git a/src/mesh_utils/global_ids_updater_inline_impl.hh b/src/mesh_utils/global_ids_updater_inline_impl.hh
index 1d976477c..e16393b47 100644
--- a/src/mesh_utils/global_ids_updater_inline_impl.hh
+++ b/src/mesh_utils/global_ids_updater_inline_impl.hh
@@ -1,128 +1,132 @@
/**
* @file global_ids_updater_inline_impl.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Oct 02 2015
* @date last modification: Sun Aug 13 2017
*
* @brief Implementation of the inline functions of GlobalIdsUpdater
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "global_ids_updater.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_HH__
-#define __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_HH__
+#ifndef AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_HH_
+#define AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt GlobalIdsUpdater::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
UInt size = 0;
if (tag == SynchronizationTag::_giu_global_conn) {
size +=
Mesh::getNbNodesPerElementList(elements) * sizeof(UInt) + sizeof(int);
#ifndef AKANTU_NDEBUG
size += sizeof(NodeFlag) * Mesh::getNbNodesPerElementList(elements);
#endif
}
return size;
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
- if (tag != SynchronizationTag::_giu_global_conn)
+ if (tag != SynchronizationTag::_giu_global_conn) {
return;
+ }
- auto & global_nodes_ids = mesh.getGlobalNodesIds();
+ const auto & global_nodes_ids = mesh.getGlobalNodesIds();
buffer << int(mesh.getCommunicator().whoAmI());
- for (auto & element : elements) {
+ for (const auto & element : elements) {
/// get element connectivity
const Vector<UInt> current_conn =
const_cast<const Mesh &>(mesh).getConnectivity(element);
/// loop on all connectivity nodes
for (auto node : current_conn) {
UInt index = -1;
if ((this->reduce and mesh.isLocalOrMasterNode(node)) or
(not this->reduce and not mesh.isPureGhostNode(node))) {
index = global_nodes_ids(node);
}
buffer << index;
#ifndef AKANTU_NDEBUG
buffer << mesh.getNodeFlag(node);
#endif
}
}
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
- if (tag != SynchronizationTag::_giu_global_conn)
+ if (tag != SynchronizationTag::_giu_global_conn) {
return;
+ }
MeshAccessor mesh_accessor(mesh);
auto & global_nodes_ids = mesh_accessor.getNodesGlobalIds();
int proc;
buffer >> proc;
- for (auto & element : elements) {
+ for (const auto & element : elements) {
/// get element connectivity
Vector<UInt> current_conn =
const_cast<const Mesh &>(mesh).getConnectivity(element);
/// loop on all connectivity nodes
for (auto node : current_conn) {
UInt index;
buffer >> index;
#ifndef AKANTU_NDEBUG
NodeFlag node_flag;
buffer >> node_flag;
- if (reduce)
+ if (reduce) {
nodes_flags[node].push_back(std::make_pair(proc, node_flag));
+ }
#endif
- if (index == UInt(-1))
+ if (index == UInt(-1)) {
continue;
+ }
if (mesh.isSlaveNode(node)) {
global_nodes_ids(node) = index;
mesh_accessor.setNodePrank(node, proc);
}
}
}
}
} // namespace akantu
-#endif /* __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_HH__ */
+#endif /* AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_HH_ */
diff --git a/src/mesh_utils/mesh_partition.cc b/src/mesh_utils/mesh_partition.cc
index 551f5e838..4f6c1f75a 100644
--- a/src/mesh_utils/mesh_partition.cc
+++ b/src/mesh_utils/mesh_partition.cc
@@ -1,557 +1,405 @@
/**
* @file mesh_partition.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 17 2010
* @date last modification: Wed Jan 24 2018
*
* @brief implementation of common part of all partitioner
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_partition.hh"
#include "aka_iterators.hh"
#include "aka_types.hh"
#include "mesh_accessor.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <numeric>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
-MeshPartition::MeshPartition(const Mesh & mesh, UInt spatial_dimension,
+MeshPartition::MeshPartition(Mesh & mesh, UInt spatial_dimension,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(mesh), spatial_dimension(spatial_dimension),
partitions("partition", id, memory_id),
ghost_partitions("ghost_partition", id, memory_id),
ghost_partitions_offset("ghost_partition_offset", id, memory_id),
saved_connectivity("saved_connectivity", id, memory_id) {
AKANTU_DEBUG_IN();
UInt nb_total_element = 0;
for (auto && type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
- linearized_offsets.push_back(std::make_pair(type, nb_total_element));
+ linearized_offsets.emplace_back(type, nb_total_element);
nb_total_element += mesh.getConnectivity(type).size();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MeshPartition::~MeshPartition() = default;
/* -------------------------------------------------------------------------- */
UInt MeshPartition::linearized(const Element & element) {
auto it =
std::find_if(linearized_offsets.begin(), linearized_offsets.end(),
[&element](auto & a) { return a.first == element.type; });
AKANTU_DEBUG_ASSERT(it != linearized_offsets.end(),
"A bug might be crawling around this corner...");
return (it->second + element.element);
}
/* -------------------------------------------------------------------------- */
Element MeshPartition::unlinearized(UInt lin_element) {
ElementType type{_not_defined};
UInt offset{0};
for (auto & pair : linearized_offsets) {
- if (lin_element < pair.second)
+ if (lin_element < pair.second) {
continue;
+ }
std::tie(type, offset) = pair;
}
return Element{type, lin_element - offset, _not_ghost};
}
/* -------------------------------------------------------------------------- */
/**
* conversion in c++ of the METIS_MeshToDual (mesh.c) function wrote by George
* in Metis (University of Minnesota)
*/
void MeshPartition::buildDualGraph(
Array<Int> & dxadj, Array<Int> & dadjncy, Array<Int> & edge_loads,
- std::function<Int(const Element &, const Element &)> edge_load_func,
+ const std::function<Int(const Element &, const Element &)> &edge_load_func,
Array<Int> & vertex_loads,
- std::function<Int(const Element &)> vertex_load_func) {
+ const std::function<Int(const Element &)> &vertex_load_func) {
CSR<Element> nodes_to_elements;
MeshUtils::buildNode2Elements(mesh, nodes_to_elements);
std::unordered_map<UInt, std::vector<UInt>> adjacent_elements;
// for each elements look for its connected elements
for_each_element(
mesh,
[&](auto && element) {
- const auto & conn = mesh.getConnectivity(element);
+ const auto & conn = const_cast<const Mesh &>(mesh).getConnectivity(element);
std::map<Element, UInt> hits;
// count the number of nodes shared with a given element
for (auto && node : conn) {
for (auto && connected_element : nodes_to_elements.getRow(node)) {
++hits[connected_element];
}
}
// define a minumum number of nodes to share to be considered as a
// ajacent element
UInt magic_number{conn.size()};
for (auto n : arange(mesh.getNbFacetTypes(element.type))) {
magic_number = std::min(
mesh.getNbNodesPerElement(mesh.getFacetType(element.type, n)),
magic_number);
}
// check all neighbors to see which ones are "adjacent"
for (auto && data : hits) {
const auto & adjacent_element = data.first;
// not adjacent to miself
- if (adjacent_element == element)
+ if (adjacent_element == element) {
continue;
+ }
// not enough shared nodes
- if (data.second < magic_number)
+ if (data.second < magic_number) {
continue;
+ }
/// Patch in order to prevent neighboring cohesive elements
/// from detecting each other
#if defined(AKANTU_COHESIVE_ELEMENT)
auto element_kind = element.kind();
auto adjacent_element_kind = adjacent_element.kind();
if (element_kind == adjacent_element_kind &&
- element_kind == _ek_cohesive)
+ element_kind == _ek_cohesive) {
continue;
+ }
#endif
adjacent_elements[this->linearized(element)].push_back(
this->linearized(adjacent_element));
}
},
_spatial_dimension = mesh.getSpatialDimension(),
_element_kind = _ek_not_defined);
// prepare the arrays
auto nb_elements{adjacent_elements.size()};
dxadj.resize(nb_elements + 1);
vertex_loads.resize(nb_elements);
for (auto && data : adjacent_elements) {
const auto & element{data.first};
const auto & neighbors{data.second};
dxadj[element] = neighbors.size();
}
/// convert the dxadj array of sizes in a csr one of offsets
- for (UInt i = 1; i < nb_elements; ++i)
+ for (UInt i = 1; i < nb_elements; ++i) {
dxadj(i) += dxadj(i - 1);
- for (UInt i = nb_elements; i > 0; --i)
+ }
+ for (UInt i = nb_elements; i > 0; --i) {
dxadj(i) = dxadj(i - 1);
+ }
dxadj(0) = 0;
dadjncy.resize(dxadj(nb_elements));
edge_loads.resize(dadjncy.size());
// fill the different arrays
for (auto && data : adjacent_elements) {
const auto & element{data.first};
const auto & neighbors{data.second};
auto unlinearized_element = unlinearized(element);
vertex_loads(element) = vertex_load_func(unlinearized_element);
auto pos = dxadj(element);
for (auto && neighbor : neighbors) {
dadjncy(pos) = neighbor;
edge_loads(pos) =
edge_load_func(unlinearized_element, unlinearized(neighbor));
++pos;
}
}
}
-/* -------------------------------------------------------------------------- */
-/**
- * TODO this function should most probably be rewritten in a more modern way
- * conversion in c++ of the GENDUALMETIS (mesh.c) function wrote by George in
- * Metis (University of Minnesota)
- */
-// void MeshPartition::buildDualGraph(
-// Array<Int> & dxadj, Array<Int> & dadjncy, Array<Int> & edge_loads,
-// std::function<Int(const Element &, const Element &)> edge_load_func,
-// Array<Int> & vertex_loads,
-// std::function<Int(const Element &)> vertex_load_func) {
-// AKANTU_DEBUG_IN();
-
-// std::map<ElementType, std::tuple<const Array<UInt> *, UInt, UInt>>
-// connectivities;
-// UInt spatial_dimension = mesh.getSpatialDimension();
-// UInt nb_total_element{0};
-
-// for (auto & type :
-// mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
-// auto type_p1 = mesh.getP1ElementType(type);
-// auto nb_nodes_per_element_p1 = mesh.getNbNodesPerElement(type_p1);
-// const auto & conn = mesh.getConnectivity(type, _not_ghost);
-
-// for (auto n : arange(mesh.getNbFacetTypes(type_p1))) {
-// auto magic_number =
-// mesh.getNbNodesPerElement(mesh.getFacetType(type_p1, n));
-// connectivities[type] =
-// std::make_tuple(&conn, nb_nodes_per_element_p1, magic_number);
-// }
-
-// nb_total_element += conn.size();
-// }
-
-// CSR<Element> node_to_elem;
-// MeshUtils::buildNode2Elements(mesh, node_to_elem);
-
-// dxadj.resize(nb_total_element + 1);
-// /// initialize the dxadj array
-// auto dxadj_it = dxadj.begin();
-// for (auto & pair : connectivities) {
-// const auto & connectivity = *std::get<0>(pair.second);
-// auto nb_nodes_per_element_p1 = std::get<1>(pair.second);
-
-// std::fill_n(dxadj_it, connectivity.size(), nb_nodes_per_element_p1);
-// dxadj_it += connectivity.size();
-// }
-
-// /// convert the dxadj_val array in a csr one
-// for (UInt i = 1; i < nb_total_element; ++i)
-// dxadj(i) += dxadj(i - 1);
-// for (UInt i = nb_total_element; i > 0; --i)
-// dxadj(i) = dxadj(i - 1);
-// dxadj(0) = 0;
-
-// dadjncy.resize(2 * dxadj(nb_total_element));
-
-// /// weight map to determine adjacency
-// std::unordered_map<UInt, UInt> weight_map;
-
-// for (auto & pair : connectivities) {
-// auto type = pair.first;
-// const auto & connectivity = *std::get<0>(pair.second);
-// auto nb_nodes_per_element = std::get<1>(pair.second);
-// auto magic_number = std::get<2>(pair.second);
-
-// Element element{type, 0, _not_ghost};
-
-// for (const auto & conn :
-// make_view(connectivity, connectivity.getNbComponent())) {
-// auto linearized_el = linearized(element);
-
-// /// fill the weight map
-// for (UInt n : arange(nb_nodes_per_element)) {
-// auto && node = conn(n);
-
-// for (auto k = node_to_elem.rbegin(node); k !=
-// node_to_elem.rend(node);
-// --k) {
-// auto & current_element = *k;
-// auto current_el = linearized(current_element);
-// AKANTU_DEBUG_ASSERT(current_el != UInt(-1),
-// "Linearized element not found");
-// if (current_el <= linearized_el)
-// break;
-
-// auto weight_map_insert =
-// weight_map.insert(std::make_pair(current_el, 1));
-// if (not weight_map_insert.second)
-// (weight_map_insert.first->second)++;
-// }
-// }
-
-// /// each element with a weight of the size of a facet are adjacent
-// for (auto & weight_pair : weight_map) {
-// auto & adjacent_el = weight_pair.first;
-// auto magic = weight_pair.second;
-// if (magic != magic_number)
-// continue;
-
-// #if defined(AKANTU_COHESIVE_ELEMENT)
-// /// Patch in order to prevent neighboring cohesive elements
-// /// from detecting each other
-// auto adjacent_element = unlinearized(adjacent_el);
-
-// auto el_kind = element.kind();
-// auto adjacent_el_kind = adjacent_element.kind();
-
-// if (el_kind == adjacent_el_kind && el_kind == _ek_cohesive)
-// continue;
-// #endif
-// UInt index_adj = dxadj(adjacent_el)++;
-// UInt index_lin = dxadj(linearized_el)++;
-
-// dadjncy(index_lin) = adjacent_el;
-// dadjncy(index_adj) = linearized_el;
-// }
-
-// element.element++;
-// weight_map.clear();
-// }
-// }
-
-// Int k_start = 0, linerized_el = 0, j = 0;
-// for (auto & pair : connectivities) {
-// const auto & connectivity = *std::get<0>(pair.second);
-// auto nb_nodes_per_element_p1 = std::get<1>(pair.second);
-// auto nb_element = connectivity.size();
-
-// for (UInt el = 0; el < nb_element; ++el, ++linerized_el) {
-// for (Int k = k_start; k < dxadj(linerized_el); ++k, ++j)
-// dadjncy(j) = dadjncy(k);
-// dxadj(linerized_el) = j;
-// k_start += nb_nodes_per_element_p1;
-// }
-// }
-
-// for (UInt i = nb_total_element; i > 0; --i)
-// dxadj(i) = dxadj(i - 1);
-// dxadj(0) = 0;
-
-// vertex_loads.resize(dxadj.size() - 1);
-// edge_loads.resize(dadjncy.size());
-// UInt adj = 0;
-// for (UInt i = 0; i < nb_total_element; ++i) {
-// auto el = unlinearized(i);
-// vertex_loads(i) = vertex_load_func(el);
-
-// UInt nb_adj = dxadj(i + 1) - dxadj(i);
-// for (UInt j = 0; j < nb_adj; ++j, ++adj) {
-// auto el_adj_id = dadjncy(dxadj(i) + j);
-// auto el_adj = unlinearized(el_adj_id);
-
-// Int load = edge_load_func(el, el_adj);
-// edge_loads(adj) = load;
-// }
-// }
-
-// AKANTU_DEBUG_OUT();
-// }
/* -------------------------------------------------------------------------- */
void MeshPartition::fillPartitionInformation(
const Mesh & mesh, const Int * linearized_partitions) {
AKANTU_DEBUG_IN();
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem);
UInt linearized_el = 0;
- for (auto & type :
+ for (const auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto & partition = partitions.alloc(nb_element, 1, type, _not_ghost);
auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
auto & ghost_partition_offset =
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
auto & ghost_partition = ghost_partitions.alloc(0, 1, type, _ghost);
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
auto conn_it = connectivity.begin(connectivity.getNbComponent());
for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
UInt part = linearized_partitions[linearized_el];
partition(el) = part;
std::list<UInt> list_adj_part;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
auto conn = Vector<UInt>(*(conn_it + el));
UInt node = conn(n);
for (const auto & adj_element : node_to_elem.getRow(node)) {
UInt adj_el = linearized(adj_element);
UInt adj_part = linearized_partitions[adj_el];
if (part != adj_part) {
list_adj_part.push_back(adj_part);
}
}
}
list_adj_part.sort();
list_adj_part.unique();
for (auto & adj_part : list_adj_part) {
ghost_part_csr.getRows().push_back(adj_part);
ghost_part_csr.rowOffset(el)++;
ghost_partition.push_back(adj_part);
ghost_partition_offset(el)++;
}
}
ghost_part_csr.countToCSR();
/// convert the ghost_partitions_offset array in an offset array
auto & ghost_partitions_offset_ptr = ghost_partitions_offset(type, _ghost);
- for (UInt i = 1; i < nb_element; ++i)
+ for (UInt i = 1; i < nb_element; ++i) {
ghost_partitions_offset_ptr(i) += ghost_partitions_offset_ptr(i - 1);
- for (UInt i = nb_element; i > 0; --i)
+ }
+ for (UInt i = nb_element; i > 0; --i) {
ghost_partitions_offset_ptr(i) = ghost_partitions_offset_ptr(i - 1);
+ }
ghost_partitions_offset_ptr(0) = 0;
}
// All Facets
for (Int sp = spatial_dimension - 1; sp >= 0; --sp) {
- for (auto & type : mesh.elementTypes(sp, _not_ghost, _ek_not_defined)) {
+ for (const auto & type : mesh.elementTypes(sp, _not_ghost, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type);
auto & partition = partitions.alloc(nb_element, 1, type, _not_ghost);
AKANTU_DEBUG_INFO("Allocating partitions for " << type);
auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
auto & ghost_partition_offset =
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
auto & ghost_partition = ghost_partitions.alloc(0, 1, type, _ghost);
AKANTU_DEBUG_INFO("Allocating ghost_partitions for " << type);
const Array<std::vector<Element>> & elem_to_subelem =
mesh.getElementToSubelement(type, _not_ghost);
// Facet loop
for (UInt i(0); i < mesh.getNbElement(type, _not_ghost); ++i) {
const auto & adjacent_elems = elem_to_subelem(i);
if (adjacent_elems.empty()) {
partition(i) = 0;
continue;
}
Element min_elem{_max_element_type, std::numeric_limits<UInt>::max(),
*(ghost_type_t{}.end())};
UInt min_part(std::numeric_limits<UInt>::max());
std::set<UInt> adjacent_parts;
for (auto adj_elem : adjacent_elems) {
if (adj_elem == ElementNull) { // case of boundary elements
continue;
}
auto adjacent_elem_part = partitions(adj_elem);
if (adjacent_elem_part < min_part) {
min_part = adjacent_elem_part;
min_elem = adj_elem;
}
adjacent_parts.insert(adjacent_elem_part);
}
partition(i) = min_part;
auto git = ghost_partitions_csr(min_elem.type, _not_ghost)
.begin(min_elem.element);
auto gend = ghost_partitions_csr(min_elem.type, _not_ghost)
.end(min_elem.element);
for (; git != gend; ++git) {
adjacent_parts.insert(*git);
}
adjacent_parts.erase(min_part);
- for (auto & part : adjacent_parts) {
+ for (const auto & part : adjacent_parts) {
ghost_part_csr.getRows().push_back(part);
ghost_part_csr.rowOffset(i)++;
ghost_partition.push_back(part);
}
ghost_partition_offset(i + 1) =
ghost_partition_offset(i + 1) + adjacent_elems.size();
}
ghost_part_csr.countToCSR();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::tweakConnectivity() {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
for (auto && type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
auto & connectivity = mesh_accessor.getConnectivity(type, _not_ghost);
auto & saved_conn = saved_connectivity.alloc(
connectivity.size(), connectivity.getNbComponent(), type, _not_ghost);
saved_conn.copy(connectivity);
for (auto && conn :
make_view(connectivity, connectivity.getNbComponent())) {
for (auto && node : conn) {
if (mesh.isPeriodicSlave(node)) {
node = mesh.getPeriodicMaster(node);
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::restoreConnectivity() {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
for (auto && type : saved_connectivity.elementTypes(
spatial_dimension, _not_ghost, _ek_not_defined)) {
auto & conn = mesh_accessor.getConnectivity(type, _not_ghost);
auto & saved_conn = saved_connectivity(type, _not_ghost);
conn.copy(saved_conn);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-bool MeshPartition::hasPartitions(const ElementType & type,
- const GhostType & ghost_type) {
+bool MeshPartition::hasPartitions(ElementType type,
+ GhostType ghost_type) {
return partitions.exists(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
void MeshPartition::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "MeshPartition ["
<< "\n";
stream << space << " + id : " << id << "\n";
stream << space << " + nb partitions: " << nb_partitions << "\n";
stream << space << " + partitions [ "
<< "\n";
partitions.printself(stream, indent + 2);
stream << space << " ]"
<< "\n";
stream << space << "]"
<< "\n";
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/mesh_utils/mesh_partition.hh b/src/mesh_utils/mesh_partition.hh
index e44f498d8..623854832 100644
--- a/src/mesh_utils/mesh_partition.hh
+++ b/src/mesh_utils/mesh_partition.hh
@@ -1,152 +1,151 @@
/**
* @file mesh_partition.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Jan 23 2018
*
* @brief tools to partitionate a mesh
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-
-/* -------------------------------------------------------------------------- */
-
-#ifndef __AKANTU_MESH_PARTITION_HH__
-#define __AKANTU_MESH_PARTITION_HH__
-
/* -------------------------------------------------------------------------- */
#include "aka_csr.hh"
-#include "aka_memory.hh"
#include "mesh.hh"
-
/* -------------------------------------------------------------------------- */
+#ifndef AKANTU_MESH_PARTITION_HH_
+#define AKANTU_MESH_PARTITION_HH_
+
+
namespace akantu {
class MeshPartition : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- MeshPartition(const Mesh & mesh, UInt spatial_dimension,
+ MeshPartition(Mesh & mesh, UInt spatial_dimension,
const ID & id = "MeshPartitioner",
const MemoryID & memory_id = 0);
~MeshPartition() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// define a partition of the mesh
virtual void partitionate(
UInt nb_part,
- std::function<Int(const Element &, const Element &)> edge_load_func =
- [](auto &&, auto &&) { return 1; },
- std::function<Int(const Element &)> vertex_load_func =
- [](auto &&) { return 1; }) = 0;
+ const std::function<Int(const Element &, const Element &)> &
+ edge_load_func =
+ [](auto && /*unused*/, auto && /*unused*/) { return 1; },
+ const std::function<Int(const Element &)> & vertex_load_func =
+ [](auto && /*unused*/) { return 1; }) = 0;
/// reorder the nodes to reduce the filling during the factorization of a
/// matrix that has a profil based on the connectivity of the mesh
virtual void reorder() = 0;
/// fill the partitions array with a given linearized partition information
void fillPartitionInformation(const Mesh & mesh,
const Int * linearized_partitions);
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// build the dual graph of the mesh, for all element of spatial_dimension
- void buildDualGraph(
- Array<Int> & dxadj, Array<Int> & dadjncy, Array<Int> & edge_loads,
- std::function<Int(const Element &, const Element &)> edge_load_func,
- Array<Int> & vertex_loads,
- std::function<Int(const Element &)> vertex_load_func);
+ void
+ buildDualGraph(Array<Int> & dxadj, Array<Int> & dadjncy,
+ Array<Int> & edge_loads,
+ const std::function<Int(const Element &, const Element &)> &
+ edge_load_func,
+ Array<Int> & vertex_loads,
+ const std::function<Int(const Element &)> & vertex_load_func);
/// tweak the mesh to handle the PBC pairs
void tweakConnectivity();
/// restore the mesh that has been tweaked
void restoreConnectivity();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
- bool hasPartitions(const ElementType & type, const GhostType & ghost_type);
+ bool hasPartitions(ElementType type, GhostType ghost_type);
AKANTU_GET_MACRO(Partitions, partitions, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Partition, partitions, UInt);
AKANTU_GET_MACRO(GhostPartitionCSR, ghost_partitions_csr,
const ElementTypeMap<CSR<UInt>> &);
AKANTU_GET_MACRO(NbPartition, nb_partitions, UInt);
AKANTU_SET_MACRO(NbPartition, nb_partitions, UInt);
protected:
UInt linearized(const Element & element);
Element unlinearized(UInt lin_element);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id
std::string id;
/// the mesh to partition
- const Mesh & mesh;
+ Mesh & mesh;
/// dimension of the elements to consider in the mesh
UInt spatial_dimension;
/// number of partitions
UInt nb_partitions;
/// partition numbers
ElementTypeMapArray<UInt> partitions;
ElementTypeMap<CSR<UInt>> ghost_partitions_csr;
ElementTypeMapArray<UInt> ghost_partitions;
ElementTypeMapArray<UInt> ghost_partitions_offset;
Array<UInt> * permutation;
ElementTypeMapArray<UInt> saved_connectivity;
// vector of pair to ensure the iteration order
std::vector<std::pair<ElementType, UInt>> linearized_offsets;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const MeshPartition & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#ifdef AKANTU_USE_SCOTCH
#include "mesh_partition_scotch.hh"
#endif
-#endif /* __AKANTU_MESH_PARTITION_HH__ */
+#endif /* AKANTU_MESH_PARTITION_HH_ */
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
index 60af3884f..a2c871d2a 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
+++ b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
@@ -1,139 +1,140 @@
/**
* @file mesh_partition_mesh_data.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Tue Feb 20 2018
*
* @brief implementation of the MeshPartitionMeshData class
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "mesh_partition_mesh_data.hh"
#if !defined(AKANTU_NDEBUG)
#include <set>
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
-MeshPartitionMeshData::MeshPartitionMeshData(const Mesh & mesh,
+MeshPartitionMeshData::MeshPartitionMeshData(Mesh & mesh,
UInt spatial_dimension,
const ID & id,
const MemoryID & memory_id)
: MeshPartition(mesh, spatial_dimension, id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MeshPartitionMeshData::MeshPartitionMeshData(
- const Mesh & mesh, const ElementTypeMapArray<UInt> & mapping,
+ Mesh & mesh, const ElementTypeMapArray<UInt> & mapping,
UInt spatial_dimension, const ID & id, const MemoryID & memory_id)
: MeshPartition(mesh, spatial_dimension, id, memory_id),
partition_mapping(&mapping) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::partitionate(
- UInt nb_part, std::function<Int(const Element &, const Element &)>,
- std::function<Int(const Element &)>) {
+ UInt nb_part,
+ const std::function<Int(const Element &, const Element &)> &/*edge_load_func*/,
+ const std::function<Int(const Element &)> &/*vertex_load_func*/) {
AKANTU_DEBUG_IN();
if (mesh.isPeriodic()) {
tweakConnectivity();
}
nb_partitions = nb_part;
auto ghost_type = _not_ghost;
auto spatial_dimension = mesh.getSpatialDimension();
UInt linearized_el = 0;
auto nb_elements = mesh.getNbElement(mesh.getSpatialDimension(), ghost_type);
- auto partition_list = new Int[nb_elements];
+ auto *partition_list = new Int[nb_elements];
#if !defined(AKANTU_NDEBUG)
std::set<UInt> partitions;
#endif
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
const auto & partition_array = (*partition_mapping)(type, ghost_type);
AKANTU_DEBUG_ASSERT(partition_array.size() ==
mesh.getNbElement(type, ghost_type),
"The partition mapping does not have the right number "
<< "of entries for type " << type
<< " and ghost type " << ghost_type << "."
<< " Tags=" << partition_array.size()
<< " Mesh=" << mesh.getNbElement(type, ghost_type));
for (auto && part : partition_array) {
partition_list[linearized_el] = part;
#if !defined(AKANTU_NDEBUG)
partitions.insert(part);
#endif
++linearized_el;
}
}
#if !defined(AKANTU_NDEBUG)
AKANTU_DEBUG_ASSERT(partitions.size() == nb_part,
"The number of real partitions does not match with the "
"number of asked partitions");
#endif
fillPartitionInformation(mesh, partition_list);
delete[] partition_list;
if (mesh.isPeriodic()) {
restoreConnectivity();
}
AKANTU_DEBUG_OUT();
} // namespace akantu
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::reorder() { AKANTU_TO_IMPLEMENT(); }
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::setPartitionMapping(
const ElementTypeMapArray<UInt> & mapping) {
partition_mapping = &mapping;
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::setPartitionMappingFromMeshData(
const std::string & data_name) {
partition_mapping = &(mesh.getData<UInt>(data_name));
}
} // namespace akantu
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
index ab32c101c..0497f0de4 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
+++ b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
@@ -1,94 +1,94 @@
/**
* @file mesh_partition_mesh_data.hh
*
* @author Dana Christen <dana.christen@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief mesh partitioning based on data provided in the mesh
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_PARTITION_MESH_DATA_HH__
-#define __AKANTU_MESH_PARTITION_MESH_DATA_HH__
+#ifndef AKANTU_MESH_PARTITION_MESH_DATA_HH_
+#define AKANTU_MESH_PARTITION_MESH_DATA_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_partition.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartitionMeshData : public MeshPartition {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- MeshPartitionMeshData(const Mesh & mesh, UInt spatial_dimension,
+ MeshPartitionMeshData(Mesh & mesh, UInt spatial_dimension,
const ID & id = "MeshPartitionerMeshData",
const MemoryID & memory_id = 0);
- MeshPartitionMeshData(const Mesh & mesh,
+ MeshPartitionMeshData(Mesh & mesh,
const ElementTypeMapArray<UInt> & mapping,
UInt spatial_dimension,
const ID & id = "MeshPartitionerMeshData",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void partitionate(
UInt nb_part,
- std::function<Int(const Element &, const Element &)> edge_load_func =
- [](auto &&, auto &&) { return 1; },
- std::function<Int(const Element &)> vertex_load_func =
- [](auto &&) { return 1; }) override;
+ const std::function<Int(const Element &, const Element &)> &edge_load_func =
+ [](auto && /*unused*/, auto && /*unused*/) { return 1; },
+ const std::function<Int(const Element &)> &vertex_load_func =
+ [](auto && /*unused*/) { return 1; }) override;
void reorder() override;
void setPartitionMapping(const ElementTypeMapArray<UInt> & mapping);
void setPartitionMappingFromMeshData(const std::string & data_name);
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const ElementTypeMapArray<UInt> * partition_mapping;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_MESH_PARTITION_MESH_DATA_HH__ */
+#endif /* AKANTU_MESH_PARTITION_MESH_DATA_HH_ */
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc b/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
index 34ae90d39..7e2848937 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
+++ b/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
@@ -1,463 +1,472 @@
/**
* @file mesh_partition_scotch.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief implementation of the MeshPartitionScotch class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_partition_scotch.hh"
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "aka_static_if.hh"
+#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <cstdio>
#include <fstream>
/* -------------------------------------------------------------------------- */
#if !defined(AKANTU_USE_PTSCOTCH)
#ifndef AKANTU_SCOTCH_NO_EXTERN
extern "C" {
#endif // AKANTU_SCOTCH_NO_EXTERN
#include <scotch.h>
#ifndef AKANTU_SCOTCH_NO_EXTERN
}
#endif // AKANTU_SCOTCH_NO_EXTERN
#else // AKANTU_USE_PTSCOTCH
#include <ptscotch.h>
#endif // AKANTU_USE_PTSCOTCH
namespace akantu {
namespace {
constexpr int scotch_version = int(SCOTCH_VERSION);
}
/* -------------------------------------------------------------------------- */
-MeshPartitionScotch::MeshPartitionScotch(const Mesh & mesh,
- UInt spatial_dimension, const ID & id,
+MeshPartitionScotch::MeshPartitionScotch(Mesh & mesh, UInt spatial_dimension,
+ const ID & id,
const MemoryID & memory_id)
: MeshPartition(mesh, spatial_dimension, id, memory_id) {
AKANTU_DEBUG_IN();
// check if the akantu types and Scotch one are consistent
static_assert(
sizeof(Int) == sizeof(SCOTCH_Num),
"The integer type of Akantu does not match the one from Scotch");
static_if(aka::bool_constant<scotch_version >= 6>{})
.then([](auto && y) { SCOTCH_randomSeed(y); })
.else_([](auto && y) { srandom(y); })(
std::forward<UInt>(RandomGenerator<UInt>::seed()));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
static SCOTCH_Mesh * createMesh(const Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes = mesh.getNbNodes();
UInt total_nb_element = 0;
UInt nb_edge = 0;
- for (auto & type : mesh.elementTypes(spatial_dimension)) {
+ for (const auto & type : mesh.elementTypes(spatial_dimension)) {
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
total_nb_element += nb_element;
nb_edge += nb_element * nb_nodes_per_element;
}
SCOTCH_Num vnodbas = 0;
SCOTCH_Num vnodnbr = nb_nodes;
SCOTCH_Num velmbas = vnodnbr;
SCOTCH_Num velmnbr = total_nb_element;
auto * verttab = new SCOTCH_Num[vnodnbr + velmnbr + 1];
SCOTCH_Num * vendtab = verttab + 1;
SCOTCH_Num * velotab = nullptr;
SCOTCH_Num * vnlotab = nullptr;
SCOTCH_Num * vlbltab = nullptr;
memset(verttab, 0, (vnodnbr + velmnbr + 1) * sizeof(SCOTCH_Num));
- for (auto & type : mesh.elementTypes(spatial_dimension)) {
- if (Mesh::getSpatialDimension(type) != spatial_dimension)
+ for (const auto & type : mesh.elementTypes(spatial_dimension)) {
+ if (Mesh::getSpatialDimension(type) != spatial_dimension) {
continue;
+ }
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
/// count number of occurrence of each node
for (UInt el = 0; el < nb_element; ++el) {
UInt * conn_val = connectivity.storage() + el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
verttab[*(conn_val++)]++;
}
}
}
/// convert the occurrence array in a csr one
- for (UInt i = 1; i < nb_nodes; ++i)
+ for (UInt i = 1; i < nb_nodes; ++i) {
verttab[i] += verttab[i - 1];
- for (UInt i = nb_nodes; i > 0; --i)
+ }
+ for (UInt i = nb_nodes; i > 0; --i) {
verttab[i] = verttab[i - 1];
+ }
verttab[0] = 0;
/// rearrange element to get the node-element list
SCOTCH_Num edgenbr = verttab[vnodnbr] + nb_edge;
auto * edgetab = new SCOTCH_Num[edgenbr];
UInt linearized_el = 0;
- for (auto & type : mesh.elementTypes(spatial_dimension)) {
- UInt nb_element = mesh.getNbElement(type);
- UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
- const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
+ for (const auto & type : mesh.elementTypes(spatial_dimension)) {
+ auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
+ const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
- for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
- UInt * conn_val = connectivity.storage() + el * nb_nodes_per_element;
- for (UInt n = 0; n < nb_nodes_per_element; ++n)
- edgetab[verttab[*(conn_val++)]++] = linearized_el + velmbas;
+ for (auto && conn : make_view(connectivity, nb_nodes_per_element)) {
+ for (auto c : conn) {
+ edgetab[verttab[c]++] = linearized_el + velmbas;
+ }
+ ++linearized_el;
}
}
- for (UInt i = nb_nodes; i > 0; --i)
+ for (UInt i = nb_nodes; i > 0; --i) {
verttab[i] = verttab[i - 1];
+ }
verttab[0] = 0;
SCOTCH_Num * verttab_tmp = verttab + vnodnbr + 1;
SCOTCH_Num * edgetab_tmp = edgetab + verttab[vnodnbr];
- for (auto & type : mesh.elementTypes(spatial_dimension)) {
- UInt nb_element = mesh.getNbElement(type);
- UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
-
- const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
+ for (const auto & type : mesh.elementTypes(spatial_dimension)) {
+ auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
+ const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
- for (UInt el = 0; el < nb_element; ++el) {
+ for (auto && conn : make_view(connectivity, nb_nodes_per_element)) {
*verttab_tmp = *(verttab_tmp - 1) + nb_nodes_per_element;
verttab_tmp++;
- UInt * conn = connectivity.storage() + el * nb_nodes_per_element;
- for (UInt i = 0; i < nb_nodes_per_element; ++i) {
- *(edgetab_tmp++) = *(conn++) + vnodbas;
+
+ for (auto c : conn) {
+ *(edgetab_tmp++) = c + vnodbas;
}
}
}
auto * meshptr = new SCOTCH_Mesh;
SCOTCH_meshInit(meshptr);
SCOTCH_meshBuild(meshptr, velmbas, vnodbas, velmnbr, vnodnbr, verttab,
vendtab, velotab, vnlotab, vlbltab, edgenbr, edgetab);
/// Check the mesh
AKANTU_DEBUG_ASSERT(SCOTCH_meshCheck(meshptr) == 0,
"Scotch mesh is not consistent");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save initial graph
FILE * fmesh = fopen("ScotchMesh.msh", "w");
SCOTCH_meshSave(meshptr, fmesh);
fclose(fmesh);
/// write geometry file
std::ofstream fgeominit;
fgeominit.open("ScotchMesh.xyz");
fgeominit << spatial_dimension << std::endl << nb_nodes << std::endl;
const Array<Real> & nodes = mesh.getNodes();
Real * nodes_val = nodes.storage();
for (UInt i = 0; i < nb_nodes; ++i) {
fgeominit << i << " ";
- for (UInt s = 0; s < spatial_dimension; ++s)
+ for (UInt s = 0; s < spatial_dimension; ++s) {
fgeominit << *(nodes_val++) << " ";
+ }
fgeominit << std::endl;
;
}
fgeominit.close();
}
#endif
AKANTU_DEBUG_OUT();
return meshptr;
}
/* -------------------------------------------------------------------------- */
static void destroyMesh(SCOTCH_Mesh * meshptr) {
AKANTU_DEBUG_IN();
- SCOTCH_Num velmbas, vnodbas, vnodnbr, velmnbr, *verttab, *vendtab, *velotab,
- *vnlotab, *vlbltab, edgenbr, *edgetab, degrptr;
+ SCOTCH_Num velmbas;
+ SCOTCH_Num vnodbas;
+ SCOTCH_Num vnodnbr;
+ SCOTCH_Num velmnbr;
+ SCOTCH_Num * verttab;
+ SCOTCH_Num * vendtab;
+ SCOTCH_Num * velotab;
+ SCOTCH_Num * vnlotab;
+ SCOTCH_Num * vlbltab;
+ SCOTCH_Num edgenbr;
+ SCOTCH_Num * edgetab;
+ SCOTCH_Num degrptr;
SCOTCH_meshData(meshptr, &velmbas, &vnodbas, &velmnbr, &vnodnbr, &verttab,
&vendtab, &velotab, &vnlotab, &vlbltab, &edgenbr, &edgetab,
&degrptr);
delete[] verttab;
delete[] edgetab;
SCOTCH_meshExit(meshptr);
delete meshptr;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionScotch::partitionate(
UInt nb_part,
- std::function<Int(const Element &, const Element &)> edge_load_func,
- std::function<Int(const Element &)> vertex_load_func) {
+ const std::function<Int(const Element &, const Element &)> & edge_load_func,
+ const std::function<Int(const Element &)> & vertex_load_func) {
AKANTU_DEBUG_IN();
nb_partitions = nb_part;
if (mesh.isPeriodic()) {
tweakConnectivity();
}
AKANTU_DEBUG_INFO("Partitioning the mesh " << mesh.getID() << " in "
<< nb_part << " parts.");
Array<Int> dxadj;
Array<Int> dadjncy;
Array<Int> edge_loads;
Array<Int> vertex_loads;
buildDualGraph(dxadj, dadjncy, edge_loads, edge_load_func, vertex_loads,
vertex_load_func);
/// variables that will hold our structures in scotch format
SCOTCH_Graph scotch_graph;
SCOTCH_Strat scotch_strat;
/// description number and arrays for struct mesh for scotch
SCOTCH_Num baseval = 0; // base numbering for element and
// nodes (0 -> C , 1 -> fortran)
SCOTCH_Num vertnbr = dxadj.size() - 1; // number of vertexes
SCOTCH_Num * parttab; // array of partitions
SCOTCH_Num edgenbr = dxadj(vertnbr); // twice the number of "edges"
//(an "edge" bounds two nodes)
SCOTCH_Num * verttab = dxadj.storage(); // array of start indices in edgetab
SCOTCH_Num * vendtab = nullptr; // array of after-last indices in edgetab
SCOTCH_Num * velotab =
vertex_loads.storage(); // integer load associated with
// every vertex ( optional )
SCOTCH_Num * edlotab = edge_loads.storage(); // integer load associated with
// every edge ( optional )
SCOTCH_Num * edgetab = dadjncy.storage(); // adjacency array of every vertex
SCOTCH_Num * vlbltab = nullptr; // vertex label array (optional)
/// Allocate space for Scotch arrays
parttab = new SCOTCH_Num[vertnbr];
/// Initialize the strategy structure
SCOTCH_stratInit(&scotch_strat);
/// Initialize the graph structure
SCOTCH_graphInit(&scotch_graph);
/// Build the graph from the adjacency arrays
SCOTCH_graphBuild(&scotch_graph, baseval, vertnbr, verttab, vendtab, velotab,
vlbltab, edgenbr, edgetab, edlotab);
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save initial graph
FILE * fgraphinit = fopen("GraphIniFile.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraphinit);
fclose(fgraphinit);
/// write geometry file
std::ofstream fgeominit;
fgeominit.open("GeomIniFile.xyz");
fgeominit << spatial_dimension << std::endl << vertnbr << std::endl;
const Array<Real> & nodes = mesh.getNodes();
auto nodes_it = nodes.begin(spatial_dimension);
UInt out_linerized_el = 0;
- for (auto & type :
+ for (const auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
- UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Vector<Real> mid(spatial_dimension);
- for (UInt el = 0; el < nb_element; ++el) {
+ for (auto && conn : make_view(connectivity, nb_nodes_per_element)) {
mid.set(0.);
- for (UInt n = 0; n < nb_nodes_per_element; ++n) {
- UInt node = connectivity.storage()[nb_nodes_per_element * el + n];
+ for (auto node : conn) {
mid += Vector<Real>(nodes_it[node]);
}
mid /= nb_nodes_per_element;
fgeominit << out_linerized_el++ << " ";
- for (UInt s = 0; s < spatial_dimension; ++s)
+ for (UInt s = 0; s < spatial_dimension; ++s) {
fgeominit << mid[s] << " ";
+ }
fgeominit << std::endl;
;
}
}
fgeominit.close();
}
#endif
/// Check the graph
AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
"Graph to partition is not consistent");
/// Partition the mesh
SCOTCH_graphPart(&scotch_graph, nb_part, &scotch_strat, parttab);
/// Check the graph
AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
"Partitioned graph is not consistent");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save the partitioned graph
FILE * fgraph = fopen("GraphFile.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraph);
fclose(fgraph);
/// save the partition map
std::ofstream fmap;
fmap.open("MapFile.map");
fmap << vertnbr << std::endl;
- for (Int i = 0; i < vertnbr; i++)
+ for (Int i = 0; i < vertnbr; i++) {
fmap << i << " " << parttab[i] << std::endl;
+ }
fmap.close();
}
#endif
/// free the scotch data structures
SCOTCH_stratExit(&scotch_strat);
SCOTCH_graphFree(&scotch_graph);
SCOTCH_graphExit(&scotch_graph);
fillPartitionInformation(mesh, parttab);
delete[] parttab;
if (mesh.isPeriodic()) {
restoreConnectivity();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionScotch::reorder() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Reordering the mesh " << mesh.getID());
SCOTCH_Mesh * scotch_mesh = createMesh(mesh);
UInt nb_nodes = mesh.getNbNodes();
SCOTCH_Strat scotch_strat;
// SCOTCH_Ordering scotch_order;
auto * permtab = new SCOTCH_Num[nb_nodes];
SCOTCH_Num * peritab = nullptr;
SCOTCH_Num cblknbr = 0;
SCOTCH_Num * rangtab = nullptr;
SCOTCH_Num * treetab = nullptr;
/// Initialize the strategy structure
SCOTCH_stratInit(&scotch_strat);
SCOTCH_Graph scotch_graph;
SCOTCH_graphInit(&scotch_graph);
SCOTCH_meshGraph(scotch_mesh, &scotch_graph);
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
FILE * fgraphinit = fopen("ScotchMesh.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraphinit);
fclose(fgraphinit);
}
#endif
/// Check the graph
// AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
// "Mesh to Graph is not consistent");
SCOTCH_graphOrder(&scotch_graph, &scotch_strat, permtab, peritab, &cblknbr,
rangtab, treetab);
SCOTCH_graphExit(&scotch_graph);
SCOTCH_stratExit(&scotch_strat);
destroyMesh(scotch_mesh);
/// Renumbering
UInt spatial_dimension = mesh.getSpatialDimension();
-
+ MeshAccessor mesh_accessor(mesh);
for (auto gt : ghost_types) {
- for (auto & type : mesh.elementTypes(_ghost_type = gt)) {
- UInt nb_element = mesh.getNbElement(type, gt);
- UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
-
- const Array<UInt> & connectivity = mesh.getConnectivity(type, gt);
-
- UInt * conn = connectivity.storage();
- for (UInt el = 0; el < nb_element * nb_nodes_per_element; ++el, ++conn) {
- *conn = permtab[*conn];
+ for (const auto & type : mesh.elementTypes(_ghost_type = gt)) {
+ auto & connectivity = mesh_accessor.getConnectivity(type, gt);
+ for (auto && c : make_view(connectivity)) {
+ c = permtab[c];
}
}
}
/// \todo think of a in-place way to do it
auto * new_coordinates = new Real[spatial_dimension * nb_nodes];
Real * old_coordinates = mesh.getNodes().storage();
for (UInt i = 0; i < nb_nodes; ++i) {
memcpy(new_coordinates + permtab[i] * spatial_dimension,
old_coordinates + i * spatial_dimension,
spatial_dimension * sizeof(Real));
}
memcpy(old_coordinates, new_coordinates,
nb_nodes * spatial_dimension * sizeof(Real));
delete[] new_coordinates;
delete[] permtab;
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh b/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
index 7683a3060..06eb2c9f2 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
+++ b/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
@@ -1,78 +1,76 @@
/**
* @file mesh_partition_scotch.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief mesh partitioning based on libScotch
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-
-/* -------------------------------------------------------------------------- */
-
-#ifndef __AKANTU_MESH_PARTITION_SCOTCH_HH__
-#define __AKANTU_MESH_PARTITION_SCOTCH_HH__
-
/* -------------------------------------------------------------------------- */
-#include "aka_common.hh"
#include "mesh_partition.hh"
+/* -------------------------------------------------------------------------- */
+
+#ifndef AKANTU_MESH_PARTITION_SCOTCH_HH_
+#define AKANTU_MESH_PARTITION_SCOTCH_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartitionScotch : public MeshPartition {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- MeshPartitionScotch(const Mesh & mesh, UInt spatial_dimension,
+ MeshPartitionScotch(Mesh & mesh, UInt spatial_dimension,
const ID & id = "mesh_partition_scotch",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
- virtual void partitionate(
+ void partitionate(
UInt nb_part,
- std::function<Int(const Element &, const Element &)> edge_load_func =
- [](auto &&, auto &&) { return 1; },
- std::function<Int(const Element &)> vertex_load_func =
- [](auto &&) { return 1; }) override;
+ const std::function<Int(const Element &, const Element &)> &
+ edge_load_func =
+ [](auto && /*unused*/, auto && /*unused*/) { return 1; },
+ const std::function<Int(const Element &)> & vertex_load_func =
+ [](auto && /*unused*/) { return 1; }) override;
void reorder() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
-#endif /* __AKANTU_MESH_PARTITION_SCOTCH_HH__ */
+#endif /* AKANTU_MESH_PARTITION_SCOTCH_HH_ */
diff --git a/src/mesh_utils/mesh_utils.cc b/src/mesh_utils/mesh_utils.cc
index 1ebd9dc3f..a9cad9e2a 100644
--- a/src/mesh_utils/mesh_utils.cc
+++ b/src/mesh_utils/mesh_utils.cc
@@ -1,1828 +1,1882 @@
/**
* @file mesh_utils.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Aug 20 2010
* @date last modification: Wed Feb 21 2018
*
* @brief All mesh utils necessary for various tasks
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_utils.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh_accessor.hh"
#include "mesh_iterators.hh"
/* -------------------------------------------------------------------------- */
#include <limits>
#include <numeric>
#include <queue>
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2Elements(const Mesh & mesh,
CSR<Element> & node_to_elem,
UInt spatial_dimension) {
AKANTU_DEBUG_IN();
- if (spatial_dimension == _all_dimensions)
+ if (spatial_dimension == _all_dimensions) {
spatial_dimension = mesh.getSpatialDimension();
+ }
/// count number of occurrence of each node
UInt nb_nodes = mesh.getNbNodes();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
- for_each_element(mesh,
- [&](auto && element) {
- Vector<UInt> conn = mesh.getConnectivity(element);
- for (auto && node : conn) {
- ++node_to_elem.rowOffset(node);
- }
- },
- _spatial_dimension = spatial_dimension,
- _element_kind = _ek_not_defined);
+ for_each_element(
+ mesh,
+ [&](auto && element) {
+ Vector<UInt> conn = mesh.getConnectivity(element);
+ for (auto && node : conn) {
+ ++node_to_elem.rowOffset(node);
+ }
+ },
+ _spatial_dimension = spatial_dimension, _element_kind = _ek_not_defined);
node_to_elem.countToCSR();
node_to_elem.resizeCols();
/// rearrange element to get the node-element list
// Element e;
node_to_elem.beginInsertions();
- for_each_element(mesh,
- [&](auto && element) {
- Vector<UInt> conn = mesh.getConnectivity(element);
- for (auto && node : conn) {
- node_to_elem.insertInRow(node, element);
- }
- },
- _spatial_dimension = spatial_dimension,
- _element_kind = _ek_not_defined);
+ for_each_element(
+ mesh,
+ [&](auto && element) {
+ Vector<UInt> conn = mesh.getConnectivity(element);
+ for (auto && node : conn) {
+ node_to_elem.insertInRow(node, element);
+ }
+ },
+ _spatial_dimension = spatial_dimension, _element_kind = _ek_not_defined);
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2ElementsElementTypeMap(const Mesh & mesh,
CSR<UInt> & node_to_elem,
- const ElementType & type,
- const GhostType & ghost_type) {
+ ElementType type,
+ GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_elements = mesh.getConnectivity(type, ghost_type).size();
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
/// count number of occurrence of each node
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
- for (UInt n = 0; n < nb_nodes_per_element; ++n)
+ for (UInt n = 0; n < nb_nodes_per_element; ++n) {
++node_to_elem.rowOffset(conn_val[el_offset + n]);
+ }
}
/// convert the occurrence array in a csr one
node_to_elem.countToCSR();
node_to_elem.resizeCols();
node_to_elem.beginInsertions();
/// save the element index in the node-element list
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
node_to_elem.insertInRow(conn_val[el_offset + n], el);
}
}
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacets(Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (auto ghost_type : ghost_types) {
- for (auto & type : mesh.elementTypes(spatial_dimension - 1, ghost_type)) {
+ for (const auto & type :
+ mesh.elementTypes(spatial_dimension - 1, ghost_type)) {
mesh.getConnectivity(type, ghost_type).resize(0);
// \todo inform the mesh event handler
}
}
buildFacetsDimension(mesh, mesh, true, spatial_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt to_dimension) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
buildAllFacets(mesh, mesh_facets, spatial_dimension, to_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt from_dimension, UInt to_dimension) {
AKANTU_DEBUG_IN();
to_dimension = std::max(to_dimension, UInt(0));
-
+
AKANTU_DEBUG_ASSERT(
mesh_facets.isMeshFacets(),
"The mesh_facets should be initialized with initMeshFacets");
/// generate facets
buildFacetsDimension(mesh, mesh_facets, false, from_dimension);
/// sort facets and generate sub-facets
for (UInt i = from_dimension - 1; i > to_dimension; --i) {
buildFacetsDimension(mesh_facets, mesh_facets, false, i);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacetsDimension(const Mesh & mesh, Mesh & mesh_facets,
bool boundary_only, UInt dimension) {
AKANTU_DEBUG_IN();
// save the current parent of mesh_facets and set it temporarly to mesh since
// mesh is the one containing the elements for which mesh_facets has the
// sub-elements
// example: if the function is called with mesh = mesh_facets
const Mesh * mesh_facets_parent = nullptr;
try {
mesh_facets_parent = &mesh_facets.getMeshParent();
} catch (...) {
}
mesh_facets.defineMeshParent(mesh);
MeshAccessor mesh_accessor(mesh_facets);
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<Real> & mesh_facets_nodes = mesh_facets.getNodes();
const auto mesh_facets_nodes_it = mesh_facets_nodes.begin(spatial_dimension);
CSR<Element> node_to_elem;
buildNode2Elements(mesh, node_to_elem, dimension);
Array<UInt> counter;
std::vector<Element> connected_elements;
NewElementsEvent event(AKANTU_CURRENT_FUNCTION);
-
+
// init the SubelementToElement data to improve performance
for (auto && ghost_type : ghost_types) {
for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
mesh_accessor.getSubelementToElement(type, ghost_type);
auto facet_types = mesh.getAllFacetTypes(type);
for (auto && ft : arange(facet_types.size())) {
auto facet_type = facet_types(ft);
mesh_accessor.getElementToSubelement(facet_type, ghost_type);
mesh_accessor.getConnectivity(facet_type, ghost_type);
}
}
}
const ElementSynchronizer * synchronizer = nullptr;
if (mesh.isDistributed()) {
synchronizer = &(mesh.getElementSynchronizer());
}
Element current_element;
for (auto && ghost_type : ghost_types) {
GhostType facet_ghost_type = ghost_type;
current_element.ghost_type = ghost_type;
for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
auto facet_types = mesh.getAllFacetTypes(type);
current_element.type = type;
for (auto && ft : arange(facet_types.size())) {
auto facet_type = facet_types(ft);
auto nb_element = mesh.getNbElement(type, ghost_type);
- auto element_to_subelement =
+ auto * element_to_subelement =
&mesh_facets.getElementToSubelement(facet_type, ghost_type);
- auto connectivity_facets =
+ auto * connectivity_facets =
&mesh_facets.getConnectivity(facet_type, ghost_type);
auto nb_nodes_per_facet = connectivity_facets->getNbComponent();
// Vector<UInt> facet(nb_nodes_per_facet);
for (UInt el = 0; el < nb_element; ++el) {
current_element.element = el;
auto && facets =
mesh.getFacetConnectivity(current_element, ft).transpose();
for (auto facet : facets) {
// facet = facets(f);
UInt first_node_nb_elements = node_to_elem.getNbCols(facet(0));
counter.resize(first_node_nb_elements);
- counter.clear();
+ counter.zero();
// loop over the other nodes to search intersecting elements,
// which are the elements that share another node with the
// starting element after first_node
for (auto && data : enumerate(node_to_elem.getRow(facet(0)))) {
auto && local_el = std::get<0>(data);
auto && first_node = std::get<1>(data);
for (auto n : arange(1, nb_nodes_per_facet)) {
auto && node_elements = node_to_elem.getRow(facet(n));
counter(local_el) += std::count(
node_elements.begin(), node_elements.end(), first_node);
}
}
// counting the number of elements connected to the facets and
// taking the minimum element number, because the facet should
// be inserted just once
UInt nb_element_connected_to_facet = 0;
Element minimum_el = ElementNull;
connected_elements.clear();
for (auto && data : enumerate(node_to_elem.getRow(facet(0)))) {
- if (not(counter(std::get<0>(data)) == nb_nodes_per_facet - 1))
+ if (not(counter(std::get<0>(data)) == nb_nodes_per_facet - 1)) {
continue;
+ }
auto && real_el = std::get<1>(data);
++nb_element_connected_to_facet;
minimum_el = std::min(minimum_el, real_el);
connected_elements.push_back(real_el);
}
- if (minimum_el != current_element)
+ if (minimum_el != current_element) {
continue;
+ }
bool full_ghost_facet = false;
UInt n = 0;
while (n < nb_nodes_per_facet && mesh.isPureGhostNode(facet(n))) {
++n;
}
- if (n == nb_nodes_per_facet)
+ if (n == nb_nodes_per_facet) {
full_ghost_facet = true;
+ }
- if (full_ghost_facet)
+ if (full_ghost_facet) {
continue;
+ }
- if (boundary_only and nb_element_connected_to_facet != 1)
+ if (boundary_only and nb_element_connected_to_facet != 1) {
continue;
+ }
std::vector<Element> elements;
// build elements_on_facets: linearized_el must come first
// in order to store the facet in the correct direction
// and avoid to invert the sign in the normal computation
+ elements.reserve(elements.size() + connected_elements.size());
for (auto && connected_element : connected_elements) {
elements.push_back(connected_element);
}
if (nb_element_connected_to_facet == 1) { /// boundary facet
elements.push_back(ElementNull);
} else if (nb_element_connected_to_facet == 2) { /// internal facet
/// check if facet is in between ghost and normal
/// elements: if it's the case, the facet is either
/// ghost or not ghost. The criterion to decide this
/// is arbitrary. It was chosen to check the processor
/// id (prank) of the two neighboring elements. If
/// prank of the ghost element is lower than prank of
/// the normal one, the facet is not ghost, otherwise
/// it's ghost
GhostType gt[2] = {_not_ghost, _not_ghost};
- for (UInt el = 0; el < connected_elements.size(); ++el)
+ for (UInt el = 0; el < connected_elements.size(); ++el) {
gt[el] = connected_elements[el].ghost_type;
+ }
if ((gt[0] == _not_ghost) xor (gt[1] == _not_ghost)) {
UInt prank[2];
for (UInt el = 0; el < 2; ++el) {
prank[el] = synchronizer->getRank(connected_elements[el]);
}
// ugly trick from Marco detected :P
bool ghost_one = (gt[0] != _ghost);
- if (prank[ghost_one] > prank[!ghost_one])
+ if (prank[ghost_one] > prank[!ghost_one]) {
facet_ghost_type = _not_ghost;
- else
+ } else {
facet_ghost_type = _ghost;
+ }
connectivity_facets =
&mesh_facets.getConnectivity(facet_type, facet_ghost_type);
element_to_subelement = &mesh_facets.getElementToSubelement(
facet_type, facet_ghost_type);
}
}
element_to_subelement->push_back(elements);
connectivity_facets->push_back(facet);
/// current facet index
UInt current_facet = connectivity_facets->size() - 1;
Element facet_element{facet_type, current_facet, facet_ghost_type};
event.getList().push_back(facet_element);
/// loop on every element connected to current facet and
/// insert current facet in the first free spot of the
/// subelement_to_element vector
for (auto & loc_el : elements) {
- if (loc_el == ElementNull)
+ if (loc_el == ElementNull) {
continue;
+ }
auto & subelement_to_element = mesh_facets.getSubelementToElement(
loc_el.type, loc_el.ghost_type);
auto && subelements = Vector<Element>(
make_view(subelement_to_element,
subelement_to_element.getNbComponent())
.begin()[loc_el.element]);
for (auto & el : subelements) {
- if (el != ElementNull)
+ if (el != ElementNull) {
continue;
+ }
el = facet_element;
break;
}
}
/// reset connectivity in case a facet was found in
/// between ghost and normal elements
if (facet_ghost_type != ghost_type) {
facet_ghost_type = ghost_type;
connectivity_facets =
&mesh_accessor.getConnectivity(facet_type, facet_ghost_type);
element_to_subelement = &mesh_accessor.getElementToSubelement(
facet_type, facet_ghost_type);
}
}
}
}
}
}
mesh_facets.sendEvent(event);
-
+
// restore the parent of mesh_facet
- if (mesh_facets_parent)
+ if (mesh_facets_parent != nullptr) {
mesh_facets.defineMeshParent(*mesh_facets_parent);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberMeshNodes(Mesh & mesh,
Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type,
Array<UInt> & old_nodes_numbers) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
std::map<UInt, UInt> renumbering_map;
for (UInt i = 0; i < old_nodes_numbers.size(); ++i) {
renumbering_map[old_nodes_numbers(i)] = i;
}
/// renumber the nodes
renumberNodesInConnectivity(local_connectivities,
(nb_local_element + nb_ghost_element) *
nb_nodes_per_element,
renumbering_map);
old_nodes_numbers.resize(renumbering_map.size());
for (auto & renumber_pair : renumbering_map) {
old_nodes_numbers(renumber_pair.second) = renumber_pair.first;
}
renumbering_map.clear();
MeshAccessor mesh_accessor(mesh);
/// copy the renumbered connectivity to the right place
auto & local_conn = mesh_accessor.getConnectivity(type);
local_conn.resize(nb_local_element);
if (nb_local_element > 0) {
memcpy(local_conn.storage(), local_connectivities.storage(),
nb_local_element * nb_nodes_per_element * sizeof(UInt));
}
auto & ghost_conn = mesh_accessor.getConnectivity(type, _ghost);
ghost_conn.resize(nb_ghost_element);
if (nb_ghost_element > 0) {
std::memcpy(ghost_conn.storage(),
local_connectivities.storage() +
nb_local_element * nb_nodes_per_element,
nb_ghost_element * nb_nodes_per_element * sizeof(UInt));
}
auto & ghost_counter = mesh_accessor.getGhostsCounters(type, _ghost);
ghost_counter.resize(nb_ghost_element, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberNodesInConnectivity(
Array<UInt> & list_nodes, UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map) {
AKANTU_DEBUG_IN();
UInt * connectivity = list_nodes.storage();
UInt new_node_num = renumbering_map.size();
for (UInt n = 0; n < nb_nodes; ++n, ++connectivity) {
UInt & node = *connectivity;
auto it = renumbering_map.find(node);
if (it == renumbering_map.end()) {
UInt old_node = node;
renumbering_map[old_node] = new_node_num;
node = new_node_num;
++new_node_num;
} else {
node = it->second;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::purifyMesh(Mesh & mesh) {
AKANTU_DEBUG_IN();
std::map<UInt, UInt> renumbering_map;
RemovedNodesEvent remove_nodes(mesh, AKANTU_CURRENT_FUNCTION);
Array<UInt> & nodes_removed = remove_nodes.getList();
for (auto ghost_type : ghost_types) {
for (auto type :
mesh.elementTypes(_all_dimensions, ghost_type, _ek_not_defined)) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_element(connectivity.size());
renumberNodesInConnectivity(
connectivity, nb_element * nb_nodes_per_element, renumbering_map);
}
}
Array<UInt> & new_numbering = remove_nodes.getNewNumbering();
std::fill(new_numbering.begin(), new_numbering.end(), UInt(-1));
for (auto && pair : renumbering_map) {
new_numbering(std::get<0>(pair)) = std::get<1>(pair);
}
for (UInt i = 0; i < new_numbering.size(); ++i) {
- if (new_numbering(i) == UInt(-1))
+ if (new_numbering(i) == UInt(-1)) {
nodes_removed.push_back(i);
+ }
}
mesh.sendEvent(remove_nodes);
AKANTU_DEBUG_OUT();
}
#if defined(AKANTU_COHESIVE_ELEMENT)
/* -------------------------------------------------------------------------- */
UInt MeshUtils::insertCohesiveElements(
Mesh & mesh, Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes, Array<Element> & new_elements,
bool only_double_facets) {
UInt spatial_dimension = mesh.getSpatialDimension();
UInt elements_to_insert = updateFacetToDouble(mesh_facets, facet_insertion);
if (elements_to_insert > 0) {
if (spatial_dimension == 1) {
doublePointFacet(mesh, mesh_facets, doubled_nodes);
} else {
doubleFacet(mesh, mesh_facets, spatial_dimension - 1, doubled_nodes,
true);
findSubfacetToDouble<false>(mesh_facets);
if (spatial_dimension == 2) {
doubleSubfacet<2>(mesh, mesh_facets, doubled_nodes);
} else if (spatial_dimension == 3) {
doubleFacet(mesh, mesh_facets, 1, doubled_nodes, false);
findSubfacetToDouble<true>(mesh_facets);
doubleSubfacet<3>(mesh, mesh_facets, doubled_nodes);
}
}
- if (!only_double_facets)
+ if (!only_double_facets) {
updateCohesiveData(mesh, mesh_facets, new_elements);
+ }
}
return elements_to_insert;
}
#endif
/* -------------------------------------------------------------------------- */
void MeshUtils::doubleNodes(Mesh & mesh, const std::vector<UInt> & old_nodes,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
Array<Real> & position = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt old_nb_nodes = position.size();
UInt new_nb_nodes = old_nb_nodes + old_nodes.size();
UInt old_nb_doubled_nodes = doubled_nodes.size();
UInt new_nb_doubled_nodes = old_nb_doubled_nodes + old_nodes.size();
position.resize(new_nb_nodes);
doubled_nodes.resize(new_nb_doubled_nodes);
Array<Real>::iterator<Vector<Real>> position_begin =
position.begin(spatial_dimension);
for (UInt n = 0; n < old_nodes.size(); ++n) {
UInt new_node = old_nb_nodes + n;
/// store doubled nodes
doubled_nodes(old_nb_doubled_nodes + n, 0) = old_nodes[n];
doubled_nodes(old_nb_doubled_nodes + n, 1) = new_node;
/// update position
std::copy(position_begin + old_nodes[n], position_begin + old_nodes[n] + 1,
position_begin + new_node);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::doubleFacet(Mesh & mesh, Mesh & mesh_facets,
UInt facet_dimension, Array<UInt> & doubled_nodes,
bool facet_mode) {
AKANTU_DEBUG_IN();
NewElementsEvent event(AKANTU_CURRENT_FUNCTION);
-
+
for (auto gt_facet : ghost_types) {
for (auto && type_facet :
mesh_facets.elementTypes(facet_dimension, gt_facet)) {
auto & facets_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
auto nb_facet_to_double = facets_to_double.size();
- if (nb_facet_to_double == 0)
+ if (nb_facet_to_double == 0) {
continue;
+ }
// this while fail if multiple facet types
// \TODO handle multiple sub-facet types
auto nb_subfacet_per_facet = Mesh::getNbFacetsPerElement(type_facet);
auto & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
auto nb_nodes_per_facet = conn_facet.getNbComponent();
auto old_nb_facet = conn_facet.size();
auto new_nb_facet = old_nb_facet + nb_facet_to_double;
#ifndef AKANTU_NDEBUG
// memory initialization are slow but help debug
conn_facet.resize(new_nb_facet, UInt(-1));
#else
conn_facet.resize(new_nb_facet);
#endif
auto conn_facet_begin = conn_facet.begin(nb_nodes_per_facet);
auto & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
#ifndef AKANTU_NDEBUG
subfacet_to_facet.resize(new_nb_facet, ElementNull);
#else
subfacet_to_facet.resize(new_nb_facet);
#endif
auto subfacet_to_facet_begin =
subfacet_to_facet.begin(nb_subfacet_per_facet);
Element new_facet{type_facet, old_nb_facet, gt_facet};
auto conn_facet_new_it = conn_facet_begin + new_facet.element;
auto subfacet_to_facet_new_it =
subfacet_to_facet_begin + new_facet.element;
event.getList().push_back(new_facet);
-
+
for (UInt facet = 0; facet < nb_facet_to_double; ++facet,
++new_facet.element, ++conn_facet_new_it,
++subfacet_to_facet_new_it) {
UInt old_facet = facets_to_double(facet);
/// adding a new facet by copying original one
/// copy connectivity in new facet
*conn_facet_new_it = conn_facet_begin[old_facet];
/// update subfacet_to_facet
*subfacet_to_facet_new_it = subfacet_to_facet_begin[old_facet];
/// loop on every subfacet
for (UInt sf = 0; sf < nb_subfacet_per_facet; ++sf) {
Element & subfacet = subfacet_to_facet(old_facet, sf);
- if (subfacet == ElementNull)
+ if (subfacet == ElementNull) {
continue;
+ }
/// update facet_to_subfacet array
mesh_facets.getElementToSubelement(subfacet).push_back(new_facet);
}
}
/// update facet_to_subfacet and _segment_3 facets if any
if (not facet_mode) {
updateSubfacetToFacet(mesh_facets, type_facet, gt_facet, true);
updateFacetToSubfacet(mesh_facets, type_facet, gt_facet, true);
updateQuadraticSegments<true>(mesh, mesh_facets, type_facet, gt_facet,
doubled_nodes);
- } else
+ } else {
updateQuadraticSegments<false>(mesh, mesh_facets, type_facet, gt_facet,
doubled_nodes);
+ }
}
}
mesh_facets.sendEvent(event);
-
+
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt MeshUtils::updateFacetToDouble(
Mesh & mesh_facets, const ElementTypeMapArray<bool> & facet_insertion) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
UInt nb_facets_to_double = 0.;
for (auto gt_facet : ghost_types) {
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
const auto & f_insertion = facet_insertion(type_facet, gt_facet);
auto & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
auto & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
Element old_facet_el{type_facet, 0, gt_facet};
UInt nb_facets = mesh_facets.getNbElement(type_facet, gt_facet);
for (UInt f = 0; f < f_insertion.size(); ++f) {
-
- if (f_insertion(f) == false)
+ if (not f_insertion(f)) {
continue;
+ }
++nb_facets_to_double;
if (element_to_facet(f)[1].type == _not_defined
#if defined(AKANTU_COHESIVE_ELEMENT)
|| element_to_facet(f)[1].kind() == _ek_cohesive
#endif
) {
AKANTU_DEBUG_WARNING("attempt to double a facet on the boundary");
continue;
}
f_to_double.push_back(f);
UInt new_facet = nb_facets + f_to_double.size() - 1;
old_facet_el.element = f;
/// update facet_to_element vector
auto & elem_to_update = element_to_facet(f)[1];
UInt el = elem_to_update.element;
auto & facet_to_element = mesh_facets.getSubelementToElement(
elem_to_update.type, elem_to_update.ghost_type);
auto el_facets = Vector<Element>(
make_view(facet_to_element, facet_to_element.getNbComponent())
.begin()[el]);
auto f_update =
std::find(el_facets.begin(), el_facets.end(), old_facet_el);
AKANTU_DEBUG_ASSERT(f_update != el_facets.end(), "Facet not found");
f_update->element = new_facet;
/// update elements connected to facet
const auto & first_facet_list = element_to_facet(f);
element_to_facet.push_back(first_facet_list);
/// set new and original facets as boundary facets
element_to_facet(new_facet)[0] = element_to_facet(new_facet)[1];
element_to_facet(new_facet)[1] = ElementNull;
element_to_facet(f)[1] = ElementNull;
}
}
}
AKANTU_DEBUG_OUT();
return nb_facets_to_double;
}
/* -------------------------------------------------------------------------- */
void MeshUtils::resetFacetToDouble(Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
for (auto gt : ghost_types) {
for (auto type : mesh_facets.elementTypes(_all_dimensions, gt)) {
mesh_facets.getDataPointer<UInt>("facet_to_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element>>(
"facets_to_subfacet_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element>>(
"elements_to_subfacet_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type, gt, 1, false);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool subsubfacet_mode>
void MeshUtils::findSubfacetToDouble(Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
- if (spatial_dimension == 1)
+ if (spatial_dimension == 1) {
return;
+ }
for (auto gt_facet : ghost_types) {
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
auto & facets_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
auto nb_facet_to_double = facets_to_double.size();
- if (nb_facet_to_double == 0)
+ if (nb_facet_to_double == 0) {
continue;
+ }
ElementType type_subfacet = Mesh::getFacetType(type_facet);
GhostType gt_subfacet = _casper;
ElementType type_subsubfacet = Mesh::getFacetType(type_subfacet);
GhostType gt_subsubfacet = _casper;
Array<UInt> * conn_subfacet = nullptr;
Array<UInt> * sf_to_double = nullptr;
Array<std::vector<Element>> * sf_to_subfacet_double = nullptr;
Array<std::vector<Element>> * f_to_subfacet_double = nullptr;
Array<std::vector<Element>> * el_to_subfacet_double = nullptr;
UInt nb_subfacet = Mesh::getNbFacetsPerElement(type_facet);
UInt nb_subsubfacet;
UInt nb_nodes_per_sf_el;
if (subsubfacet_mode) {
nb_nodes_per_sf_el = Mesh::getNbNodesPerElement(type_subsubfacet);
nb_subsubfacet = Mesh::getNbFacetsPerElement(type_subfacet);
- } else
+ } else {
nb_nodes_per_sf_el = Mesh::getNbNodesPerElement(type_subfacet);
+ }
Array<Element> & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
Array<Element> * subsubfacet_to_subfacet = nullptr;
UInt old_nb_facet = subfacet_to_facet.size() - nb_facet_to_double;
Element current_facet{type_facet, 0, gt_facet};
std::vector<Element> element_list;
std::vector<Element> facet_list;
std::vector<Element> * subfacet_list;
- if (subsubfacet_mode)
+ if (subsubfacet_mode) {
subfacet_list = new std::vector<Element>;
+ }
/// map to filter subfacets
Array<std::vector<Element>> * facet_to_subfacet = nullptr;
/// this is used to make sure that both new and old facets are
/// checked
UInt facets[2];
/// loop on every facet
for (UInt f_index = 0; f_index < 2; ++f_index) {
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
facets[bool(f_index)] = facets_to_double(facet);
facets[!bool(f_index)] = old_nb_facet + facet;
UInt old_facet = facets[0];
UInt new_facet = facets[1];
Element & starting_element = element_to_facet(new_facet)[0];
current_facet.element = old_facet;
/// loop on every subfacet
for (UInt sf = 0; sf < nb_subfacet; ++sf) {
Element & subfacet = subfacet_to_facet(old_facet, sf);
- if (subfacet == ElementNull)
+ if (subfacet == ElementNull) {
continue;
+ }
if (gt_subfacet != subfacet.ghost_type) {
gt_subfacet = subfacet.ghost_type;
if (subsubfacet_mode) {
subsubfacet_to_subfacet = &mesh_facets.getSubelementToElement(
type_subfacet, gt_subfacet);
} else {
conn_subfacet =
&mesh_facets.getConnectivity(type_subfacet, gt_subfacet);
sf_to_double = &mesh_facets.getData<UInt>(
"facet_to_double", type_subfacet, gt_subfacet);
f_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subfacet,
gt_subfacet);
el_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_subfacet,
gt_subfacet);
facet_to_subfacet = &mesh_facets.getElementToSubelement(
type_subfacet, gt_subfacet);
}
}
if (subsubfacet_mode) {
/// loop on every subsubfacet
for (UInt ssf = 0; ssf < nb_subsubfacet; ++ssf) {
Element & subsubfacet =
(*subsubfacet_to_subfacet)(subfacet.element, ssf);
- if (subsubfacet == ElementNull)
+ if (subsubfacet == ElementNull) {
continue;
+ }
if (gt_subsubfacet != subsubfacet.ghost_type) {
gt_subsubfacet = subsubfacet.ghost_type;
conn_subfacet = &mesh_facets.getConnectivity(type_subsubfacet,
gt_subsubfacet);
sf_to_double = &mesh_facets.getData<UInt>(
"facet_to_double", type_subsubfacet, gt_subsubfacet);
sf_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subsubfacet,
gt_subsubfacet);
f_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subsubfacet,
gt_subsubfacet);
el_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_subsubfacet,
gt_subsubfacet);
facet_to_subfacet = &mesh_facets.getElementToSubelement(
type_subsubfacet, gt_subsubfacet);
}
UInt global_ssf = subsubfacet.element;
Vector<UInt> subsubfacet_connectivity(
conn_subfacet->storage() + global_ssf * nb_nodes_per_sf_el,
nb_nodes_per_sf_el);
/// check if subsubfacet is to be doubled
- if (findElementsAroundSubfacet<true>(
+ if (not findElementsAroundSubfacet<true>(
mesh_facets, starting_element, current_facet,
subsubfacet_connectivity, element_list, facet_list,
- subfacet_list) == false &&
- removeElementsInVector(*subfacet_list,
- (*facet_to_subfacet)(global_ssf)) ==
- false) {
+ subfacet_list) and
+ not removeElementsInVector(
+ *subfacet_list, (*facet_to_subfacet)(global_ssf))) {
sf_to_double->push_back(global_ssf);
sf_to_subfacet_double->push_back(*subfacet_list);
f_to_subfacet_double->push_back(facet_list);
el_to_subfacet_double->push_back(element_list);
}
}
} else {
const UInt global_sf = subfacet.element;
Vector<UInt> subfacet_connectivity(
conn_subfacet->storage() + global_sf * nb_nodes_per_sf_el,
nb_nodes_per_sf_el);
/// check if subfacet is to be doubled
- if (findElementsAroundSubfacet<false>(
+ if (not findElementsAroundSubfacet<false>(
mesh_facets, starting_element, current_facet,
- subfacet_connectivity, element_list,
- facet_list) == false &&
- removeElementsInVector(
- facet_list, (*facet_to_subfacet)(global_sf)) == false) {
+ subfacet_connectivity, element_list, facet_list) and
+ not removeElementsInVector(facet_list,
+ (*facet_to_subfacet)(global_sf))) {
sf_to_double->push_back(global_sf);
f_to_subfacet_double->push_back(facet_list);
el_to_subfacet_double->push_back(element_list);
}
}
}
}
}
- if (subsubfacet_mode)
+ if (subsubfacet_mode) {
delete subfacet_list;
+ }
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
void MeshUtils::updateCohesiveData(Mesh & mesh, Mesh & mesh_facets,
Array<Element> & new_elements) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
bool third_dimension = spatial_dimension == 3;
MeshAccessor mesh_facets_accessor(mesh_facets);
for (auto gt_facet : ghost_types) {
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.size();
- if (nb_facet_to_double == 0)
+ if (nb_facet_to_double == 0) {
continue;
+ }
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
auto & facet_to_coh_element =
mesh_facets_accessor.getSubelementToElement(type_cohesive, gt_facet);
auto & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
auto & conn_cohesive = mesh.getConnectivity(type_cohesive, gt_facet);
UInt nb_nodes_per_facet = Mesh::getNbNodesPerElement(type_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
UInt old_nb_cohesive_elements = conn_cohesive.size();
UInt new_nb_cohesive_elements = conn_cohesive.size() + nb_facet_to_double;
UInt old_nb_facet = element_to_facet.size() - nb_facet_to_double;
facet_to_coh_element.resize(new_nb_cohesive_elements);
conn_cohesive.resize(new_nb_cohesive_elements);
UInt new_elements_old_size = new_elements.size();
new_elements.resize(new_elements_old_size + nb_facet_to_double);
Element c_element{type_cohesive, 0, gt_facet};
Element f_element{type_facet, 0, gt_facet};
UInt facets[2];
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
/// (in 3D cohesive elements connectivity is inverted)
facets[third_dimension ? 1 : 0] = f_to_double(facet);
facets[third_dimension ? 0 : 1] = old_nb_facet + facet;
UInt cohesive_element = old_nb_cohesive_elements + facet;
/// store doubled facets
f_element.element = facets[0];
facet_to_coh_element(cohesive_element, 0) = f_element;
f_element.element = facets[1];
facet_to_coh_element(cohesive_element, 1) = f_element;
/// modify cohesive elements' connectivity
for (UInt n = 0; n < nb_nodes_per_facet; ++n) {
conn_cohesive(cohesive_element, n) = conn_facet(facets[0], n);
conn_cohesive(cohesive_element, n + nb_nodes_per_facet) =
conn_facet(facets[1], n);
}
/// update element_to_facet vectors
c_element.element = cohesive_element;
element_to_facet(facets[0])[1] = c_element;
element_to_facet(facets[1])[1] = c_element;
/// add cohesive element to the element event list
new_elements(new_elements_old_size + facet) = c_element;
}
}
}
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
void MeshUtils::doublePointFacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
- if (spatial_dimension != 1)
+ if (spatial_dimension != 1) {
return;
+ }
auto & position = mesh.getNodes();
for (auto gt_facet : ghost_types) {
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
auto & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
auto & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
const auto & facets_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
auto nb_facet_to_double = facets_to_double.size();
auto new_nb_facet = element_to_facet.size();
auto old_nb_facet = element_to_facet.size() - nb_facet_to_double;
auto old_nb_nodes = position.size();
auto new_nb_nodes = old_nb_nodes + nb_facet_to_double;
position.resize(new_nb_nodes);
conn_facet.resize(new_nb_facet);
auto old_nb_doubled_nodes = doubled_nodes.size();
doubled_nodes.resize(old_nb_doubled_nodes + nb_facet_to_double);
for (auto && data_facet : enumerate(facets_to_double)) {
const auto & old_facet = std::get<1>(data_facet);
auto facet = std::get<0>(data_facet);
auto new_facet = old_nb_facet + facet;
auto el = element_to_facet(new_facet)[0];
auto old_node = conn_facet(old_facet);
auto new_node = old_nb_nodes + facet;
/// update position
position(new_node) = position(old_node);
conn_facet(new_facet) = new_node;
Vector<UInt> conn_segment = mesh.getConnectivity(el);
/// update facet connectivity
auto it = std::find(conn_segment.begin(), conn_segment.end(), old_node);
*it = new_node;
doubled_nodes(old_nb_doubled_nodes + facet, 0) = old_node;
doubled_nodes(old_nb_doubled_nodes + facet, 1) = new_node;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool third_dim_segments>
void MeshUtils::updateQuadraticSegments(Mesh & mesh, Mesh & mesh_facets,
ElementType type_facet,
GhostType gt_facet,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
- if (type_facet != _segment_3)
+ if (type_facet != _segment_3) {
return;
+ }
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.size();
UInt old_nb_facet =
mesh_facets.getNbElement(type_facet, gt_facet) - nb_facet_to_double;
Array<UInt> & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
/// this ones matter only for segments in 3D
Array<std::vector<Element>> * el_to_subfacet_double = nullptr;
Array<std::vector<Element>> * f_to_subfacet_double = nullptr;
if (third_dim_segments) {
el_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_facet, gt_facet);
f_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_facet, gt_facet);
}
std::vector<UInt> middle_nodes;
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt node = conn_facet(old_facet, 2);
- if (!mesh.isPureGhostNode(node))
+ if (!mesh.isPureGhostNode(node)) {
middle_nodes.push_back(node);
+ }
}
UInt n = doubled_nodes.size();
doubleNodes(mesh, middle_nodes, doubled_nodes);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt old_node = conn_facet(old_facet, 2);
- if (mesh.isPureGhostNode(old_node))
+ if (mesh.isPureGhostNode(old_node)) {
continue;
+ }
UInt new_node = doubled_nodes(n, 1);
UInt new_facet = old_nb_facet + facet;
conn_facet(new_facet, 2) = new_node;
if (third_dim_segments) {
updateElementalConnectivity(mesh_facets, old_node, new_node,
element_to_facet(new_facet));
updateElementalConnectivity(mesh, old_node, new_node,
(*el_to_subfacet_double)(facet),
&(*f_to_subfacet_double)(facet));
} else {
updateElementalConnectivity(mesh, old_node, new_node,
element_to_facet(new_facet));
}
++n;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateSubfacetToFacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode) {
AKANTU_DEBUG_IN();
Array<UInt> & sf_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_subfacet, gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.size();
/// update subfacet_to_facet vector
ElementType type_facet = _not_defined;
GhostType gt_facet = _casper;
Array<Element> * subfacet_to_facet = nullptr;
UInt nb_subfacet_per_facet = 0;
UInt old_nb_subfacet = mesh_facets.getNbElement(type_subfacet, gt_subfacet) -
nb_subfacet_to_double;
Array<std::vector<Element>> * facet_list = nullptr;
- if (facet_mode)
+ if (facet_mode) {
facet_list = &mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subfacet, gt_subfacet);
- else
+ } else {
facet_list = &mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subfacet, gt_subfacet);
+ }
Element old_subfacet_el{type_subfacet, 0, gt_subfacet};
Element new_subfacet_el{type_subfacet, 0, gt_subfacet};
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
old_subfacet_el.element = sf_to_double(sf);
new_subfacet_el.element = old_nb_subfacet + sf;
for (UInt f = 0; f < (*facet_list)(sf).size(); ++f) {
Element & facet = (*facet_list)(sf)[f];
if (facet.type != type_facet || facet.ghost_type != gt_facet) {
type_facet = facet.type;
gt_facet = facet.ghost_type;
subfacet_to_facet =
&mesh_facets.getSubelementToElement(type_facet, gt_facet);
nb_subfacet_per_facet = subfacet_to_facet->getNbComponent();
}
Element * sf_update = std::find(
subfacet_to_facet->storage() + facet.element * nb_subfacet_per_facet,
subfacet_to_facet->storage() + facet.element * nb_subfacet_per_facet +
nb_subfacet_per_facet,
old_subfacet_el);
AKANTU_DEBUG_ASSERT(subfacet_to_facet->storage() +
facet.element * nb_subfacet_per_facet !=
subfacet_to_facet->storage() +
facet.element * nb_subfacet_per_facet +
nb_subfacet_per_facet,
"Subfacet not found");
*sf_update = new_subfacet_el;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateFacetToSubfacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode) {
AKANTU_DEBUG_IN();
Array<UInt> & sf_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_subfacet, gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.size();
Array<std::vector<Element>> & facet_to_subfacet =
mesh_facets.getElementToSubelement(type_subfacet, gt_subfacet);
Array<std::vector<Element>> * facet_to_subfacet_double = nullptr;
if (facet_mode) {
facet_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subfacet, gt_subfacet);
} else {
facet_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subfacet, gt_subfacet);
}
UInt old_nb_subfacet = facet_to_subfacet.size();
facet_to_subfacet.resize(old_nb_subfacet + nb_subfacet_to_double);
- for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf)
+ for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
facet_to_subfacet(old_nb_subfacet + sf) = (*facet_to_subfacet_double)(sf);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MeshUtils::doubleSubfacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
- if (spatial_dimension == 1)
+ if (spatial_dimension == 1) {
return;
+ }
for (auto gt_subfacet : ghost_types) {
for (auto type_subfacet : mesh_facets.elementTypes(0, gt_subfacet)) {
auto & sf_to_double = mesh_facets.getData<UInt>(
"facet_to_double", type_subfacet, gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.size();
- if (nb_subfacet_to_double == 0)
+ if (nb_subfacet_to_double == 0) {
continue;
+ }
AKANTU_DEBUG_ASSERT(
type_subfacet == _point_1,
"Only _point_1 subfacet doubling is supported at the moment");
auto & conn_subfacet =
mesh_facets.getConnectivity(type_subfacet, gt_subfacet);
UInt old_nb_subfacet = conn_subfacet.size();
UInt new_nb_subfacet = old_nb_subfacet + nb_subfacet_to_double;
conn_subfacet.resize(new_nb_subfacet);
std::vector<UInt> nodes_to_double;
UInt old_nb_doubled_nodes = doubled_nodes.size();
/// double nodes
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt old_subfacet = sf_to_double(sf);
nodes_to_double.push_back(conn_subfacet(old_subfacet));
}
doubleNodes(mesh, nodes_to_double, doubled_nodes);
/// add new nodes in connectivity
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt new_subfacet = old_nb_subfacet + sf;
UInt new_node = doubled_nodes(old_nb_doubled_nodes + sf, 1);
conn_subfacet(new_subfacet) = new_node;
}
/// update facet and element connectivity
Array<std::vector<Element>> & f_to_subfacet_double =
mesh_facets.getData<std::vector<Element>>("facets_to_subfacet_double",
type_subfacet, gt_subfacet);
Array<std::vector<Element>> & el_to_subfacet_double =
mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_subfacet, gt_subfacet);
Array<std::vector<Element>> * sf_to_subfacet_double = nullptr;
- if (spatial_dimension == 3)
+ if (spatial_dimension == 3) {
sf_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subfacet, gt_subfacet);
+ }
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt old_node = doubled_nodes(old_nb_doubled_nodes + sf, 0);
UInt new_node = doubled_nodes(old_nb_doubled_nodes + sf, 1);
updateElementalConnectivity(mesh, old_node, new_node,
el_to_subfacet_double(sf),
&f_to_subfacet_double(sf));
updateElementalConnectivity(mesh_facets, old_node, new_node,
f_to_subfacet_double(sf));
- if (spatial_dimension == 3)
+ if (spatial_dimension == 3) {
updateElementalConnectivity(mesh_facets, old_node, new_node,
(*sf_to_subfacet_double)(sf));
+ }
}
if (spatial_dimension == 2) {
updateSubfacetToFacet(mesh_facets, type_subfacet, gt_subfacet, true);
updateFacetToSubfacet(mesh_facets, type_subfacet, gt_subfacet, true);
} else if (spatial_dimension == 3) {
updateSubfacetToFacet(mesh_facets, type_subfacet, gt_subfacet, false);
updateFacetToSubfacet(mesh_facets, type_subfacet, gt_subfacet, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::flipFacets(
Mesh & mesh_facets,
const ElementTypeMapArray<UInt> & remote_global_connectivities,
GhostType gt_facet) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
/// get global connectivity for local mesh
ElementTypeMapArray<UInt> local_global_connectivities(
"local_global_connectivity", mesh_facets.getID(),
mesh_facets.getMemoryID());
local_global_connectivities.initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_ghost_type = gt_facet, _with_nb_nodes_per_element = true,
_with_nb_element = true);
mesh_facets.getGlobalConnectivity(local_global_connectivities);
/// loop on every facet
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
auto & connectivity = mesh_facets.getConnectivity(type_facet, gt_facet);
auto & local_global_connectivity =
local_global_connectivities(type_facet, gt_facet);
const auto & remote_global_connectivity =
remote_global_connectivities(type_facet, gt_facet);
auto & element_per_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
auto & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
auto nb_nodes_per_facet = connectivity.getNbComponent();
auto nb_nodes_per_P1_facet =
Mesh::getNbNodesPerElement(Mesh::getP1ElementType(type_facet));
for (auto && data :
zip(make_view(connectivity, nb_nodes_per_facet),
make_view(local_global_connectivity, nb_nodes_per_facet),
make_view(remote_global_connectivity, nb_nodes_per_facet),
make_view(subfacet_to_facet, subfacet_to_facet.getNbComponent()),
make_view(element_per_facet))) {
auto & conn = std::get<0>(data);
auto & local_gconn = std::get<1>(data);
const auto & remote_gconn = std::get<2>(data);
/// skip facet if connectivities are the same
- if (local_gconn == remote_gconn)
+ if (local_gconn == remote_gconn) {
continue;
-
+ }
+
/// re-arrange connectivity
auto conn_tmp = conn;
auto begin = local_gconn.begin();
auto end = local_gconn.end();
AKANTU_DEBUG_ASSERT(std::is_permutation(begin, end, remote_gconn.begin()),
- "This facets are not just permutation of each other, "
- << local_gconn << " and " << remote_gconn);
+ "This facets are not just permutation of each other, "
+ << local_gconn << " and " << remote_gconn);
for (auto && data : enumerate(remote_gconn)) {
auto it = std::find(begin, end, std::get<1>(data));
AKANTU_DEBUG_ASSERT(it != end, "Node not found");
UInt new_position = it - begin;
- conn(new_position) = conn_tmp(std::get<0>(data));;
+ conn(new_position) = conn_tmp(std::get<0>(data));
+ ;
}
// std::transform(remote_gconn.begin(), remote_gconn.end(), conn.begin(),
// [&](auto && gnode) {
// auto it = std::find(begin, end, gnode);
// AKANTU_DEBUG_ASSERT(it != end, "Node not found");
// return conn_tmp(it - begin);
- // });
+ // });
-
/// if 3D, check if facets are just rotated
if (spatial_dimension == 3) {
auto begin = remote_gconn.begin();
/// find first node
auto it = std::find(begin, remote_gconn.end(), local_gconn(0));
- UInt n, start = it - begin;
+ UInt n;
+ UInt start = it - begin;
/// count how many nodes in the received connectivity follow
/// the same order of those in the local connectivity
for (n = 1; n < nb_nodes_per_P1_facet &&
local_gconn(n) ==
remote_gconn((start + n) % nb_nodes_per_P1_facet);
- ++n)
+ ++n) {
;
+ }
/// skip the facet inversion if facet is just rotated
if (n == nb_nodes_per_P1_facet) {
continue;
-
}
}
/// update data to invert facet
auto & element_per_facet = std::get<4>(data);
- if (element_per_facet[1] != ElementNull) // by convention the first facet
- // cannot be a ElementNull
+ if (element_per_facet[1] !=
+ ElementNull) { // by convention the first facet
+ // cannot be a ElementNull
std::swap(element_per_facet[0], element_per_facet[1]);
+ }
auto & subfacets_of_facet = std::get<3>(data);
std::swap(subfacets_of_facet(0), subfacets_of_facet(1));
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::fillElementToSubElementsData(Mesh & mesh) {
AKANTU_DEBUG_IN();
if (mesh.getNbElement(mesh.getSpatialDimension() - 1) == 0) {
AKANTU_DEBUG_INFO("There are not facets, add them in the mesh file or call "
"the buildFacet method.");
return;
}
UInt spatial_dimension = mesh.getSpatialDimension();
ElementTypeMapArray<Real> barycenters("barycenter_tmp", mesh.getID(),
mesh.getMemoryID());
barycenters.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = _all_dimensions);
Element element;
for (auto ghost_type : ghost_types) {
element.ghost_type = ghost_type;
- for (auto & type : mesh.elementTypes(_all_dimensions, ghost_type)) {
+ for (const auto & type : mesh.elementTypes(_all_dimensions, ghost_type)) {
element.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<Real> & barycenters_arr = barycenters(type, ghost_type);
barycenters_arr.resize(nb_element);
auto bary = barycenters_arr.begin(spatial_dimension);
auto bary_end = barycenters_arr.end(spatial_dimension);
for (UInt el = 0; bary != bary_end; ++bary, ++el) {
element.element = el;
mesh.getBarycenter(element, *bary);
}
}
}
MeshAccessor mesh_accessor(mesh);
for (Int sp(spatial_dimension); sp >= 1; --sp) {
- if (mesh.getNbElement(sp) == 0)
+ if (mesh.getNbElement(sp) == 0) {
continue;
+ }
for (auto ghost_type : ghost_types) {
- for (auto & type : mesh.elementTypes(sp, ghost_type)) {
+ for (const auto & type : mesh.elementTypes(sp, ghost_type)) {
mesh_accessor.getSubelementToElement(type, ghost_type)
.resize(mesh.getNbElement(type, ghost_type));
mesh_accessor.getSubelementToElement(type, ghost_type).set(ElementNull);
}
- for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
+ for (const auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
mesh_accessor.getElementToSubelement(type, ghost_type)
.resize(mesh.getNbElement(type, ghost_type));
- mesh.getElementToSubelement(type, ghost_type).clear();
+ mesh.getElementToSubelement(type, ghost_type).zero();
}
}
CSR<Element> nodes_to_elements;
buildNode2Elements(mesh, nodes_to_elements, sp);
Element facet_element;
for (auto ghost_type : ghost_types) {
facet_element.ghost_type = ghost_type;
- for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
+ for (const auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
facet_element.type = type;
auto & element_to_subelement =
mesh.getElementToSubelement(type, ghost_type);
const auto & connectivity = mesh.getConnectivity(type, ghost_type);
for (auto && data : enumerate(
make_view(connectivity, mesh.getNbNodesPerElement(type)))) {
const auto & facet = std::get<1>(data);
facet_element.element = std::get<0>(data);
std::map<Element, UInt> element_seen_counter;
auto nb_nodes_per_facet =
mesh.getNbNodesPerElement(Mesh::getP1ElementType(type));
// count the number of node in common between the facet and the other
// element connected to the nodes of the facet
for (auto node : arange(nb_nodes_per_facet)) {
for (auto & elem : nodes_to_elements.getRow(facet(node))) {
auto cit = element_seen_counter.find(elem);
if (cit != element_seen_counter.end()) {
cit->second++;
} else {
element_seen_counter[elem] = 1;
}
}
}
// check which are the connected elements
std::vector<Element> connected_elements;
for (auto && cit : element_seen_counter) {
- if (cit.second == nb_nodes_per_facet)
+ if (cit.second == nb_nodes_per_facet) {
connected_elements.push_back(cit.first);
+ }
}
// add the connected elements as sub-elements
for (auto & connected_element : connected_elements) {
element_to_subelement(facet_element.element)
.push_back(connected_element);
}
// add the element as sub-element to the connected elements
for (auto & connected_element : connected_elements) {
Vector<Element> subelements_to_element =
mesh.getSubelementToElement(connected_element);
// find the position where to insert the element
auto it = std::find(subelements_to_element.begin(),
subelements_to_element.end(), ElementNull);
AKANTU_DEBUG_ASSERT(
it != subelements_to_element.end(),
"The element "
<< connected_element << " seems to have too many facets!! ("
<< (it - subelements_to_element.begin()) << " < "
<< mesh.getNbFacetsPerElement(connected_element.type)
<< ")");
*it = facet_element;
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool third_dim_points>
bool MeshUtils::findElementsAroundSubfacet(
const Mesh & mesh_facets, const Element & starting_element,
const Element & end_facet, const Vector<UInt> & subfacet_connectivity,
std::vector<Element> & element_list, std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list) {
AKANTU_DEBUG_IN();
bool facet_matched = false;
element_list.clear();
facet_list.clear();
if (third_dim_points) {
subfacet_list->clear();
}
element_list.push_back(starting_element);
std::queue<Element> elements_to_check;
elements_to_check.push(starting_element);
/// keep going as long as there are elements to check
while (not elements_to_check.empty()) {
/// check current element
Element & current_element = elements_to_check.front();
const Vector<Element> facets_to_element =
mesh_facets.getSubelementToElement(current_element);
// for every facet of the element
- for (auto & current_facet : facets_to_element) {
- if (current_facet == ElementNull)
+ for (const auto & current_facet : facets_to_element) {
+ if (current_facet == ElementNull) {
continue;
+ }
- if (current_facet == end_facet)
+ if (current_facet == end_facet) {
facet_matched = true;
+ }
// facet already listed
if (std::find(facet_list.begin(), facet_list.end(), current_facet) !=
- facet_list.end())
+ facet_list.end()) {
continue;
+ }
// subfacet_connectivity is not in the connectivity of current_facet;
if ((std::find(facet_list.begin(), facet_list.end(), current_facet) !=
facet_list.end()) or
not hasElement(mesh_facets.getConnectivity(current_facet),
- subfacet_connectivity))
+ subfacet_connectivity)) {
continue;
+ }
facet_list.push_back(current_facet);
if (third_dim_points) {
const Vector<Element> subfacets_of_facet =
mesh_facets.getSubelementToElement(current_facet);
/// check subfacets
for (const auto & current_subfacet : subfacets_of_facet) {
- if (current_subfacet == ElementNull)
+ if (current_subfacet == ElementNull) {
continue;
+ }
if ((std::find(subfacet_list->begin(), subfacet_list->end(),
current_subfacet) == subfacet_list->end()) and
hasElement(mesh_facets.getConnectivity(current_subfacet),
- subfacet_connectivity))
+ subfacet_connectivity)) {
subfacet_list->push_back(current_subfacet);
+ }
}
}
/// consider opposing element
const auto & elements_to_facet =
mesh_facets.getElementToSubelement(current_facet);
UInt opposing = 0;
- if (elements_to_facet[0] == current_element)
+ if (elements_to_facet[0] == current_element) {
opposing = 1;
+ }
- auto & opposing_element = elements_to_facet[opposing];
+ const auto & opposing_element = elements_to_facet[opposing];
/// skip null elements since they are on a boundary
- if (opposing_element == ElementNull)
+ if (opposing_element == ElementNull) {
continue;
+ }
/// skip this element if already added
if (std::find(element_list.begin(), element_list.end(),
- opposing_element) != element_list.end())
+ opposing_element) != element_list.end()) {
continue;
+ }
/// only regular elements have to be checked
- if (opposing_element.kind() == _ek_regular)
+ if (opposing_element.kind() == _ek_regular) {
elements_to_check.push(opposing_element);
+ }
element_list.push_back(opposing_element);
AKANTU_DEBUG_ASSERT(
hasElement(
mesh_facets.getMeshParent().getConnectivity(opposing_element),
subfacet_connectivity),
"Subfacet doesn't belong to this element");
}
/// erased checked element from the list
elements_to_check.pop();
}
AKANTU_DEBUG_OUT();
return facet_matched;
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateElementalConnectivity(
Mesh & mesh, UInt old_node, UInt new_node,
const std::vector<Element> & element_list,
const std::vector<Element> *
#if defined(AKANTU_COHESIVE_ELEMENT)
facet_list
#endif
) {
AKANTU_DEBUG_IN();
- for (auto & element : element_list) {
- if (element.type == _not_defined)
+ for (const auto & element : element_list) {
+ if (element.type == _not_defined) {
continue;
+ }
Vector<UInt> connectivity = mesh.getConnectivity(element);
#if defined(AKANTU_COHESIVE_ELEMENT)
if (element.kind() == _ek_cohesive) {
AKANTU_DEBUG_ASSERT(
facet_list != nullptr,
"Provide a facet list in order to update cohesive elements");
const Vector<Element> facets =
mesh.getMeshFacets().getSubelementToElement(element);
auto facet_nb_nodes = connectivity.size() / 2;
/// loop over cohesive element's facets
for (const auto & facet : enumerate(facets)) {
/// skip facets if not present in the list
if (std::find(facet_list->begin(), facet_list->end(),
std::get<1>(facet)) == facet_list->end()) {
continue;
}
auto n = std::get<0>(facet);
- auto begin = connectivity.begin() + n * facet_nb_nodes;
+ auto begin =
+ connectivity.begin() +
+ n * facet_nb_nodes; // NOLINT(bugprone-narrowing-conversions)
auto end = begin + facet_nb_nodes;
auto it = std::find(begin, end, old_node);
AKANTU_DEBUG_ASSERT(it != end, "Node not found in current element");
*it = new_node;
}
} else
#endif
{
auto it = std::find(connectivity.begin(), connectivity.end(), old_node);
AKANTU_DEBUG_ASSERT(it != connectivity.end(),
"Node not found in current element");
/// update connectivity
*it = new_node;
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/mesh_utils.hh b/src/mesh_utils/mesh_utils.hh
index 88a918424..3c3fdec08 100644
--- a/src/mesh_utils/mesh_utils.hh
+++ b/src/mesh_utils/mesh_utils.hh
@@ -1,227 +1,228 @@
/**
* @file mesh_utils.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief All mesh utils necessary for various tasks
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_UTILS_HH__
-#define __AKANTU_MESH_UTILS_HH__
+#ifndef AKANTU_MESH_UTILS_HH_
+#define AKANTU_MESH_UTILS_HH_
namespace akantu {
class MeshUtils {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build a CSR<Element> that contains for each node the list of connected
/// elements of a given spatial dimension
static void buildNode2Elements(const Mesh & mesh, CSR<Element> & node_to_elem,
UInt spatial_dimension = _all_dimensions);
/// build a CSR<UInt> that contains for each node the number of
/// the connected elements of a given ElementType
static void
buildNode2ElementsElementTypeMap(const Mesh & mesh, CSR<UInt> & node_to_elem,
- const ElementType & type,
- const GhostType & ghost_type = _not_ghost);
+ ElementType type,
+ GhostType ghost_type = _not_ghost);
/// build the facets elements on the boundaries of a mesh
static void buildFacets(Mesh & mesh);
/// build all the facets elements: boundary and internals and store them in
/// the mesh_facets for element of dimension from_dimension to to_dimension
static void buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt from_dimension, UInt to_dimension);
/// build all the facets elements: boundary and internals and store them in
/// the mesh_facets
static void buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt to_dimension = 0);
/// build facets for a given spatial dimension
static void buildFacetsDimension(const Mesh & mesh, Mesh & mesh_facets,
bool boundary_only, UInt dimension);
/// take the local_connectivity array as the array of local and ghost
/// connectivity, renumber the nodes and set the connectivity of the mesh
static void renumberMeshNodes(Mesh & mesh, Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type, Array<UInt> & old_nodes);
/// compute pbc pair for a given direction
- static void computePBCMap(const Mesh & mymesh, const UInt dir,
+ static void computePBCMap(const Mesh & mymesh, UInt dir,
std::map<UInt, UInt> & pbc_pair);
/// compute pbc pair for a surface pair
static void computePBCMap(const Mesh & mymesh,
const std::pair<ID, ID> & surface_pair,
std::map<UInt, UInt> & pbc_pair);
/// remove not connected nodes /!\ this functions renumbers the nodes.
static void purifyMesh(Mesh & mesh);
#if defined(AKANTU_COHESIVE_ELEMENT)
/// function to insert cohesive elements on the selected facets
/// @return number of facets that have been doubled
static UInt
insertCohesiveElements(Mesh & mesh, Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes,
Array<Element> & new_elements,
bool only_double_facets);
#endif
/// fill the subelement to element and the elements to subelements data
static void fillElementToSubElementsData(Mesh & mesh);
/// flip facets based on global connectivity
- static void flipFacets(Mesh & mesh_facets,
- const ElementTypeMapArray<UInt> & global_connectivity,
- GhostType gt_facet);
+ static void
+ flipFacets(Mesh & mesh_facets,
+ const ElementTypeMapArray<UInt> & remote_global_connectivities,
+ GhostType gt_facet);
/// provide list of elements around a node and check if a given
/// facet is reached
template <bool third_dim_points>
static bool findElementsAroundSubfacet(
const Mesh & mesh_facets, const Element & starting_element,
const Element & end_facet, const Vector<UInt> & subfacet_connectivity,
- std::vector<Element> & elem_list, std::vector<Element> & facet_list,
+ std::vector<Element> & element_list, std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list = nullptr);
/// function to check if a node belongs to a given element
static inline bool hasElement(const Vector<UInt> & nodes_element,
const Vector<UInt> & nodes);
/// reset facet_to_double arrays in the Mesh
static void resetFacetToDouble(Mesh & mesh_facets);
private:
/// match pairs that are on the associated pbc's
- static void matchPBCPairs(const Mesh & mymesh, const UInt dir,
+ static void matchPBCPairs(const Mesh & mymesh, UInt dir,
Array<UInt> & selected_left,
Array<UInt> & selected_right,
std::map<UInt, UInt> & pbc_pair);
/// function used by all the renumbering functions
static void
renumberNodesInConnectivity(Array<UInt> & list_nodes, UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map);
/// update facet_to_subfacet
static void updateFacetToSubfacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode);
/// update subfacet_to_facet
static void updateSubfacetToFacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode);
/// function to double a given facet and update the list of doubled
/// nodes
static void doubleFacet(Mesh & mesh, Mesh & mesh_facets, UInt facet_dimension,
Array<UInt> & doubled_nodes, bool facet_mode);
/// function to double a subfacet given start and end index for
/// local facet_to_subfacet vector, and update the list of doubled
/// nodes
template <UInt spatial_dimension>
static void doubleSubfacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes);
/// double a node
static void doubleNodes(Mesh & mesh, const std::vector<UInt> & old_nodes,
Array<UInt> & doubled_nodes);
/// fill facet_to_double array in the mesh
/// returns the number of facets to be doubled
static UInt
updateFacetToDouble(Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion);
/// find subfacets to be doubled
template <bool subsubfacet_mode>
static void findSubfacetToDouble(Mesh & mesh_facets);
/// double facets (points) in 1D
static void doublePointFacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes);
#if defined(AKANTU_COHESIVE_ELEMENT)
/// update cohesive element data
static void updateCohesiveData(Mesh & mesh, Mesh & mesh_facets,
Array<Element> & new_elements);
#endif
/// update elemental connectivity after doubling a node
inline static void updateElementalConnectivity(
Mesh & mesh, UInt old_node, UInt new_node,
const std::vector<Element> & element_list,
const std::vector<Element> * facet_list = nullptr);
/// double middle nodes if facets are _segment_3
template <bool third_dim_segments>
static void updateQuadraticSegments(Mesh & mesh, Mesh & mesh_facets,
ElementType type_facet,
GhostType gt_facet,
Array<UInt> & doubled_nodes);
/// remove elements on a vector
inline static bool
removeElementsInVector(const std::vector<Element> & elem_to_remove,
std::vector<Element> & elem_list);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "mesh_utils_inline_impl.hh"
-#endif /* __AKANTU_MESH_UTILS_HH__ */
+#endif /* AKANTU_MESH_UTILS_HH_ */
diff --git a/src/mesh_utils/mesh_utils_distribution.cc b/src/mesh_utils/mesh_utils_distribution.cc
index 147726140..b9e7ad2ad 100644
--- a/src/mesh_utils/mesh_utils_distribution.cc
+++ b/src/mesh_utils/mesh_utils_distribution.cc
@@ -1,160 +1,162 @@
/**
* @file mesh_utils_distribution.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 08 2016
* @date last modification: Tue Nov 07 2017
*
* @brief Implementation of the methods of mesh utils distribute
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_utils_distribution.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "mesh_partition.hh"
#include "mesh_utils.hh"
#include "node_info_per_processor.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace MeshUtilsDistribution {
/* ------------------------------------------------------------------------ */
- void distributeMeshCentralized(Mesh & mesh, UInt,
+ void distributeMeshCentralized(Mesh & mesh, UInt /*unused*/,
const MeshPartition & partition) {
MeshAccessor mesh_accessor(mesh);
ElementSynchronizer & element_synchronizer =
mesh_accessor.getElementSynchronizer();
NodeSynchronizer & node_synchronizer = mesh_accessor.getNodeSynchronizer();
const Communicator & comm = element_synchronizer.getCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
mesh_accessor.setNbGlobalNodes(mesh.getNbNodes());
auto & gids = mesh_accessor.getNodesGlobalIds();
- if (nb_proc == 1)
+ if (nb_proc == 1) {
return;
+ }
gids.resize(0);
mesh.synchronizeGroupNames();
AKANTU_DEBUG_ASSERT(
partition.getNbPartition() == nb_proc,
"The number of partition does not match the number of processors: "
<< partition.getNbPartition() << " != " << nb_proc);
/**
* connectivity and communications scheme construction
*/
UInt count = 0;
/* --- MAIN LOOP ON TYPES --- */
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
/// \todo change this ugly way to avoid a problem if an element
/// type is present in the mesh but not in the partitions
try {
partition.getPartition(type, _not_ghost);
} catch (...) {
continue;
}
MasterElementInfoPerProc proc_infos(element_synchronizer, count, my_rank,
type, partition);
proc_infos.synchronize();
++count;
}
{ /// Ending the synchronization of elements by sending a stop message
MasterElementInfoPerProc proc_infos(element_synchronizer, count, my_rank,
_not_defined, partition);
proc_infos.synchronize();
++count;
}
/**
* Nodes synchronization
*/
MasterNodeInfoPerProc node_proc_infos(node_synchronizer, count, my_rank);
node_proc_infos.synchronize();
MeshUtils::fillElementToSubElementsData(mesh);
mesh_accessor.setDistributed();
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------ */
void distributeMeshCentralized(Mesh & mesh, UInt root) {
MeshAccessor mesh_accessor(mesh);
ElementSynchronizer & element_synchronizer =
mesh_accessor.getElementSynchronizer();
NodeSynchronizer & node_synchronizer = mesh_accessor.getNodeSynchronizer();
const Communicator & comm = element_synchronizer.getCommunicator();
UInt nb_proc = comm.getNbProc();
mesh_accessor.getNodesGlobalIds().resize(0);
- if (nb_proc == 1)
+ if (nb_proc == 1) {
return;
+ }
mesh.synchronizeGroupNames();
/**
* connectivity and communications scheme construction on distant
* processors
*/
UInt count = 0;
bool need_synchronize = true;
do {
/* --------<<<<-SIZE--------------------------------------------------- */
SlaveElementInfoPerProc proc_infos(element_synchronizer, count, root);
need_synchronize = proc_infos.synchronize();
++count;
} while (need_synchronize);
/**
* Nodes synchronization
*/
SlaveNodeInfoPerProc node_proc_infos(node_synchronizer, count, root);
node_proc_infos.synchronize();
MeshUtils::fillElementToSubElementsData(mesh);
mesh_accessor.setDistributed();
}
} // namespace MeshUtilsDistribution
} // namespace akantu
diff --git a/src/mesh_utils/mesh_utils_distribution.hh b/src/mesh_utils/mesh_utils_distribution.hh
index 4ec00ddd8..f8c768f12 100644
--- a/src/mesh_utils/mesh_utils_distribution.hh
+++ b/src/mesh_utils/mesh_utils_distribution.hh
@@ -1,54 +1,54 @@
/**
* @file mesh_utils_distribution.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sat Apr 01 2017
*
* @brief Mesh utils to distribute a mesh
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_UTILS_DISTRIBUTION_HH__
-#define __AKANTU_MESH_UTILS_DISTRIBUTION_HH__
+#ifndef AKANTU_MESH_UTILS_DISTRIBUTION_HH_
+#define AKANTU_MESH_UTILS_DISTRIBUTION_HH_
namespace akantu {
class Mesh;
class MeshPartition;
} // namespace akantu
namespace akantu {
namespace MeshUtilsDistribution {
/// Master call to distribute a mesh in a centralized manner (the UInt is just
/// to avoid some shitty access from the slave...)
- void distributeMeshCentralized(Mesh & mesh, UInt,
+ void distributeMeshCentralized(Mesh & mesh, UInt /*unused*/,
const MeshPartition & partition);
/// Slave call to distribute a mesh in a centralized manner
void distributeMeshCentralized(Mesh & mesh, UInt root);
} // namespace MeshUtilsDistribution
} // namespace akantu
-#endif /* __AKANTU_MESH_UTILS_DISTRIBUTION_HH__ */
+#endif /* AKANTU_MESH_UTILS_DISTRIBUTION_HH_ */
diff --git a/src/mesh_utils/mesh_utils_inline_impl.hh b/src/mesh_utils/mesh_utils_inline_impl.hh
index 01057936a..8cb648176 100644
--- a/src/mesh_utils/mesh_utils_inline_impl.hh
+++ b/src/mesh_utils/mesh_utils_inline_impl.hh
@@ -1,86 +1,87 @@
/**
* @file mesh_utils_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Aug 20 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Mesh utils inline functions
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_UTILS_INLINE_IMPL_HH__
-#define __AKANTU_MESH_UTILS_INLINE_IMPL_HH__
+#ifndef AKANTU_MESH_UTILS_INLINE_IMPL_HH_
+#define AKANTU_MESH_UTILS_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline bool MeshUtils::hasElement(const Vector<UInt> & nodes_element,
const Vector<UInt> & nodes) {
// one of the nodes of nodes is not in nodes_element stops
auto it = std::mismatch(nodes.begin(), nodes.end(), nodes_element.begin(),
[&](auto && node, auto && /*node2*/) -> bool {
auto it = std::find(nodes_element.begin(),
nodes_element.end(), node);
return (it != nodes_element.end());
});
// true if all nodes where found in nodes_element
return (it.first == nodes.end());
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
inline bool
MeshUtils::removeElementsInVector(const std::vector<Element> & elem_to_remove,
std::vector<Element> & elem_list) {
- if (elem_list.size() <= elem_to_remove.size())
+ if (elem_list.size() <= elem_to_remove.size()) {
return true;
+ }
auto el_it = elem_to_remove.begin();
auto el_last = elem_to_remove.end();
std::vector<Element>::iterator el_del;
UInt deletions = 0;
for (; el_it != el_last; ++el_it) {
el_del = std::find(elem_list.begin(), elem_list.end(), *el_it);
if (el_del != elem_list.end()) {
elem_list.erase(el_del);
++deletions;
}
}
AKANTU_DEBUG_ASSERT(deletions == 0 || deletions == elem_to_remove.size(),
"Not all elements have been erased");
return deletions == 0;
}
} // namespace akantu
-#endif /* __AKANTU_MESH_UTILS_INLINE_IMPL_HH__ */
+#endif /* AKANTU_MESH_UTILS_INLINE_IMPL_HH_ */
diff --git a/src/mesh_utils/mesh_utils_pbc.cc b/src/mesh_utils/mesh_utils_pbc.cc
index 7c71e3481..b491caba8 100644
--- a/src/mesh_utils/mesh_utils_pbc.cc
+++ b/src/mesh_utils/mesh_utils_pbc.cc
@@ -1,298 +1,309 @@
/**
* @file mesh_utils_pbc.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Wed Feb 09 2011
* @date last modification: Tue Feb 20 2018
*
* @brief periodic boundary condition connectivity tweak
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/// class that sorts a set of nodes of same coordinates in 'dir' direction
class CoordinatesComparison {
public:
CoordinatesComparison(const UInt dimension, const UInt dir_1,
const UInt dir_2, Real normalization, Real tolerance,
const Array<Real> & coords)
: dim(dimension), dir_1(dir_1), dir_2(dir_2),
normalization(normalization), tolerance(tolerance),
coords_it(coords.begin(dim)) {}
// answers the question whether n2 is larger or equal to n1
bool operator()(const UInt n1, const UInt n2) {
Vector<Real> coords_n1 = coords_it[n1];
Vector<Real> coords_n2 = coords_it[n2];
return this->operator()(coords_n1, coords_n2);
}
bool operator()(const Vector<Real> & coords_n1,
- const Vector<Real> & coords_n2) {
+ const Vector<Real> & coords_n2) const {
Real diff = coords_n1(dir_1) - coords_n2(dir_1);
;
- if (dim == 2 || std::abs(diff) / normalization > tolerance)
- return diff > 0. ? false : true;
- else if (dim > 2) {
+ if (dim == 2 || std::abs(diff) / normalization > tolerance) {
+ return (diff <= 0.);
+ }
+ if (dim > 2) {
diff = coords_n1(dir_2) - coords_n2(dir_2);
- ;
- return diff > 0 ? false : true;
+ return (diff <= 0);
}
return true;
}
private:
UInt dim;
UInt dir_1;
UInt dir_2;
Real normalization;
Real tolerance;
const Array<Real>::const_vector_iterator coords_it;
};
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh, const UInt dir,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_left;
Array<UInt> selected_right;
const UInt dim = mesh.getSpatialDimension();
auto it = mesh.getNodes().begin(dim);
auto end = mesh.getNodes().end(dim);
- if (dim <= dir)
+ if (dim <= dir) {
return;
+ }
const Vector<Real> & lower_bounds = mesh.getLowerBounds();
const Vector<Real> & upper_bounds = mesh.getUpperBounds();
AKANTU_DEBUG_INFO("min " << lower_bounds(dir));
AKANTU_DEBUG_INFO("max " << upper_bounds(dir));
for (UInt node = 0; it != end; ++it, ++node) {
const Vector<Real> & coords = *it;
AKANTU_DEBUG_TRACE("treating " << coords(dir));
if (Math::are_float_equal(coords(dir), lower_bounds(dir))) {
AKANTU_DEBUG_TRACE("pushing node " << node << " on the left side");
selected_left.push_back(node);
} else if (Math::are_float_equal(coords(dir), upper_bounds(dir))) {
selected_right.push_back(node);
AKANTU_DEBUG_TRACE("pushing node " << node << " on the right side");
}
}
AKANTU_DEBUG_INFO("found "
<< selected_left.size() << " and " << selected_right.size()
<< " nodes at each boundary for direction " << dir);
// match pairs
MeshUtils::matchPBCPairs(mesh, dir, selected_left, selected_right, pbc_pair);
}
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh,
const std::pair<ID, ID> & surface_pair,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_first;
Array<UInt> selected_second;
// find nodes on surfaces
const ElementGroup & first_surf = mesh.getElementGroup(surface_pair.first);
const ElementGroup & second_surf = mesh.getElementGroup(surface_pair.second);
// if this surface pair is not on this proc
if (first_surf.getNbNodes() == 0 || second_surf.getNbNodes() == 0) {
AKANTU_DEBUG_WARNING("computePBCMap has at least one surface without any "
"nodes. I will ignore it.");
return;
}
// copy nodes from element group
selected_first.copy(first_surf.getNodeGroup().getNodes());
selected_second.copy(second_surf.getNodeGroup().getNodes());
// coordinates
const Array<Real> & coords = mesh.getNodes();
const UInt dim = mesh.getSpatialDimension();
// variables to find min and max of surfaces
- Real first_max[3], first_min[3];
- Real second_max[3], second_min[3];
+ Real first_max[3];
+ Real first_min[3];
+ Real second_max[3];
+ Real second_min[3];
for (UInt i = 0; i < dim; ++i) {
first_min[i] = std::numeric_limits<Real>::max();
second_min[i] = std::numeric_limits<Real>::max();
first_max[i] = -std::numeric_limits<Real>::max();
second_max[i] = -std::numeric_limits<Real>::max();
}
// find min and max of surface nodes
for (auto it = selected_first.begin(); it != selected_first.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
- if (first_min[i] > coords(*it, i))
+ if (first_min[i] > coords(*it, i)) {
first_min[i] = coords(*it, i);
- if (first_max[i] < coords(*it, i))
+ }
+ if (first_max[i] < coords(*it, i)) {
first_max[i] = coords(*it, i);
+ }
}
}
for (auto it = selected_second.begin(); it != selected_second.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
- if (second_min[i] > coords(*it, i))
+ if (second_min[i] > coords(*it, i)) {
second_min[i] = coords(*it, i);
- if (second_max[i] < coords(*it, i))
+ }
+ if (second_max[i] < coords(*it, i)) {
second_max[i] = coords(*it, i);
+ }
}
}
// find direction of pbc
Int first_dir = -1;
#ifndef AKANTU_NDEBUG
Int second_dir = -2;
#endif
for (UInt i = 0; i < dim; ++i) {
if (Math::are_float_equal(first_min[i], first_max[i])) {
first_dir = i;
}
#ifndef AKANTU_NDEBUG
if (Math::are_float_equal(second_min[i], second_max[i])) {
second_dir = i;
}
#endif
}
AKANTU_DEBUG_ASSERT(first_dir == second_dir,
"Surface pair has not same direction. Surface "
<< surface_pair.first << " dir=" << first_dir
<< " ; Surface " << surface_pair.second
<< " dir=" << second_dir);
UInt dir = first_dir;
// match pairs
- if (first_min[dir] < second_min[dir])
+ if (first_min[dir] < second_min[dir]) {
MeshUtils::matchPBCPairs(mesh, dir, selected_first, selected_second,
pbc_pair);
- else
+ } else {
MeshUtils::matchPBCPairs(mesh, dir, selected_second, selected_first,
pbc_pair);
+ }
}
/* -------------------------------------------------------------------------- */
void MeshUtils::matchPBCPairs(const Mesh & mesh, const UInt dir,
Array<UInt> & selected_left,
Array<UInt> & selected_right,
std::map<UInt, UInt> & pbc_pair) {
// tolerance is that large because most meshers generate points coordinates
// with single precision only (it is the case of GMSH for instance)
Real tolerance = 1e-7;
const UInt dim = mesh.getSpatialDimension();
Real normalization = mesh.getUpperBounds()(dir) - mesh.getLowerBounds()(dir);
AKANTU_DEBUG_ASSERT(std::abs(normalization) > Math::getTolerance(),
"In matchPBCPairs: The normalization is zero. "
<< "Did you compute the bounding box of the mesh?");
- auto odir_1 = UInt(-1), odir_2 = UInt(-1);
+ auto odir_1 = UInt(-1);
+ auto odir_2 = UInt(-1);
if (dim == 3) {
if (dir == _x) {
odir_1 = _y;
odir_2 = _z;
} else if (dir == _y) {
odir_1 = _x;
odir_2 = _z;
} else if (dir == _z) {
odir_1 = _x;
odir_2 = _y;
}
} else if (dim == 2) {
if (dir == _x) {
odir_1 = _y;
} else if (dir == _y) {
odir_1 = _x;
}
}
CoordinatesComparison compare_nodes(dim, odir_1, odir_2, normalization,
tolerance, mesh.getNodes());
std::sort(selected_left.begin(), selected_left.end(), compare_nodes);
std::sort(selected_right.begin(), selected_right.end(), compare_nodes);
auto it_left = selected_left.begin();
auto end_left = selected_left.end();
auto it_right = selected_right.begin();
auto end_right = selected_right.end();
auto nit = mesh.getNodes().begin(dim);
while ((it_left != end_left) && (it_right != end_right)) {
UInt i1 = *it_left;
UInt i2 = *it_right;
Vector<Real> coords1 = nit[i1];
Vector<Real> coords2 = nit[i2];
AKANTU_DEBUG_TRACE("do I pair? " << i1 << "(" << coords1 << ") with" << i2
<< "(" << coords2 << ") in direction "
<< dir);
Real dx = 0.0;
Real dy = 0.0;
- if (dim >= 2)
+ if (dim >= 2) {
dx = coords1(odir_1) - coords2(odir_1);
- if (dim == 3)
+ }
+ if (dim == 3) {
dy = coords1(odir_2) - coords2(odir_2);
+ }
if (std::abs(dx * dx + dy * dy) / normalization < tolerance) {
// then i match these pairs
- if (pbc_pair.count(i2)) {
+ if (pbc_pair.count(i2) != 0U) {
i2 = pbc_pair[i2];
}
pbc_pair[i1] = i2;
AKANTU_DEBUG_TRACE("pairing " << i1 << "(" << coords1 << ") with" << i2
<< "(" << coords2 << ") in direction "
<< dir);
++it_left;
++it_right;
} else if (compare_nodes(coords1, coords2)) {
++it_left;
} else {
++it_right;
}
}
AKANTU_DEBUG_INFO("found " << pbc_pair.size() << " pairs for direction "
<< dir);
}
} // namespace akantu
diff --git a/src/model/common/boundary_condition/boundary_condition.hh b/src/model/common/boundary_condition/boundary_condition.hh
index f8520f161..0067f7dd9 100644
--- a/src/model/common/boundary_condition/boundary_condition.hh
+++ b/src/model/common/boundary_condition/boundary_condition.hh
@@ -1,100 +1,100 @@
/**
* @file boundary_condition.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief XXX
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_BOUNDARY_CONDITION_HH__
-#define __AKANTU_BOUNDARY_CONDITION_HH__
+#ifndef AKANTU_BOUNDARY_CONDITION_HH_
+#define AKANTU_BOUNDARY_CONDITION_HH_
#include "aka_common.hh"
#include "boundary_condition_functor.hh"
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace akantu {
template <class ModelType> class BoundaryCondition {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
/* ------------------------------------------------------------------------ */
/* Constructors / Destructors / Initializers */
/* ------------------------------------------------------------------------ */
public:
BoundaryCondition() : model(nullptr) {}
/// Initialize the boundary conditions
- void initBC(ModelType & ptr, Array<Real> & primal, Array<Real> & dual);
- void initBC(ModelType & ptr, Array<Real> & primal,
+ void initBC(ModelType & model, Array<Real> & primal, Array<Real> & dual);
+ void initBC(ModelType & model, Array<Real> & primal,
Array<Real> & primal_increment, Array<Real> & dual);
/* ------------------------------------------------------------------------ */
/* Methods and accessors */
/* ------------------------------------------------------------------------ */
public:
// inline void initBoundaryCondition();
template <typename FunctorType>
/// Apply the boundary conditions
inline void applyBC(const FunctorType & func);
template <class FunctorType>
inline void applyBC(const FunctorType & func, const std::string & group_name);
template <class FunctorType>
inline void applyBC(const FunctorType & func,
const ElementGroup & element_group);
AKANTU_GET_MACRO_NOT_CONST(Model, *model, ModelType &);
AKANTU_GET_MACRO_NOT_CONST(Primal, *primal, Array<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Dual, *dual, Array<Real> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
template <class FunctorType, BC::Functor::Type type = FunctorType::type>
struct TemplateFunctionWrapper;
private:
ModelType * model;
Array<Real> * primal{nullptr};
Array<Real> * dual{nullptr};
Array<Real> * primal_increment{nullptr};
};
} // namespace akantu
#include "boundary_condition_tmpl.hh"
-#endif /* __AKANTU_BOUNDARY_CONDITION_HH__ */
+#endif /* AKANTU_BOUNDARY_CONDITION_HH_ */
diff --git a/src/model/common/boundary_condition/boundary_condition_functor.hh b/src/model/common/boundary_condition/boundary_condition_functor.hh
index 67119c358..d793cb055 100644
--- a/src/model/common/boundary_condition/boundary_condition_functor.hh
+++ b/src/model/common/boundary_condition/boundary_condition_functor.hh
@@ -1,213 +1,213 @@
/**
* @file boundary_condition_functor.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Tue Feb 20 2018
*
* @brief Definitions of the functors to apply boundary conditions
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "fe_engine.hh"
#include "integration_point.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__
-#define __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__
+#ifndef AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH_
+#define AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
namespace BC {
using Axis = ::akantu::SpatialDirection;
/* ---------------------------------------------------------------------- */
struct Functor {
enum Type { _dirichlet, _neumann };
virtual ~Functor() = default;
};
/* ---------------------------------------------------------------------- */
namespace Dirichlet {
class DirichletFunctor : public Functor {
public:
DirichletFunctor() = default;
explicit DirichletFunctor(Axis ax) : axis(ax) {}
virtual void operator()(__attribute__((unused)) UInt node,
__attribute__((unused)) Vector<bool> & flags,
__attribute__((unused)) Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
AKANTU_TO_IMPLEMENT();
}
public:
static const Type type = _dirichlet;
protected:
Axis axis{_x};
};
/* ---------------------------------------------------------------------- */
class FlagOnly : public DirichletFunctor {
public:
explicit FlagOnly(Axis ax = _x) : DirichletFunctor(ax) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
- const Vector<Real> & coord) const;
+ const Vector<Real> & coord) const override;
};
/* ---------------------------------------------------------------------- */
// class FreeBoundary : public DirichletFunctor {
// public:
// explicit FreeBoundary(Axis ax = _x) : DirichletFunctor(ax) {}
// public:
// inline void operator()(UInt node, Vector<bool> & flags,
// Vector<Real> & primal,
// const Vector<Real> & coord) const;
// };
/* ---------------------------------------------------------------------- */
class FixedValue : public DirichletFunctor {
public:
FixedValue(Real val, Axis ax = _x) : DirichletFunctor(ax), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
- const Vector<Real> & coord) const;
+ const Vector<Real> & coord) const override;
protected:
Real value;
};
/* ---------------------------------------------------------------------- */
class IncrementValue : public DirichletFunctor {
public:
IncrementValue(Real val, Axis ax = _x)
: DirichletFunctor(ax), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
- const Vector<Real> & coord) const;
+ const Vector<Real> & coord) const override;
inline void setIncrement(Real val) { this->value = val; }
protected:
Real value;
};
/* ---------------------------------------------------------------------- */
class Increment : public DirichletFunctor {
public:
explicit Increment(const Vector<Real> & val)
: DirichletFunctor(_x), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
- const Vector<Real> & coord) const;
+ const Vector<Real> & coord) const override;
inline void setIncrement(const Vector<Real> & val) { this->value = val; }
protected:
Vector<Real> value;
};
} // namespace Dirichlet
/* ------------------------------------------------------------------------ */
/* Neumann */
/* ------------------------------------------------------------------------ */
namespace Neumann {
class NeumannFunctor : public Functor {
protected:
NeumannFunctor() = default;
public:
virtual void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const = 0;
- virtual ~NeumannFunctor() = default;
+ ~NeumannFunctor() override = default;
public:
static const Type type = _neumann;
};
/* ---------------------------------------------------------------------- */
class FromHigherDim : public NeumannFunctor {
public:
explicit FromHigherDim(const Matrix<Real> & mat) : bc_data(mat) {}
~FromHigherDim() override = default;
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const override;
protected:
Matrix<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FromSameDim : public NeumannFunctor {
public:
explicit FromSameDim(const Vector<Real> & vec) : bc_data(vec) {}
~FromSameDim() override = default;
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const override;
protected:
Vector<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FreeBoundary : public NeumannFunctor {
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const override;
};
} // namespace Neumann
} // namespace BC
} // namespace akantu
#include "boundary_condition_functor_inline_impl.hh"
-#endif /* __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__ */
+#endif /* AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH_ */
diff --git a/src/model/common/boundary_condition/boundary_condition_functor_inline_impl.hh b/src/model/common/boundary_condition/boundary_condition_functor_inline_impl.hh
index 443383287..c0778f666 100644
--- a/src/model/common/boundary_condition/boundary_condition_functor_inline_impl.hh
+++ b/src/model/common/boundary_condition/boundary_condition_functor_inline_impl.hh
@@ -1,154 +1,154 @@
/**
* @file boundary_condition_functor_inline_impl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Mon Feb 19 2018
*
* @brief implementation of the BC::Functors
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition_functor.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_HH__
-#define __AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_HH__
+#ifndef AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_HH_
+#define AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_HH_
/* -------------------------------------------------------------------------- */
#define DIRICHLET_SANITY_CHECK \
AKANTU_DEBUG_ASSERT( \
coord.size() <= flags.size(), \
"The coordinates and flags vectors given to the boundary" \
<< " condition functor have different sizes!"); \
AKANTU_DEBUG_ASSERT( \
primal.size() <= coord.size(), \
"The primal vector and coordinates vector given" \
<< " to the boundary condition functor have different sizes!");
#define NEUMANN_SANITY_CHECK \
AKANTU_DEBUG_ASSERT( \
coord.size() <= normals.size(), \
"The coordinates and normals vectors given to the" \
<< " boundary condition functor have different sizes!"); \
AKANTU_DEBUG_ASSERT( \
dual.size() <= coord.size(), \
"The dual vector and coordinates vector given to" \
<< " the boundary condition functor have different sizes!");
namespace akantu {
namespace BC {
/* ---------------------------------------------------------------------- */
namespace Dirichlet {
inline void FlagOnly::
operator()(__attribute__((unused)) UInt node, Vector<bool> & flags,
__attribute__((unused)) Vector<Real> & primal,
__attribute__((unused)) const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
}
/* ---------------------------------------------------------------------- */
// inline void FreeBoundary::
// operator()(__attribute__((unused)) UInt node, Vector<bool> & flags,
// __attribute__((unused)) Vector<Real> & primal,
// __attribute__((unused)) const Vector<Real> & coord) const {
// DIRICHLET_SANITY_CHECK;
// flags(this->axis) = false;
// }
/* ---------------------------------------------------------------------- */
inline void FixedValue::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
primal(this->axis) = value;
}
/* ---------------------------------------------------------------------- */
inline void IncrementValue::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
primal(this->axis) += value;
}
/* ---------------------------------------------------------------------- */
inline void Increment::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags.set(true);
primal += value;
}
} // namespace Dirichlet
/* ------------------------------------------------------------------------ */
/* Neumann */
/* ------------------------------------------------------------------------ */
namespace Neumann {
inline void FreeBoundary::
operator()(__attribute__((unused)) const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused)) const Vector<Real> & coord,
__attribute__((unused)) const Vector<Real> & normals) const {
for (UInt i(0); i < dual.size(); ++i) {
dual(i) = 0.0;
}
}
/* ---------------------------------------------------------------------- */
inline void FromHigherDim::operator()(__attribute__((unused))
const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused))
const Vector<Real> & coord,
const Vector<Real> & normals) const {
dual.mul<false>(this->bc_data, normals);
}
/* ---------------------------------------------------------------------- */
inline void FromSameDim::
operator()(__attribute__((unused)) const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused)) const Vector<Real> & coord,
__attribute__((unused)) const Vector<Real> & normals) const {
dual = this->bc_data;
}
} // namespace Neumann
} // namespace BC
} // namespace akantu
-#endif /* __AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_HH__ */
+#endif /* AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_HH_ */
diff --git a/src/model/common/boundary_condition/boundary_condition_tmpl.hh b/src/model/common/boundary_condition/boundary_condition_tmpl.hh
index 85c20a94e..2a62798ff 100644
--- a/src/model/common/boundary_condition/boundary_condition_tmpl.hh
+++ b/src/model/common/boundary_condition/boundary_condition_tmpl.hh
@@ -1,229 +1,231 @@
/**
* @file boundary_condition_tmpl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Tue Feb 20 2018
*
* @brief implementation of the applyBC
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition.hh"
#include "element_group.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_BOUNDARY_CONDITION_TMPL_HH__
-#define __AKANTU_BOUNDARY_CONDITION_TMPL_HH__
+#ifndef AKANTU_BOUNDARY_CONDITION_TMPL_HH_
+#define AKANTU_BOUNDARY_CONDITION_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename ModelType>
void BoundaryCondition<ModelType>::initBC(ModelType & model,
Array<Real> & primal,
Array<Real> & dual) {
this->model = &model;
this->primal = &primal;
this->dual = &dual;
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
void BoundaryCondition<ModelType>::initBC(ModelType & model,
Array<Real> & primal,
Array<Real> & primal_increment,
Array<Real> & dual) {
this->initBC(model, primal, dual);
this->primal_increment = &primal_increment;
}
/* -------------------------------------------------------------------------- */
/* Partial specialization for DIRICHLET functors */
template <typename ModelType>
template <typename FunctorType>
struct BoundaryCondition<ModelType>::TemplateFunctionWrapper<
FunctorType, BC::Functor::_dirichlet> {
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance) {
auto & model = bc_instance.getModel();
auto & primal = bc_instance.getPrimal();
const auto & coords = model.getMesh().getNodes();
auto & boundary_flags = model.getBlockedDOFs();
UInt dim = model.getMesh().getSpatialDimension();
auto primal_iter = primal.begin(primal.getNbComponent());
auto coords_iter = coords.begin(dim);
auto flags_iter = boundary_flags.begin(boundary_flags.getNbComponent());
for (auto n : group.getNodeGroup()) {
Vector<bool> flag(flags_iter[n]);
Vector<Real> primal(primal_iter[n]);
Vector<Real> coords(coords_iter[n]);
func(n, flag, primal, coords);
}
}
};
/* -------------------------------------------------------------------------- */
/* Partial specialization for NEUMANN functors */
template <typename ModelType>
template <typename FunctorType>
struct BoundaryCondition<ModelType>::TemplateFunctionWrapper<
FunctorType, BC::Functor::_neumann> {
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance) {
UInt dim = bc_instance.getModel().getSpatialDimension();
switch (dim) {
case 1: {
AKANTU_TO_IMPLEMENT();
break;
}
case 2:
case 3: {
applyBC(func, group, bc_instance, _not_ghost);
applyBC(func, group, bc_instance, _ghost);
break;
}
}
}
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance,
GhostType ghost_type) {
auto & model = bc_instance.getModel();
auto & dual = bc_instance.getDual();
const auto & mesh = model.getMesh();
const auto & nodes_coords = mesh.getNodes();
const auto & fem_boundary = model.getFEEngineBoundary();
UInt dim = model.getSpatialDimension();
UInt nb_degree_of_freedom = dual.getNbComponent();
IntegrationPoint quad_point;
quad_point.ghost_type = ghost_type;
// Loop over the boundary element types
for (auto && type : group.elementTypes(dim - 1, ghost_type)) {
const auto & element_ids = group.getElements(type, ghost_type);
UInt nb_quad_points =
fem_boundary.getNbIntegrationPoints(type, ghost_type);
UInt nb_elements = element_ids.size();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> dual_before_integ(nb_elements * nb_quad_points,
nb_degree_of_freedom, 0.);
Array<Real> quad_coords(nb_elements * nb_quad_points, dim);
const auto & normals_on_quad =
fem_boundary.getNormalsOnIntegrationPoints(type, ghost_type);
fem_boundary.interpolateOnIntegrationPoints(
nodes_coords, quad_coords, dim, type, ghost_type, element_ids);
auto normals_begin = normals_on_quad.begin(dim);
decltype(normals_begin) normals_iter;
auto quad_coords_iter = quad_coords.begin(dim);
auto dual_iter = dual_before_integ.begin(nb_degree_of_freedom);
quad_point.type = type;
for (auto el : element_ids) {
quad_point.element = el;
normals_iter = normals_begin + el * nb_quad_points;
for (auto q : arange(nb_quad_points)) {
quad_point.num_point = q;
func(quad_point, *dual_iter, *quad_coords_iter, *normals_iter);
++dual_iter;
++quad_coords_iter;
++normals_iter;
}
}
Array<Real> dual_by_shapes(nb_elements * nb_quad_points,
nb_degree_of_freedom * nb_nodes_per_element);
fem_boundary.computeNtb(dual_before_integ, dual_by_shapes, type,
ghost_type, element_ids);
Array<Real> dual_by_shapes_integ(nb_elements, nb_degree_of_freedom *
nb_nodes_per_element);
fem_boundary.integrate(dual_by_shapes, dual_by_shapes_integ,
nb_degree_of_freedom * nb_nodes_per_element, type,
ghost_type, element_ids);
// assemble the result into force vector
model.getDOFManager().assembleElementalArrayLocalArray(
dual_by_shapes_integ, dual, type, ghost_type, 1., element_ids);
}
}
};
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void BoundaryCondition<ModelType>::applyBC(const FunctorType & func) {
auto bit = model->getMesh().getGroupManager().element_group_begin();
auto bend = model->getMesh().getGroupManager().element_group_end();
- for (; bit != bend; ++bit)
+ for (; bit != bend; ++bit) {
applyBC(func, *bit);
+ }
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void
BoundaryCondition<ModelType>::applyBC(const FunctorType & func,
const std::string & group_name) {
try {
const ElementGroup & element_group =
model->getMesh().getElementGroup(group_name);
applyBC(func, element_group);
} catch (akantu::debug::Exception & e) {
AKANTU_EXCEPTION("Error applying a boundary condition onto \""
<< group_name << "\"! [" << e.what() << "]");
}
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void
BoundaryCondition<ModelType>::applyBC(const FunctorType & func,
const ElementGroup & element_group) {
#if !defined(AKANTU_NDEBUG)
- if (element_group.getDimension() != model->getSpatialDimension() - 1)
+ if (element_group.getDimension() != model->getSpatialDimension() - 1) {
AKANTU_DEBUG_WARNING("The group "
<< element_group.getName()
<< " does not contain only boundaries elements");
+ }
#endif
TemplateFunctionWrapper<FunctorType>::applyBC(func, element_group, *this);
}
-#endif /* __AKANTU_BOUNDARY_CONDITION_TMPL_HH__ */
+#endif /* AKANTU_BOUNDARY_CONDITION_TMPL_HH_ */
} // namespace akantu
diff --git a/src/model/common/dof_manager/dof_manager.cc b/src/model/common/dof_manager/dof_manager.cc
index 91f9ea4df..f5b0847bf 100644
--- a/src/model/common/dof_manager/dof_manager.cc
+++ b/src/model/common/dof_manager/dof_manager.cc
@@ -1,1014 +1,1017 @@
/**
* @file dof_manager.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the common parts of the DOFManagers
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
#include "communicator.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
#include "node_synchronizer.hh"
#include "non_linear_solver.hh"
#include "periodic_node_synchronizer.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), dofs_flag(0, 1, std::string(id + ":dofs_type")),
global_equation_number(0, 1, "global_equation_number"),
communicator(Communicator::getStaticCommunicator()) {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(Mesh & mesh, const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(&mesh),
dofs_flag(0, 1, std::string(id + ":dofs_type")),
global_equation_number(0, 1, "global_equation_number"),
communicator(mesh.getCommunicator()) {
this->mesh->registerEventHandler(*this, _ehp_dof_manager);
}
/* -------------------------------------------------------------------------- */
-DOFManager::~DOFManager() {
- // if (mesh) {
- // this->mesh->unregisterEventHandler(*this);
- // }
-}
-
-/* -------------------------------------------------------------------------- */
-// void DOFManager::getEquationsNumbers(const ID &, Array<UInt> &) {
-// AKANTU_TO_IMPLEMENT();
-// }
+DOFManager::~DOFManager() = default;
/* -------------------------------------------------------------------------- */
std::vector<ID> DOFManager::getDOFIDs() const {
std::vector<ID> keys;
- for (const auto & dof_data : this->dofs)
+ for (const auto & dof_data : this->dofs) {
keys.push_back(dof_data.first);
+ }
return keys;
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayLocalArray(
const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
- const ElementType & type, const GhostType & ghost_type, Real scale_factor,
+ ElementType type, GhostType ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_element;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
UInt * filter_it = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filter_it = filter_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
AKANTU_DEBUG_ASSERT(elementary_vect.size() == nb_element,
"The vector elementary_vect("
<< elementary_vect.getID()
<< ") has not the good size.");
const Array<UInt> & connectivity =
this->mesh->getConnectivity(type, ghost_type);
Array<Real>::const_matrix_iterator elem_it =
elementary_vect.begin(nb_degree_of_freedom, nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el, ++elem_it) {
UInt element = el;
if (filter_it != nullptr) {
// conn_it = conn_begin + *filter_it;
element = *filter_it;
}
// const Vector<UInt> & conn = *conn_it;
const Matrix<Real> & elemental_val = *elem_it;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt offset_node = connectivity(element, n) * nb_degree_of_freedom;
Vector<Real> assemble(array_assembeled.storage() + offset_node,
nb_degree_of_freedom);
Vector<Real> elem_val = elemental_val(n);
assemble.aXplusY(elem_val, scale_factor);
}
- if (filter_it != nullptr)
+ if (filter_it != nullptr) {
++filter_it;
+ }
// else
// ++conn_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayToResidual(
const ID & dof_id, const Array<Real> & elementary_vect,
- const ElementType & type, const GhostType & ghost_type, Real scale_factor,
+ ElementType type, GhostType ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
nb_degree_of_freedom);
- array_localy_assembeled.clear();
+ array_localy_assembeled.zero();
this->assembleElementalArrayLocalArray(
elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
filter_elements);
this->assembleToResidual(dof_id, array_localy_assembeled, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayToLumpedMatrix(
const ID & dof_id, const Array<Real> & elementary_vect,
- const ID & lumped_mtx, const ElementType & type,
- const GhostType & ghost_type, Real scale_factor,
+ const ID & lumped_mtx, ElementType type,
+ GhostType ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
nb_degree_of_freedom);
- array_localy_assembeled.clear();
+ array_localy_assembeled.zero();
this->assembleElementalArrayLocalArray(
elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
filter_elements);
this->assembleToLumpedMatrix(dof_id, array_localy_assembeled, lumped_mtx, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleMatMulDOFsToResidual(const ID & A_id,
Real scale_factor) {
for (auto & pair : this->dofs) {
const auto & dof_id = pair.first;
auto & dof_data = *pair.second;
this->assembleMatMulVectToResidual(dof_id, A_id, *dof_data.dof,
scale_factor);
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::splitSolutionPerDOFs() {
for (auto && data : this->dofs) {
auto & dof_data = *data.second;
dof_data.solution.resize(dof_data.dof->size() *
dof_data.dof->getNbComponent());
this->getSolutionPerDOFs(data.first, dof_data.solution);
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->getSolution(), solution_array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::getLumpedMatrixPerDOFs(const ID & dof_id,
const ID & lumped_mtx,
Array<Real> & lumped) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->getLumpedMatrix(lumped_mtx), lumped);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleToResidual(const ID & dof_id,
Array<Real> & array_to_assemble,
Real scale_factor) {
AKANTU_DEBUG_IN();
// this->makeConsistentForPeriodicity(dof_id, array_to_assemble);
this->assembleToGlobalArray(dof_id, array_to_assemble, this->getResidual(),
scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleToLumpedMatrix(const ID & dof_id,
Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor) {
AKANTU_DEBUG_IN();
// this->makeConsistentForPeriodicity(dof_id, array_to_assemble);
auto & lumped = this->getLumpedMatrix(lumped_mtx);
this->assembleToGlobalArray(dof_id, array_to_assemble, lumped, scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::DOFData(const ID & dof_id)
- : support_type(_dst_generic), group_support("__mesh__"), dof(nullptr),
- blocked_dofs(nullptr), increment(nullptr), previous(nullptr),
+ : support_type(_dst_generic), group_support("__mesh__"),
solution(0, 1, dof_id + ":solution"),
local_equation_number(0, 1, dof_id + ":local_equation_number"),
associated_nodes(0, 1, dof_id + "associated_nodes") {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::~DOFData() = default;
/* -------------------------------------------------------------------------- */
template <typename Func>
auto DOFManager::countDOFsForNodes(const DOFData & dof_data, UInt nb_nodes,
Func && getNode) {
auto nb_local_dofs = nb_nodes;
decltype(nb_local_dofs) nb_pure_local = 0;
for (auto n : arange(nb_nodes)) {
UInt node = getNode(n);
// http://www.open-std.org/jtc1/sc22/open/n2356/conv.html
// bool are by convention casted to 0 and 1 when promoted to int
nb_pure_local += this->mesh->isLocalOrMasterNode(node);
nb_local_dofs -= this->mesh->isPeriodicSlave(node);
}
const auto & dofs_array = *dof_data.dof;
nb_pure_local *= dofs_array.getNbComponent();
nb_local_dofs *= dofs_array.getNbComponent();
return std::make_pair(nb_local_dofs, nb_pure_local);
}
/* -------------------------------------------------------------------------- */
auto DOFManager::getNewDOFDataInternal(const ID & dof_id) -> DOFData & {
auto it = this->dofs.find(dof_id);
if (it != this->dofs.end()) {
AKANTU_EXCEPTION("This dof array has already been registered");
}
std::unique_ptr<DOFData> dof_data_ptr = this->getNewDOFData(dof_id);
DOFData & dof_data = *dof_data_ptr;
this->dofs[dof_id] = std::move(dof_data_ptr);
return dof_data;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type) {
auto & dofs_storage = this->getNewDOFDataInternal(dof_id);
dofs_storage.support_type = support_type;
this->registerDOFsInternal(dof_id, dofs_array);
resizeGlobalArrays();
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & support_group) {
auto & dofs_storage = this->getNewDOFDataInternal(dof_id);
dofs_storage.support_type = _dst_nodal;
dofs_storage.group_support = support_group;
this->registerDOFsInternal(dof_id, dofs_array);
resizeGlobalArrays();
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt, UInt>
DOFManager::registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array) {
DOFData & dof_data = this->getDOFData(dof_id);
dof_data.dof = &dofs_array;
UInt nb_local_dofs = 0;
UInt nb_pure_local = 0;
const auto & support_type = dof_data.support_type;
switch (support_type) {
case _dst_nodal: {
const auto & group = dof_data.group_support;
std::function<UInt(UInt)> getNode;
if (group == "__mesh__") {
AKANTU_DEBUG_ASSERT(
dofs_array.size() == this->mesh->getNbNodes(),
"The array of dof is too short to be associated to nodes.");
std::tie(nb_local_dofs, nb_pure_local) = countDOFsForNodes(
dof_data, this->mesh->getNbNodes(), [](auto && n) { return n; });
} else {
const auto & node_group =
this->mesh->getElementGroup(group).getNodeGroup().getNodes();
AKANTU_DEBUG_ASSERT(
dofs_array.size() == node_group.size(),
"The array of dof is too shot to be associated to nodes.");
std::tie(nb_local_dofs, nb_pure_local) =
countDOFsForNodes(dof_data, node_group.size(),
[&node_group](auto && n) { return node_group(n); });
}
break;
}
case _dst_generic: {
nb_local_dofs = nb_pure_local =
dofs_array.size() * dofs_array.getNbComponent();
break;
}
default: { AKANTU_EXCEPTION("This type of dofs is not handled yet."); }
}
dof_data.local_nb_dofs = nb_local_dofs;
dof_data.pure_local_nb_dofs = nb_pure_local;
dof_data.ghosts_nb_dofs = nb_local_dofs - nb_pure_local;
this->pure_local_system_size += nb_pure_local;
this->local_system_size += nb_local_dofs;
auto nb_total_pure_local = nb_pure_local;
communicator.allReduce(nb_total_pure_local, SynchronizerOperation::_sum);
this->system_size += nb_total_pure_local;
// updating the dofs data after counting is finished
switch (support_type) {
case _dst_nodal: {
const auto & group = dof_data.group_support;
if (group != "__mesh__") {
auto & support_nodes =
this->mesh->getElementGroup(group).getNodeGroup().getNodes();
this->updateDOFsData(
dof_data, nb_local_dofs, nb_pure_local, support_nodes.size(),
[&support_nodes](UInt node) -> UInt { return support_nodes[node]; });
} else {
this->updateDOFsData(dof_data, nb_local_dofs, nb_pure_local,
mesh->getNbNodes(),
[](UInt node) -> UInt { return node; });
}
break;
}
case _dst_generic: {
this->updateDOFsData(dof_data, nb_local_dofs, nb_pure_local);
break;
}
}
return std::make_tuple(nb_local_dofs, nb_pure_local, nb_total_pure_local);
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsPrevious(const ID & dof_id, Array<Real> & array) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.previous != nullptr) {
AKANTU_EXCEPTION("The previous dofs array for "
<< dof_id << " has already been registered");
}
dof.previous = &array;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsIncrement(const ID & dof_id, Array<Real> & array) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.increment != nullptr) {
AKANTU_EXCEPTION("The dofs increment array for "
<< dof_id << " has already been registered");
}
dof.increment = &array;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsDerivative(const ID & dof_id, UInt order,
Array<Real> & dofs_derivative) {
DOFData & dof = this->getDOFData(dof_id);
std::vector<Array<Real> *> & derivatives = dof.dof_derivatives;
if (derivatives.size() < order) {
derivatives.resize(order, nullptr);
} else {
if (derivatives[order - 1] != nullptr) {
AKANTU_EXCEPTION("The dof derivatives of order "
<< order << " already been registered for this dof ("
<< dof_id << ")");
}
}
derivatives[order - 1] = &dofs_derivative;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerBlockedDOFs(const ID & dof_id,
Array<bool> & blocked_dofs) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.blocked_dofs != nullptr) {
AKANTU_EXCEPTION("The blocked dofs array for "
<< dof_id << " has already been registered");
}
dof.blocked_dofs = &blocked_dofs;
}
/* -------------------------------------------------------------------------- */
SparseMatrix &
DOFManager::registerSparseMatrix(const ID & matrix_id,
std::unique_ptr<SparseMatrix> & matrix) {
auto it = this->matrices.find(matrix_id);
if (it != this->matrices.end()) {
AKANTU_EXCEPTION("The matrix " << matrix_id << " already exists in "
<< this->id);
}
auto & ret = *matrix;
this->matrices[matrix_id] = std::move(matrix);
return ret;
}
/* -------------------------------------------------------------------------- */
/// Get an instance of a new SparseMatrix
SolverVector &
DOFManager::registerLumpedMatrix(const ID & matrix_id,
std::unique_ptr<SolverVector> & matrix) {
auto it = this->lumped_matrices.find(matrix_id);
if (it != this->lumped_matrices.end()) {
AKANTU_EXCEPTION("The lumped matrix " << matrix_id << " already exists in "
<< this->id);
}
auto & ret = *matrix;
this->lumped_matrices[matrix_id] = std::move(matrix);
ret.resize();
return ret;
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & DOFManager::registerNonLinearSolver(
const ID & non_linear_solver_id,
std::unique_ptr<NonLinearSolver> & non_linear_solver) {
NonLinearSolversMap::const_iterator it =
this->non_linear_solvers.find(non_linear_solver_id);
if (it != this->non_linear_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
<< " already exists in "
<< this->id);
}
NonLinearSolver & ret = *non_linear_solver;
this->non_linear_solvers[non_linear_solver_id] = std::move(non_linear_solver);
return ret;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManager::registerTimeStepSolver(
const ID & time_step_solver_id,
std::unique_ptr<TimeStepSolver> & time_step_solver) {
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
if (it != this->time_step_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
<< " already exists in "
<< this->id);
}
TimeStepSolver & ret = *time_step_solver;
this->time_step_solvers[time_step_solver_id] = std::move(time_step_solver);
return ret;
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManager::getMatrix(const ID & id) {
ID matrix_id = this->id + ":mtx:" + id;
SparseMatricesMap::const_iterator it = this->matrices.find(matrix_id);
if (it == this->matrices.end()) {
AKANTU_SILENT_EXCEPTION("The matrix " << matrix_id << " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasMatrix(const ID & id) const {
ID mtx_id = this->id + ":mtx:" + id;
auto it = this->matrices.find(mtx_id);
return it != this->matrices.end();
}
/* -------------------------------------------------------------------------- */
SolverVector & DOFManager::getLumpedMatrix(const ID & id) {
ID matrix_id = this->id + ":lumped_mtx:" + id;
LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
if (it == this->lumped_matrices.end()) {
AKANTU_SILENT_EXCEPTION("The lumped matrix "
<< matrix_id << " does not exists in " << this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
const SolverVector & DOFManager::getLumpedMatrix(const ID & id) const {
ID matrix_id = this->id + ":lumped_mtx:" + id;
auto it = this->lumped_matrices.find(matrix_id);
if (it == this->lumped_matrices.end()) {
AKANTU_SILENT_EXCEPTION("The lumped matrix "
<< matrix_id << " does not exists in " << this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasLumpedMatrix(const ID & id) const {
ID mtx_id = this->id + ":lumped_mtx:" + id;
auto it = this->lumped_matrices.find(mtx_id);
return it != this->lumped_matrices.end();
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & DOFManager::getNonLinearSolver(const ID & id) {
ID non_linear_solver_id = this->id + ":nls:" + id;
NonLinearSolversMap::const_iterator it =
this->non_linear_solvers.find(non_linear_solver_id);
if (it == this->non_linear_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
<< " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasNonLinearSolver(const ID & id) const {
ID solver_id = this->id + ":nls:" + id;
auto it = this->non_linear_solvers.find(solver_id);
return it != this->non_linear_solvers.end();
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManager::getTimeStepSolver(const ID & id) {
ID time_step_solver_id = this->id + ":tss:" + id;
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
if (it == this->time_step_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
<< " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasTimeStepSolver(const ID & solver_id) const {
ID time_step_solver_id = this->id + ":tss:" + solver_id;
auto it = this->time_step_solvers.find(time_step_solver_id);
return it != this->time_step_solvers.end();
}
/* -------------------------------------------------------------------------- */
void DOFManager::savePreviousDOFs(const ID & dofs_id) {
this->getPreviousDOFs(dofs_id).copy(this->getDOFs(dofs_id));
}
/* -------------------------------------------------------------------------- */
-void DOFManager::clearResidual() { this->residual->clear(); }
+void DOFManager::zeroResidual() { this->residual->zero(); }
/* -------------------------------------------------------------------------- */
-void DOFManager::clearMatrix(const ID & mtx) { this->getMatrix(mtx).clear(); }
+void DOFManager::zeroMatrix(const ID & mtx) { this->getMatrix(mtx).zero(); }
/* -------------------------------------------------------------------------- */
-void DOFManager::clearLumpedMatrix(const ID & mtx) {
- this->getLumpedMatrix(mtx).clear();
+void DOFManager::zeroLumpedMatrix(const ID & mtx) {
+ this->getLumpedMatrix(mtx).zero();
}
/* -------------------------------------------------------------------------- */
/* Mesh Events */
/* -------------------------------------------------------------------------- */
std::pair<UInt, UInt>
DOFManager::updateNodalDOFs(const ID & dof_id, const Array<UInt> & nodes_list) {
auto & dof_data = this->getDOFData(dof_id);
- UInt nb_new_local_dofs, nb_new_pure_local;
+ UInt nb_new_local_dofs;
+ UInt nb_new_pure_local;
std::tie(nb_new_local_dofs, nb_new_pure_local) =
countDOFsForNodes(dof_data, nodes_list.size(),
[&nodes_list](auto && n) { return nodes_list(n); });
this->pure_local_system_size += nb_new_pure_local;
this->local_system_size += nb_new_local_dofs;
UInt nb_new_global = nb_new_pure_local;
communicator.allReduce(nb_new_global, SynchronizerOperation::_sum);
this->system_size += nb_new_global;
dof_data.solution.resize(local_system_size);
updateDOFsData(dof_data, nb_new_local_dofs, nb_new_pure_local,
nodes_list.size(),
[&nodes_list](UInt pos) -> UInt { return nodes_list[pos]; });
return std::make_pair(nb_new_local_dofs, nb_new_pure_local);
}
/* -------------------------------------------------------------------------- */
void DOFManager::resizeGlobalArrays() {
// resize all relevant arrays
this->residual->resize();
this->solution->resize();
this->data_cache->resize();
- for (auto & lumped_matrix : lumped_matrices)
+ for (auto & lumped_matrix : lumped_matrices) {
lumped_matrix.second->resize();
+ }
for (auto & matrix : matrices) {
matrix.second->clearProfile();
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::onNodesAdded(const Array<UInt> & nodes_list,
- const NewNodesEvent &) {
+ const NewNodesEvent & /*unused*/) {
for (auto & pair : this->dofs) {
const auto & dof_id = pair.first;
auto & dof_data = this->getDOFData(dof_id);
- if (dof_data.support_type != _dst_nodal)
+ if (dof_data.support_type != _dst_nodal) {
continue;
+ }
const auto & group = dof_data.group_support;
if (group == "__mesh__") {
this->updateNodalDOFs(dof_id, nodes_list);
} else {
const auto & node_group =
this->mesh->getElementGroup(group).getNodeGroup();
Array<UInt> new_nodes_list;
for (const auto & node : nodes_list) {
- if (node_group.find(node) != UInt(-1))
+ if (node_group.find(node) != UInt(-1)) {
new_nodes_list.push_back(node);
+ }
}
this->updateNodalDOFs(dof_id, new_nodes_list);
}
}
this->resizeGlobalArrays();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class GlobalDOFInfoDataAccessor : public DataAccessor<UInt> {
public:
using size_type =
typename std::unordered_map<UInt, std::vector<UInt>>::size_type;
GlobalDOFInfoDataAccessor(DOFManager::DOFData & dof_data,
DOFManager & dof_manager)
: dof_data(dof_data), dof_manager(dof_manager) {
for (auto && pair :
zip(dof_data.local_equation_number, dof_data.associated_nodes)) {
UInt node;
Int dof;
std::tie(dof, node) = pair;
dofs_per_node[node].push_back(dof);
}
}
UInt getNbData(const Array<UInt> & nodes,
const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_ask_nodes or
tag == SynchronizationTag::_giu_global_conn) {
return nodes.size() * dof_data.dof->getNbComponent() * sizeof(Int);
}
return 0;
}
void packData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_ask_nodes or
tag == SynchronizationTag::_giu_global_conn) {
- for (auto & node : nodes) {
- auto & dofs = dofs_per_node.at(node);
- for (auto & dof : dofs) {
+ for (const auto & node : nodes) {
+ const auto & dofs = dofs_per_node.at(node);
+ for (const auto & dof : dofs) {
buffer << dof_manager.global_equation_number(dof);
}
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) override {
if (tag == SynchronizationTag::_ask_nodes or
tag == SynchronizationTag::_giu_global_conn) {
- for (auto & node : nodes) {
- auto & dofs = dofs_per_node[node];
- for (auto dof : dofs) {
+ for (const auto & node : nodes) {
+ const auto & dofs = dofs_per_node[node];
+ for (const auto & dof : dofs) {
Int global_dof;
buffer >> global_dof;
AKANTU_DEBUG_ASSERT(
(dof_manager.global_equation_number(dof) == -1 or
dof_manager.global_equation_number(dof) == global_dof),
"This dof already had a global_dof_id which is different from "
"the received one. "
<< dof_manager.global_equation_number(dof)
<< " != " << global_dof);
dof_manager.global_equation_number(dof) = global_dof;
dof_manager.global_to_local_mapping[global_dof] = dof;
}
}
}
}
protected:
std::unordered_map<UInt, std::vector<Int>> dofs_per_node;
DOFManager::DOFData & dof_data;
DOFManager & dof_manager;
};
/* -------------------------------------------------------------------------- */
auto DOFManager::computeFirstDOFIDs(UInt nb_new_local_dofs,
UInt nb_new_pure_local) {
// determine the first local/global dof id to use
UInt offset = 0;
this->communicator.exclusiveScan(nb_new_pure_local, offset);
auto first_global_dof_id = this->first_global_dof_id + offset;
auto first_local_dof_id = this->local_system_size - nb_new_local_dofs;
offset = nb_new_pure_local;
this->communicator.allReduce(offset);
this->first_global_dof_id += offset;
return std::make_pair(first_local_dof_id, first_global_dof_id);
}
/* -------------------------------------------------------------------------- */
void DOFManager::updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local, UInt nb_node,
const std::function<UInt(UInt)> & getNode) {
auto nb_local_dofs_added = nb_node * dof_data.dof->getNbComponent();
auto first_dof_pos = dof_data.local_equation_number.size();
dof_data.local_equation_number.reserve(dof_data.local_equation_number.size() +
nb_local_dofs_added);
dof_data.associated_nodes.reserve(dof_data.associated_nodes.size() +
nb_local_dofs_added);
this->dofs_flag.resize(this->local_system_size, NodeFlag::_normal);
this->global_equation_number.resize(this->local_system_size, -1);
std::unordered_map<std::pair<UInt, UInt>, UInt> masters_dofs;
// update per dof info
- UInt local_eq_num, first_global_dof_id;
+ UInt local_eq_num;
+ UInt first_global_dof_id;
std::tie(local_eq_num, first_global_dof_id) =
computeFirstDOFIDs(nb_new_local_dofs, nb_new_pure_local);
for (auto d : arange(nb_local_dofs_added)) {
auto node = getNode(d / dof_data.dof->getNbComponent());
auto dof_flag = this->mesh->getNodeFlag(node);
dof_data.associated_nodes.push_back(node);
auto is_local_dof = this->mesh->isLocalOrMasterNode(node);
auto is_periodic_slave = this->mesh->isPeriodicSlave(node);
auto is_periodic_master = this->mesh->isPeriodicMaster(node);
if (is_periodic_slave) {
dof_data.local_equation_number.push_back(-1);
continue;
}
// update equation numbers
this->dofs_flag(local_eq_num) = dof_flag;
dof_data.local_equation_number.push_back(local_eq_num);
if (is_local_dof) {
this->global_equation_number(local_eq_num) = first_global_dof_id;
this->global_to_local_mapping[first_global_dof_id] = local_eq_num;
++first_global_dof_id;
} else {
this->global_equation_number(local_eq_num) = -1;
}
if (is_periodic_master) {
auto node = getNode(d / dof_data.dof->getNbComponent());
auto dof = d % dof_data.dof->getNbComponent();
masters_dofs.insert(
std::make_pair(std::make_pair(node, dof), local_eq_num));
}
++local_eq_num;
}
// correct periodic slave equation numbers
if (this->mesh->isPeriodic()) {
auto assoc_begin = dof_data.associated_nodes.begin();
for (auto d : arange(nb_local_dofs_added)) {
auto node = dof_data.associated_nodes(first_dof_pos + d);
- if (not this->mesh->isPeriodicSlave(node))
+ if (not this->mesh->isPeriodicSlave(node)) {
continue;
+ }
auto master_node = this->mesh->getPeriodicMaster(node);
auto dof = d % dof_data.dof->getNbComponent();
dof_data.local_equation_number(first_dof_pos + d) =
masters_dofs[std::make_pair(master_node, dof)];
}
}
// synchronize the global numbering for slaves nodes
if (this->mesh->isDistributed()) {
GlobalDOFInfoDataAccessor data_accessor(dof_data, *this);
if (this->mesh->isPeriodic()) {
mesh->getPeriodicNodeSynchronizer().synchronizeOnce(
data_accessor, SynchronizationTag::_giu_global_conn);
}
auto & node_synchronizer = this->mesh->getNodeSynchronizer();
node_synchronizer.synchronizeOnce(data_accessor,
SynchronizationTag::_ask_nodes);
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local) {
dof_data.local_equation_number.reserve(dof_data.local_equation_number.size() +
nb_new_local_dofs);
- UInt first_local_dof_id, first_global_dof_id;
+ UInt first_local_dof_id;
+ UInt first_global_dof_id;
std::tie(first_local_dof_id, first_global_dof_id) =
computeFirstDOFIDs(nb_new_local_dofs, nb_new_pure_local);
this->dofs_flag.resize(this->local_system_size, NodeFlag::_normal);
this->global_equation_number.resize(this->local_system_size, -1);
// update per dof info
for (auto _ [[gnu::unused]] : arange(nb_new_local_dofs)) {
// update equation numbers
this->dofs_flag(first_local_dof_id) = NodeFlag::_normal;
dof_data.local_equation_number.push_back(first_local_dof_id);
this->global_equation_number(first_local_dof_id) = first_global_dof_id;
this->global_to_local_mapping[first_global_dof_id] = first_local_dof_id;
++first_global_dof_id;
++first_local_dof_id;
}
}
/* -------------------------------------------------------------------------- */
-void DOFManager::onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
- const RemovedNodesEvent &) {}
+void DOFManager::onNodesRemoved(const Array<UInt> & /*unused*/,
+ const Array<UInt> & /*unused*/,
+ const RemovedNodesEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
-void DOFManager::onElementsAdded(const Array<Element> &,
- const NewElementsEvent &) {}
+void DOFManager::onElementsAdded(const Array<Element> & /*unused*/,
+ const NewElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
-void DOFManager::onElementsRemoved(const Array<Element> &,
- const ElementTypeMapArray<UInt> &,
- const RemovedElementsEvent &) {}
+void DOFManager::onElementsRemoved(const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const RemovedElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
-void DOFManager::onElementsChanged(const Array<Element> &,
- const Array<Element> &,
- const ElementTypeMapArray<UInt> &,
- const ChangedElementsEvent &) {}
+void DOFManager::onElementsChanged(const Array<Element> & /*unused*/,
+ const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const ChangedElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
void DOFManager::updateGlobalBlockedDofs() {
this->previous_global_blocked_dofs.copy(this->global_blocked_dofs);
this->global_blocked_dofs.reserve(this->local_system_size, 0);
this->previous_global_blocked_dofs_release =
this->global_blocked_dofs_release;
for (auto & pair : dofs) {
- if (!this->hasBlockedDOFs(pair.first))
+ if (!this->hasBlockedDOFs(pair.first)) {
continue;
+ }
DOFData & dof_data = *pair.second;
for (auto && data : zip(dof_data.getLocalEquationsNumbers(),
make_view(*dof_data.blocked_dofs))) {
const auto & dof = std::get<0>(data);
const auto & is_blocked = std::get<1>(data);
if (is_blocked) {
this->global_blocked_dofs.push_back(dof);
}
}
}
std::sort(this->global_blocked_dofs.begin(), this->global_blocked_dofs.end());
auto last = std::unique(this->global_blocked_dofs.begin(),
this->global_blocked_dofs.end());
this->global_blocked_dofs.resize(last - this->global_blocked_dofs.begin());
auto are_equal =
global_blocked_dofs.size() == previous_global_blocked_dofs.size() and
std::equal(global_blocked_dofs.begin(), global_blocked_dofs.end(),
previous_global_blocked_dofs.begin());
- if (not are_equal)
+ if (not are_equal) {
++this->global_blocked_dofs_release;
+ }
}
/* -------------------------------------------------------------------------- */
void DOFManager::applyBoundary(const ID & matrix_id) {
auto & J = this->getMatrix(matrix_id);
if (this->jacobian_release == J.getRelease()) {
auto are_equal = this->global_blocked_dofs_release ==
this->previous_global_blocked_dofs_release;
// std::equal(global_blocked_dofs.begin(), global_blocked_dofs.end(),
// previous_global_blocked_dofs.begin());
- if (not are_equal)
+ if (not are_equal) {
J.applyBoundary();
+ }
previous_global_blocked_dofs.copy(global_blocked_dofs);
} else {
J.applyBoundary();
}
this->jacobian_release = J.getRelease();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleMatMulVectToGlobalArray(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
SolverVector & array,
Real scale_factor) {
auto & A = this->getMatrix(A_id);
- data_cache->clear();
+ data_cache->zero();
this->assembleToGlobalArray(dof_id, x, *data_cache, 1.);
A.matVecMul(*data_cache, array, scale_factor, 1.);
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor) {
assembleMatMulVectToGlobalArray(dof_id, A_id, x, *residual, scale_factor);
}
} // namespace akantu
diff --git a/src/model/common/dof_manager/dof_manager.hh b/src/model/common/dof_manager/dof_manager.hh
index c8a953e9d..1dfd7a573 100644
--- a/src/model/common/dof_manager/dof_manager.hh
+++ b/src/model/common/dof_manager/dof_manager.hh
@@ -1,717 +1,715 @@
/**
* @file dof_manager.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Wed Feb 21 2018
*
* @brief Class handling the different types of dofs
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DOF_MANAGER_HH__
-#define __AKANTU_DOF_MANAGER_HH__
+#ifndef AKANTU_DOF_MANAGER_HH_
+#define AKANTU_DOF_MANAGER_HH_
namespace akantu {
class TermsToAssemble;
class NonLinearSolver;
class TimeStepSolver;
class SparseMatrix;
class SolverVector;
class SolverCallback;
} // namespace akantu
namespace akantu {
class DOFManager : protected Memory, protected MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
protected:
struct DOFData;
public:
DOFManager(const ID & id = "dof_manager", const MemoryID & memory_id = 0);
DOFManager(Mesh & mesh, const ID & id = "dof_manager",
const MemoryID & memory_id = 0);
~DOFManager() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register an array of degree of freedom
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type);
/// the dof as an implied type of _dst_nodal and is defined only on a subset
/// of nodes
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
- const ID & group_support);
+ const ID & support_group);
/// register an array of previous values of the degree of freedom
virtual void registerDOFsPrevious(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of increment of degree of freedom
virtual void registerDOFsIncrement(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of derivatives for a particular dof array
virtual void registerDOFsDerivative(const ID & dof_id, UInt order,
Array<Real> & dofs_derivative);
/// register array representing the blocked degree of freedoms
virtual void registerBlockedDOFs(const ID & dof_id,
Array<bool> & blocked_dofs);
/// Assemble an array to the global residual array
virtual void assembleToResidual(const ID & dof_id,
Array<Real> & array_to_assemble,
Real scale_factor = 1.);
/// Assemble an array to the global lumped matrix array
virtual void assembleToLumpedMatrix(const ID & dof_id,
Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor = 1.);
/**
* Assemble elementary values to a local array of the size nb_nodes *
* nb_dof_per_node. The dof number is implicitly considered as
* conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayLocalArray(
const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayToResidual(
const ID & dof_id, const Array<Real> & elementary_vect,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to a global array corresponding to a lumped
* matrix
*/
virtual void assembleElementalArrayToLumpedMatrix(
const ID & dof_id, const Array<Real> & elementary_vect,
- const ID & lumped_mtx, const ElementType & type,
- const GhostType & ghost_type, Real scale_factor = 1.,
+ const ID & lumped_mtx, ElementType type,
+ GhostType ghost_type, Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d. With 0 <
* n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
- const Array<Real> & elementary_mat, const ElementType & type,
- const GhostType & ghost_type = _not_ghost,
+ const Array<Real> & elementary_mat, ElementType type,
+ GhostType ghost_type = _not_ghost,
const MatrixType & elemental_matrix_type = _symmetric,
const Array<UInt> & filter_elements = empty_filter) = 0;
/// multiply a vector by a matrix and assemble the result to the residual
virtual void assembleMatMulVectToArray(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor = 1) = 0;
/// multiply a vector by a lumped matrix and assemble the result to the
/// residual
virtual void assembleLumpedMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) = 0;
/// assemble coupling terms between to dofs
virtual void assemblePreassembledMatrix(const ID & dof_id_m,
const ID & dof_id_n,
const ID & matrix_id,
const TermsToAssemble & terms) = 0;
/// multiply a vector by a matrix and assemble the result to the residual
virtual void assembleMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1);
/// multiply the dofs by a matrix and assemble the result to the residual
virtual void assembleMatMulDOFsToResidual(const ID & A_id,
Real scale_factor = 1);
/// updates the global blocked_dofs array
virtual void updateGlobalBlockedDofs();
/// sets the residual to 0
- virtual void clearResidual();
+ virtual void zeroResidual();
/// sets the matrix to 0
- virtual void clearMatrix(const ID & mtx);
+ virtual void zeroMatrix(const ID & mtx);
/// sets the lumped matrix to 0
- virtual void clearLumpedMatrix(const ID & mtx);
+ virtual void zeroLumpedMatrix(const ID & mtx);
virtual void applyBoundary(const ID & matrix_id = "J");
// virtual void applyBoundaryLumped(const ID & matrix_id = "J");
/// extract a lumped matrix part corresponding to a given dof
virtual void getLumpedMatrixPerDOFs(const ID & dof_id, const ID & lumped_mtx,
Array<Real> & lumped);
/// splits the solution storage from a global view to the per dof storages
void splitSolutionPerDOFs();
private:
/// dispatch the creation of the dof data and register it
DOFData & getNewDOFDataInternal(const ID & dof_id);
protected:
/// common function to help registering dofs the return values are the add new
/// numbers of local dofs, pure local dofs, and system size
virtual std::tuple<UInt, UInt, UInt>
registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array);
/// minimum functionality to implement per derived version of the DOFManager
/// to allow the splitSolutionPerDOFs function to work
virtual void getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array);
/// fill a Vector with the equation numbers corresponding to the given
/// connectivity
- inline void extractElementEquationNumber(const Array<Int> & equation_numbers,
- const Vector<UInt> & connectivity,
- UInt nb_degree_of_freedom,
- Vector<Int> & local_equation_number);
+ static inline void extractElementEquationNumber(
+ const Array<Int> & equation_numbers, const Vector<UInt> & connectivity,
+ UInt nb_degree_of_freedom, Vector<Int> & element_equation_number);
/// Assemble a array to a global one
void assembleMatMulVectToGlobalArray(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
SolverVector & array,
Real scale_factor = 1.);
/// common function that can be called by derived class with proper matrice
/// types
template <typename Mat>
void assemblePreassembledMatrix_(Mat & A, const ID & dof_id_m,
const ID & dof_id_n,
const TermsToAssemble & terms);
template <typename Mat>
void assembleElementalMatricesToMatrix_(
Mat & A, const ID & dof_id, const Array<Real> & elementary_mat,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements);
template <typename Vec>
void assembleMatMulVectToArray_(const ID & dof_id, const ID & A_id,
const Array<Real> & x, Array<Real> & array,
Real scale_factor);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the location type of a given dof
inline bool isLocalOrMasterDOF(UInt local_dof_num);
/// Answer to the question is a dof a slave dof ?
inline bool isSlaveDOF(UInt local_dof_num);
/// Answer to the question is a dof a slave dof ?
inline bool isPureGhostDOF(UInt local_dof_num);
/// tells if the dof manager knows about a global dof
bool hasGlobalEquationNumber(Int global) const;
/// return the local index of the global equation number
inline Int globalToLocalEquationNumber(Int global) const;
/// converts local equation numbers to global equation numbers;
inline Int localToGlobalEquationNumber(Int local) const;
/// get the array of dof types (use only if you know what you do...)
inline NodeFlag getDOFFlag(Int local_id) const;
/// Global number of dofs
AKANTU_GET_MACRO(SystemSize, this->system_size, UInt);
/// Local number of dofs
AKANTU_GET_MACRO(LocalSystemSize, this->local_system_size, UInt);
/// Pure local number of dofs
AKANTU_GET_MACRO(PureLocalSystemSize, this->pure_local_system_size, UInt);
/// Retrieve all the registered DOFs
std::vector<ID> getDOFIDs() const;
/* ------------------------------------------------------------------------ */
/* DOFs and derivatives accessors */
/* ------------------------------------------------------------------------ */
/// Get a reference to the registered dof array for a given id
inline Array<Real> & getDOFs(const ID & dofs_id);
/// Get the support type of a given dof
inline DOFSupportType getSupportType(const ID & dofs_id) const;
/// are the dofs registered
- inline bool hasDOFs(const ID & dofs_id) const;
+ inline bool hasDOFs(const ID & dof_id) const;
/// Get a reference to the registered dof derivatives array for a given id
inline Array<Real> & getDOFsDerivatives(const ID & dofs_id, UInt order);
/// Does the dof has derivatives
inline bool hasDOFsDerivatives(const ID & dofs_id, UInt order) const;
/// Get a reference to the blocked dofs array registered for the given id
inline const Array<bool> & getBlockedDOFs(const ID & dofs_id) const;
/// Does the dof has a blocked array
inline bool hasBlockedDOFs(const ID & dofs_id) const;
/// Get a reference to the registered dof increment array for a given id
inline Array<Real> & getDOFsIncrement(const ID & dofs_id);
/// Does the dof has a increment array
inline bool hasDOFsIncrement(const ID & dofs_id) const;
/// Does the dof has a previous array
inline Array<Real> & getPreviousDOFs(const ID & dofs_id);
/// Get a reference to the registered dof array for previous step values a
/// given id
inline bool hasPreviousDOFs(const ID & dofs_id) const;
/// saves the values from dofs to previous dofs
virtual void savePreviousDOFs(const ID & dofs_id);
/// Get a reference to the solution array registered for the given id
inline const Array<Real> & getSolution(const ID & dofs_id) const;
/// Get a reference to the solution array registered for the given id
inline Array<Real> & getSolution(const ID & dofs_id);
/// Get the blocked dofs array
AKANTU_GET_MACRO(GlobalBlockedDOFs, global_blocked_dofs, const Array<Int> &);
/// Get the blocked dofs array
AKANTU_GET_MACRO(PreviousGlobalBlockedDOFs, previous_global_blocked_dofs,
const Array<Int> &);
/* ------------------------------------------------------------------------ */
/* Matrices accessors */
/* ------------------------------------------------------------------------ */
/// Get an instance of a new SparseMatrix
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) = 0;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) = 0;
/// Get the equation numbers corresponding to a dof_id. This might be used to
/// access the matrix.
inline const Array<Int> & getLocalEquationsNumbers(const ID & dof_id) const;
protected:
/// get the array of dof types (use only if you know what you do...)
inline const Array<UInt> & getDOFsAssociatedNodes(const ID & dof_id) const;
protected:
/* ------------------------------------------------------------------------ */
/// register a matrix
SparseMatrix & registerSparseMatrix(const ID & matrix_id,
std::unique_ptr<SparseMatrix> & matrix);
/// register a lumped matrix (aka a Vector)
SolverVector & registerLumpedMatrix(const ID & matrix_id,
std::unique_ptr<SolverVector> & matrix);
/// register a non linear solver instantiated by a derived class
NonLinearSolver &
registerNonLinearSolver(const ID & non_linear_solver_id,
std::unique_ptr<NonLinearSolver> & non_linear_solver);
/// register a time step solver instantiated by a derived class
TimeStepSolver &
registerTimeStepSolver(const ID & time_step_solver_id,
std::unique_ptr<TimeStepSolver> & time_step_solver);
template <class NLSType, class DMType>
NonLinearSolver & registerNonLinearSolver(DMType & dm, const ID & id,
const NonLinearSolverType & type) {
ID non_linear_solver_id = this->id + ":nls:" + id;
std::unique_ptr<NonLinearSolver> nls = std::make_unique<NLSType>(
dm, type, non_linear_solver_id, this->memory_id);
return this->registerNonLinearSolver(non_linear_solver_id, nls);
}
template <class TSSType, class DMType>
TimeStepSolver & registerTimeStepSolver(DMType & dm, const ID & id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback) {
ID time_step_solver_id = this->id + ":tss:" + id;
std::unique_ptr<TimeStepSolver> tss =
std::make_unique<TSSType>(dm, type, non_linear_solver, solver_callback,
time_step_solver_id, this->memory_id);
return this->registerTimeStepSolver(time_step_solver_id, tss);
}
template <class MatType, class DMType>
SparseMatrix & registerSparseMatrix(DMType & dm, const ID & id,
const MatrixType & matrix_type) {
ID matrix_id = this->id + ":mtx:" + id;
std::unique_ptr<SparseMatrix> sm =
std::make_unique<MatType>(dm, matrix_type, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
template <class MatType>
SparseMatrix & registerSparseMatrix(const ID & id,
const ID & matrix_to_copy_id) {
ID matrix_id = this->id + ":mtx:" + id;
auto & sm_to_copy =
aka::as_type<MatType>(this->getMatrix(matrix_to_copy_id));
std::unique_ptr<SparseMatrix> sm =
std::make_unique<MatType>(sm_to_copy, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
template <class MatType, class DMType>
SolverVector & registerLumpedMatrix(DMType & dm, const ID & id) {
ID matrix_id = this->id + ":lumped_mtx:" + id;
std::unique_ptr<SolverVector> sm = std::make_unique<MatType>(dm, matrix_id);
return this->registerLumpedMatrix(matrix_id, sm);
}
protected:
virtual void makeConsistentForPeriodicity(const ID & dof_id,
SolverVector & array) = 0;
virtual void assembleToGlobalArray(const ID & dof_id,
const Array<Real> & array_to_assemble,
SolverVector & global_array,
Real scale_factor) = 0;
public:
/// extract degrees of freedom (identified by ID) from a global solver array
virtual void getArrayPerDOFs(const ID & dof_id, const SolverVector & global,
Array<Real> & local) = 0;
/// Get the reference of an existing matrix
SparseMatrix & getMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasMatrix(const ID & matrix_id) const;
/// Get an instance of a new lumped matrix
virtual SolverVector & getNewLumpedMatrix(const ID & matrix_id) = 0;
/// Get the lumped version of a given matrix
const SolverVector & getLumpedMatrix(const ID & matrix_id) const;
/// Get the lumped version of a given matrix
SolverVector & getLumpedMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasLumpedMatrix(const ID & matrix_id) const;
/* ------------------------------------------------------------------------ */
/* Non linear system solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a non linear solver
virtual NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & _non_linear_solver_type) = 0;
/// get instance of a non linear solver
virtual NonLinearSolver & getNonLinearSolver(const ID & nls_solver_id);
/// check if the given solver exists
bool hasNonLinearSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
/* Time-Step Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a time step solver
virtual TimeStepSolver &
getNewTimeStepSolver(const ID & time_step_solver_id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback) = 0;
/// get instance of a time step solver
virtual TimeStepSolver & getTimeStepSolver(const ID & time_step_solver_id);
/// check if the given solver exists
bool hasTimeStepSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
const Mesh & getMesh() {
- if (mesh) {
+ if (mesh != nullptr) {
return *mesh;
- } else {
- AKANTU_EXCEPTION("No mesh registered in this dof manager");
}
+ AKANTU_EXCEPTION("No mesh registered in this dof manager");
}
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO(Communicator, communicator, const auto &);
AKANTU_GET_MACRO_NOT_CONST(Communicator, communicator, auto &);
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO(Solution, *(solution.get()), const auto &);
AKANTU_GET_MACRO_NOT_CONST(Solution, *(solution.get()), auto &);
AKANTU_GET_MACRO(Residual, *(residual.get()), const auto &);
AKANTU_GET_MACRO_NOT_CONST(Residual, *(residual.get()), auto &);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler interface */
/* ------------------------------------------------------------------------ */
protected:
friend class GlobalDOFInfoDataAccessor;
/// helper function for the DOFManager::onNodesAdded method
virtual std::pair<UInt, UInt> updateNodalDOFs(const ID & dof_id,
const Array<UInt> & nodes_list);
template <typename Func>
auto countDOFsForNodes(const DOFData & dof_data, UInt nb_nodes,
Func && getNode);
void updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local, UInt nb_nodes,
const std::function<UInt(UInt)> & getNode);
void updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local);
auto computeFirstDOFIDs(UInt nb_new_local_dofs, UInt nb_new_pure_local);
/// resize all the global information and takes the needed measure like
/// cleaning matrices profiles
virtual void resizeGlobalArrays();
public:
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
/// function to implement to react on akantu::RemovedNodesEvent
void onNodesRemoved(const Array<UInt> & nodes_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) override;
/// function to implement to react on akantu::NewElementsEvent
void onElementsAdded(const Array<Element> & elements_list,
const NewElementsEvent & event) override;
/// function to implement to react on akantu::RemovedElementsEvent
void onElementsRemoved(const Array<Element> & elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
/// function to implement to react on akantu::ChangedElementsEvent
void onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) override;
protected:
inline DOFData & getDOFData(const ID & dof_id);
inline const DOFData & getDOFData(const ID & dof_id) const;
- template <class _DOFData>
- inline _DOFData & getDOFDataTyped(const ID & dof_id);
- template <class _DOFData>
- inline const _DOFData & getDOFDataTyped(const ID & dof_id) const;
+ template <class DOFData_>
+ inline DOFData_ & getDOFDataTyped(const ID & dof_id);
+ template <class DOFData_>
+ inline const DOFData_ & getDOFDataTyped(const ID & dof_id) const;
virtual std::unique_ptr<DOFData> getNewDOFData(const ID & dof_id) = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// dof representations in the dof manager
struct DOFData {
DOFData() = delete;
explicit DOFData(const ID & dof_id);
virtual ~DOFData();
/// DOF support type (nodal, general) this is needed to determine how the
/// dof are shared among processors
DOFSupportType support_type;
ID group_support;
/// Degree of freedom array
Array<Real> * dof{nullptr};
/// Blocked degree of freedoms array
Array<bool> * blocked_dofs{nullptr};
/// Degree of freedoms increment
Array<Real> * increment{nullptr};
/// Degree of freedoms at previous step
Array<Real> * previous{nullptr};
/// Solution associated to the dof
Array<Real> solution;
/* ---------------------------------------------------------------------- */
/* data for dynamic simulations */
/* ---------------------------------------------------------------------- */
/// Degree of freedom derivatives arrays
std::vector<Array<Real> *> dof_derivatives;
/* ---------------------------------------------------------------------- */
/// number of dofs to consider locally for this dof id
UInt local_nb_dofs{0};
/// Number of purely local dofs
UInt pure_local_nb_dofs{0};
/// number of ghost dofs
UInt ghosts_nb_dofs{0};
/// local numbering equation numbers
Array<Int> local_equation_number;
/// associated node for _dst_nodal dofs only
Array<UInt> associated_nodes;
virtual Array<Int> & getLocalEquationsNumbers() {
return local_equation_number;
}
};
/// type to store dofs information
using DOFStorage = std::map<ID, std::unique_ptr<DOFData>>;
/// type to store all the matrices
using SparseMatricesMap = std::map<ID, std::unique_ptr<SparseMatrix>>;
/// type to store all the lumped matrices
using LumpedMatricesMap = std::map<ID, std::unique_ptr<SolverVector>>;
/// type to store all the non linear solver
using NonLinearSolversMap = std::map<ID, std::unique_ptr<NonLinearSolver>>;
/// type to store all the time step solver
using TimeStepSolversMap = std::map<ID, std::unique_ptr<TimeStepSolver>>;
/// store a reference to the dof arrays
DOFStorage dofs;
/// list of sparse matrices that where created
SparseMatricesMap matrices;
/// list of lumped matrices
LumpedMatricesMap lumped_matrices;
/// non linear solvers storage
NonLinearSolversMap non_linear_solvers;
/// time step solvers storage
TimeStepSolversMap time_step_solvers;
/// reference to the underlying mesh
Mesh * mesh{nullptr};
/// Total number of degrees of freedom (size with the ghosts)
UInt local_system_size{0};
/// Number of purely local dofs (size without the ghosts)
UInt pure_local_system_size{0};
/// Total number of degrees of freedom
UInt system_size{0};
/// rhs to the system of equation corresponding to the residual linked to the
/// different dofs
std::unique_ptr<SolverVector> residual;
/// solution of the system of equation corresponding to the different dofs
std::unique_ptr<SolverVector> solution;
/// a vector that helps internally to perform some tasks
std::unique_ptr<SolverVector> data_cache;
/// define the dofs type, local, shared, ghost
Array<NodeFlag> dofs_flag;
/// equation number in global numbering
Array<Int> global_equation_number;
using equation_numbers_map = std::unordered_map<Int, Int>;
/// dual information of global_equation_number
equation_numbers_map global_to_local_mapping;
/// Communicator used for this manager, should be the same as in the mesh if a
/// mesh is registered
Communicator & communicator;
/// accumulator to know what would be the next global id to use
UInt first_global_dof_id{0};
/// Release at last apply boundary on jacobian
UInt jacobian_release{0};
/// blocked degree of freedom in the system equation corresponding to the
/// different dofs
Array<Int> global_blocked_dofs;
UInt global_blocked_dofs_release{0};
/// blocked degree of freedom in the system equation corresponding to the
/// different dofs
Array<Int> previous_global_blocked_dofs;
UInt previous_global_blocked_dofs_release{0};
private:
/// This is for unit testing
friend class DOFManagerTester;
};
using DefaultDOFManagerFactory =
Factory<DOFManager, ID, const ID &, const MemoryID &>;
using DOFManagerFactory =
Factory<DOFManager, ID, Mesh &, const ID &, const MemoryID &>;
} // namespace akantu
#include "dof_manager_inline_impl.hh"
-#endif /* __AKANTU_DOF_MANAGER_HH__ */
+#endif /* AKANTU_DOF_MANAGER_HH_ */
diff --git a/src/model/common/dof_manager/dof_manager_default.cc b/src/model/common/dof_manager/dof_manager_default.cc
index 8cca2aef5..4caf6a746 100644
--- a/src/model/common/dof_manager/dof_manager_default.cc
+++ b/src/model/common/dof_manager/dof_manager_default.cc
@@ -1,491 +1,499 @@
/**
* @file dof_manager_default.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Thu Feb 08 2018
*
* @brief Implementation of the default DOFManager
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "element_group.hh"
#include "non_linear_solver_default.hh"
#include "periodic_node_synchronizer.hh"
#include "solver_vector_default.hh"
#include "solver_vector_distributed.hh"
#include "sparse_matrix_aij.hh"
#include "time_step_solver_default.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <memory>
#include <numeric>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(const ID & id, const MemoryID & memory_id)
: DOFManager(id, memory_id), synchronizer(nullptr) {
residual = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":residual"));
solution = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":solution"));
data_cache = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":data_cache"));
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: DOFManager(mesh, id, memory_id), synchronizer(nullptr) {
if (this->mesh->isDistributed()) {
this->synchronizer = std::make_unique<DOFSynchronizer>(
*this, this->id + ":dof_synchronizer", this->memory_id);
residual = std::make_unique<SolverVectorDistributed>(
*this, std::string(id + ":residual"));
solution = std::make_unique<SolverVectorDistributed>(
*this, std::string(id + ":solution"));
data_cache = std::make_unique<SolverVectorDistributed>(
*this, std::string(id + ":data_cache"));
} else {
residual = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":residual"));
solution = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":solution"));
data_cache = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":data_cache"));
}
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::~DOFManagerDefault() = default;
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::makeConsistentForPeriodicity(const ID & dof_id,
SolverVector & array) {
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
- if (dof_data.support_type != _dst_nodal)
+ if (dof_data.support_type != _dst_nodal) {
return;
+ }
- if (not mesh->isPeriodic())
+ if (not mesh->isPeriodic()) {
return;
+ }
this->mesh->getPeriodicNodeSynchronizer()
.reduceSynchronizeWithPBCSlaves<AddOperation>(
aka::as_type<SolverVectorDefault>(array).getVector());
}
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFManagerDefault::assembleToGlobalArray(
const ID & dof_id, const Array<T> & array_to_assemble,
Array<T> & global_array, T scale_factor) {
AKANTU_DEBUG_IN();
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
AKANTU_DEBUG_ASSERT(dof_data.local_equation_number.size() ==
array_to_assemble.size() *
array_to_assemble.getNbComponent(),
"The array to assemble does not have a correct size."
<< " (" << array_to_assemble.getID() << ")");
if (dof_data.support_type == _dst_nodal and mesh->isPeriodic()) {
for (auto && data :
zip(dof_data.local_equation_number, dof_data.associated_nodes,
make_view(array_to_assemble))) {
auto && equ_num = std::get<0>(data);
// auto && node = std::get<1>(data);
auto && arr = std::get<2>(data);
// Guillaume to Nico:
// This filter of periodic slave should not be.
// Indeed you want to get the contribution even
// from periodic slaves and cumulate to the right
// equation number.
global_array(equ_num) += scale_factor * (arr);
// scale_factor * (arr) * (not this->mesh->isPeriodicSlave(node));
}
} else {
for (auto && data :
zip(dof_data.local_equation_number, make_view(array_to_assemble))) {
auto && equ_num = std::get<0>(data);
auto && arr = std::get<1>(data);
global_array(equ_num) += scale_factor * (arr);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleToGlobalArray(
const ID & dof_id, const Array<Real> & array_to_assemble,
SolverVector & global_array_v, Real scale_factor) {
assembleToGlobalArray(
dof_id, array_to_assemble,
aka::as_type<SolverVectorDefault>(global_array_v).getVector(),
scale_factor);
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFDataDefault::DOFDataDefault(const ID & dof_id)
: DOFData(dof_id) {}
/* -------------------------------------------------------------------------- */
auto DOFManagerDefault::getNewDOFData(const ID & dof_id)
-> std::unique_ptr<DOFData> {
return std::make_unique<DOFDataDefault>(dof_id);
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt, UInt>
DOFManagerDefault::registerDOFsInternal(const ID & dof_id,
Array<Real> & dofs_array) {
auto ret = DOFManager::registerDOFsInternal(dof_id, dofs_array);
// update the synchronizer if needed
- if (this->synchronizer)
+ if (this->synchronizer) {
this->synchronizer->registerDOFs(dof_id);
+ }
return ret;
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const MatrixType & matrix_type) {
return this->registerSparseMatrix<SparseMatrixAIJ>(*this, id, matrix_type);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const ID & matrix_to_copy_id) {
return this->registerSparseMatrix<SparseMatrixAIJ>(id, matrix_to_copy_id);
}
/* -------------------------------------------------------------------------- */
SolverVector & DOFManagerDefault::getNewLumpedMatrix(const ID & id) {
return this->registerLumpedMatrix<SolverVectorDefault>(*this, id);
}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ & DOFManagerDefault::getMatrix(const ID & id) {
auto & matrix = DOFManager::getMatrix(id);
return aka::as_type<SparseMatrixAIJ>(matrix);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver &
DOFManagerDefault::getNewNonLinearSolver(const ID & id,
const NonLinearSolverType & type) {
switch (type) {
#if defined(AKANTU_USE_MUMPS)
case NonLinearSolverType::_newton_raphson:
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it */
case NonLinearSolverType::_newton_raphson_modified: {
return this->registerNonLinearSolver<NonLinearSolverNewtonRaphson>(
*this, id, type);
}
case NonLinearSolverType::_linear: {
return this->registerNonLinearSolver<NonLinearSolverLinear>(*this, id,
type);
}
#endif
case NonLinearSolverType::_lumped: {
return this->registerNonLinearSolver<NonLinearSolverLumped>(*this, id,
type);
}
default:
AKANTU_EXCEPTION("The asked type of non linear solver is not supported by "
"this dof manager");
}
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManagerDefault::getNewTimeStepSolver(
const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, SolverCallback & solver_callback) {
return this->registerTimeStepSolver<TimeStepSolverDefault>(
*this, id, type, non_linear_solver, solver_callback);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFManagerDefault::getArrayPerDOFs(const ID & dof_id,
const Array<T> & global_array,
Array<T> & local_array) const {
AKANTU_DEBUG_IN();
const Array<Int> & equation_number = this->getLocalEquationsNumbers(dof_id);
UInt nb_degree_of_freedoms = equation_number.size();
local_array.resize(nb_degree_of_freedoms / local_array.getNbComponent());
auto loc_it = local_array.begin_reinterpret(nb_degree_of_freedoms);
auto equ_it = equation_number.begin();
for (UInt d = 0; d < nb_degree_of_freedoms; ++d, ++loc_it, ++equ_it) {
(*loc_it) = global_array(*equ_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::getArrayPerDOFs(const ID & dof_id,
const SolverVector & global_array,
Array<Real> & local_array) {
getArrayPerDOFs(dof_id,
aka::as_type<SolverVectorDefault>(global_array).getVector(),
local_array);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleLumpedMatMulVectToResidual(
const ID & dof_id, const ID & A_id, const Array<Real> & x,
Real scale_factor) {
const Array<Real> & A = this->getLumpedMatrix(A_id);
auto & cache = aka::as_type<SolverVectorArray>(*this->data_cache);
- cache.clear();
+ cache.zero();
this->assembleToGlobalArray(dof_id, x, cache.getVector(), scale_factor);
for (auto && data : zip(make_view(A), make_view(cache.getVector()),
make_view(this->getResidualArray()))) {
const auto & A = std::get<0>(data);
const auto & x = std::get<1>(data);
auto & r = std::get<2>(data);
r += A * x;
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id, const Array<Real> & elementary_mat,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) {
this->addToProfile(matrix_id, dof_id, type, ghost_type);
auto & A = getMatrix(matrix_id);
DOFManager::assembleElementalMatricesToMatrix_(
A, dof_id, elementary_mat, type, ghost_type, elemental_matrix_type,
filter_elements);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assemblePreassembledMatrix(
const ID & dof_id_m, const ID & dof_id_n, const ID & matrix_id,
const TermsToAssemble & terms) {
auto & A = getMatrix(matrix_id);
DOFManager::assemblePreassembledMatrix_(A, dof_id_m, dof_id_n, terms);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleMatMulVectToArray(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor) {
if (mesh->isDistributed()) {
DOFManager::assembleMatMulVectToArray_<SolverVectorDistributed>(
dof_id, A_id, x, array, scale_factor);
} else {
DOFManager::assembleMatMulVectToArray_<SolverVectorDefault>(
dof_id, A_id, x, array, scale_factor);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::addToProfile(const ID & matrix_id, const ID & dof_id,
- const ElementType & type,
- const GhostType & ghost_type) {
+ ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
const auto & dof_data = this->getDOFData(dof_id);
- if (dof_data.support_type != _dst_nodal)
+ if (dof_data.support_type != _dst_nodal) {
return;
+ }
auto mat_dof = std::make_pair(matrix_id, dof_id);
auto type_pair = std::make_pair(type, ghost_type);
auto prof_it = this->matrix_profiled_dofs.find(mat_dof);
if (prof_it != this->matrix_profiled_dofs.end() &&
std::find(prof_it->second.begin(), prof_it->second.end(), type_pair) !=
- prof_it->second.end())
+ prof_it->second.end()) {
return;
+ }
auto nb_degree_of_freedom_per_node = dof_data.dof->getNbComponent();
const auto & equation_number = this->getLocalEquationsNumbers(dof_id);
auto & A = this->getMatrix(matrix_id);
A.resize(system_size);
auto size = A.size();
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto & connectivity = this->mesh->getConnectivity(type, ghost_type);
auto cbegin = connectivity.begin(nb_nodes_per_element);
auto cit = cbegin;
auto nb_elements = connectivity.size();
UInt * ge_it = nullptr;
if (dof_data.group_support != "__mesh__") {
const auto & group_elements =
this->mesh->getElementGroup(dof_data.group_support)
.getElements(type, ghost_type);
ge_it = group_elements.storage();
nb_elements = group_elements.size();
}
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom_per_node;
Vector<Int> element_eq_nb(size_mat);
for (UInt e = 0; e < nb_elements; ++e) {
- if (ge_it)
+ if (ge_it != nullptr) {
cit = cbegin + *ge_it;
+ }
this->extractElementEquationNumber(
equation_number, *cit, nb_degree_of_freedom_per_node, element_eq_nb);
std::transform(
element_eq_nb.storage(), element_eq_nb.storage() + element_eq_nb.size(),
element_eq_nb.storage(),
[&](auto & local) { return this->localToGlobalEquationNumber(local); });
- if (ge_it)
+ if (ge_it != nullptr) {
++ge_it;
- else
+ } else {
++cit;
+ }
for (UInt i = 0; i < size_mat; ++i) {
UInt c_irn = element_eq_nb(i);
if (c_irn < size) {
for (UInt j = 0; j < size_mat; ++j) {
UInt c_jcn = element_eq_nb(j);
if (c_jcn < size) {
A.add(c_irn, c_jcn);
}
}
}
}
}
this->matrix_profiled_dofs[mat_dof].push_back(type_pair);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Array<Real> & DOFManagerDefault::getSolutionArray() {
return dynamic_cast<SolverVectorDefault *>(this->solution.get())->getVector();
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManagerDefault::getResidualArray() const {
return dynamic_cast<SolverVectorDefault *>(this->residual.get())->getVector();
}
/* -------------------------------------------------------------------------- */
Array<Real> & DOFManagerDefault::getResidualArray() {
return dynamic_cast<SolverVectorDefault *>(this->residual.get())->getVector();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) {
DOFManager::onNodesAdded(nodes_list, event);
- if (this->synchronizer)
+ if (this->synchronizer) {
this->synchronizer->onNodesAdded(nodes_list);
+ }
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::resizeGlobalArrays() {
DOFManager::resizeGlobalArrays();
- this->global_blocked_dofs.resize(this->local_system_size, true);
- this->previous_global_blocked_dofs.resize(this->local_system_size, true);
+ this->global_blocked_dofs.resize(this->local_system_size, 1);
+ this->previous_global_blocked_dofs.resize(this->local_system_size, 1);
matrix_profiled_dofs.clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::updateGlobalBlockedDofs() {
DOFManager::updateGlobalBlockedDofs();
if (this->global_blocked_dofs_release ==
- this->previous_global_blocked_dofs_release)
+ this->previous_global_blocked_dofs_release) {
return;
+ }
global_blocked_dofs_uint.resize(local_system_size);
global_blocked_dofs_uint.set(false);
for (const auto & dof : global_blocked_dofs) {
global_blocked_dofs_uint[dof] = true;
}
}
/* -------------------------------------------------------------------------- */
Array<bool> & DOFManagerDefault::getBlockedDOFs() {
return global_blocked_dofs_uint;
}
/* -------------------------------------------------------------------------- */
const Array<bool> & DOFManagerDefault::getBlockedDOFs() const {
return global_blocked_dofs_uint;
}
/* -------------------------------------------------------------------------- */
// register in factory
// static bool default_dof_manager_is_registered [[gnu::unused]] =
// DefaultDOFManagerFactory::getInstance().registerAllocator(
// "default",
// [](const ID & id,
// const MemoryID & mem_id) -> std::unique_ptr<DOFManager> {
// return std::make_unique<DOFManagerDefault>(id, mem_id);
// });
static bool dof_manager_is_registered [[gnu::unused]] =
DOFManagerFactory::getInstance().registerAllocator(
"default",
[](Mesh & mesh, const ID & id,
const MemoryID & mem_id) -> std::unique_ptr<DOFManager> {
return std::make_unique<DOFManagerDefault>(mesh, id, mem_id);
});
static bool dof_manager_is_registered_mumps [[gnu::unused]] =
DOFManagerFactory::getInstance().registerAllocator(
"mumps",
[](Mesh & mesh, const ID & id,
const MemoryID & mem_id) -> std::unique_ptr<DOFManager> {
return std::make_unique<DOFManagerDefault>(mesh, id, mem_id);
});
} // namespace akantu
diff --git a/src/model/common/dof_manager/dof_manager_default.hh b/src/model/common/dof_manager/dof_manager_default.hh
index 9682e3e5b..3e962e315 100644
--- a/src/model/common/dof_manager/dof_manager_default.hh
+++ b/src/model/common/dof_manager/dof_manager_default.hh
@@ -1,255 +1,255 @@
/**
* @file dof_manager_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Default implementation of the dof manager
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DOF_MANAGER_DEFAULT_HH__
-#define __AKANTU_DOF_MANAGER_DEFAULT_HH__
+#ifndef AKANTU_DOF_MANAGER_DEFAULT_HH_
+#define AKANTU_DOF_MANAGER_DEFAULT_HH_
namespace akantu {
class SparseMatrixAIJ;
class NonLinearSolverDefault;
class TimeStepSolverDefault;
class DOFSynchronizer;
} // namespace akantu
namespace akantu {
class DOFManagerDefault : public DOFManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManagerDefault(const ID & id = "dof_manager_default",
const MemoryID & memory_id = 0);
DOFManagerDefault(Mesh & mesh, const ID & id = "dof_manager_default",
const MemoryID & memory_id = 0);
~DOFManagerDefault() override;
protected:
struct DOFDataDefault : public DOFData {
explicit DOFDataDefault(const ID & dof_id);
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
// /// register an array of degree of freedom
// void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
// const DOFSupportType & support_type) override;
// /// the dof as an implied type of _dst_nodal and is defined only on a
// subset
// /// of nodes
// void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
// const ID & group_support) override;
/**
* Assemble elementary values to the global matrix. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
- const Array<Real> & elementary_mat, const ElementType & type,
- const GhostType & ghost_type, const MatrixType & elemental_matrix_type,
+ const Array<Real> & elementary_mat, ElementType type,
+ GhostType ghost_type, const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) override;
void assembleMatMulVectToArray(const ID & dof_id, const ID & A_id,
const Array<Real> & x, Array<Real> & array,
Real scale_factor = 1.) override;
/// multiply a vector by a lumped matrix and assemble the result to the
/// residual
void assembleLumpedMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) override;
/// assemble coupling terms between to dofs
void assemblePreassembledMatrix(const ID & dof_id_m, const ID & dof_id_n,
const ID & matrix_id,
const TermsToAssemble & terms) override;
protected:
void assembleToGlobalArray(const ID & dof_id,
const Array<Real> & array_to_assemble,
SolverVector & global_array,
Real scale_factor) override;
template <typename T>
void assembleToGlobalArray(const ID & dof_id,
const Array<T> & array_to_assemble,
Array<T> & global_array, T scale_factor);
void getArrayPerDOFs(const ID & dof_id, const SolverVector & global,
Array<Real> & local) override;
template <typename T>
void getArrayPerDOFs(const ID & dof_id, const Array<T> & global_array,
Array<T> & local_array) const;
void makeConsistentForPeriodicity(const ID & dof_id,
SolverVector & array) override;
public:
/// update the global dofs vector
void updateGlobalBlockedDofs() override;
// /// apply boundary conditions to jacobian matrix
// void applyBoundary(const ID & matrix_id = "J") override;
private:
/// Add a symmetric matrices to a symmetric sparse matrix
void addSymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<Int> & equation_numbers, UInt max_size);
/// Add a unsymmetric matrices to a symmetric sparse matrix (i.e. cohesive
/// elements)
void addUnsymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<Int> & equation_numbers, UInt max_size);
/// Add a matrices to a unsymmetric sparse matrix
void addElementalMatrixToUnsymmetric(SparseMatrixAIJ & matrix,
const Matrix<Real> & element_mat,
const Vector<Int> & equation_numbers,
UInt max_size);
void addToProfile(const ID & matrix_id, const ID & dof_id,
- const ElementType & type, const GhostType & ghost_type);
+ ElementType type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler interface */
/* ------------------------------------------------------------------------ */
protected:
std::tuple<UInt, UInt, UInt>
registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array) override;
// std::pair<UInt, UInt>
// updateNodalDOFs(const ID & dof_id, const Array<UInt> & nodes_list)
// override;
void resizeGlobalArrays() override;
public:
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get an instance of a new SparseMatrix
SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) override;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) override;
/// Get the reference of an existing matrix
SparseMatrixAIJ & getMatrix(const ID & matrix_id);
/// Get an instance of a new lumped matrix
SolverVector & getNewLumpedMatrix(const ID & matrix_id) override;
/* ------------------------------------------------------------------------ */
/* Non Linear Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a non linear solver
NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & _non_linear_solver_type) override;
/* ------------------------------------------------------------------------ */
/* Time-Step Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a time step solver
TimeStepSolver &
getNewTimeStepSolver(const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback) override;
/* ------------------------------------------------------------------------ */
private:
/// Get the solution array
Array<Real> & getSolutionArray();
/// Get the residual array
const Array<Real> & getResidualArray() const;
/// Get the residual array
Array<Real> & getResidualArray();
public:
/// access the internal dof_synchronizer
AKANTU_GET_MACRO_NOT_CONST(Synchronizer, *synchronizer, DOFSynchronizer &);
/// access the internal dof_synchronizer
bool hasSynchronizer() const { return synchronizer != nullptr; }
Array<bool> & getBlockedDOFs();
const Array<bool> & getBlockedDOFs() const;
protected:
std::unique_ptr<DOFData> getNewDOFData(const ID & dof_id) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
using DOFToMatrixProfile =
std::map<std::pair<ID, ID>,
std::vector<std::pair<ElementType, GhostType>>>;
/// contains the the dofs that where added to the profile of a given matrix.
DOFToMatrixProfile matrix_profiled_dofs;
/// synchronizer to maintain coherency in dof fields
std::unique_ptr<DOFSynchronizer> synchronizer;
friend class DOFSynchronizer;
/// Array containing the true or false if the node is in global_blocked_dofs
Array<bool> global_blocked_dofs_uint;
};
} // namespace akantu
#include "dof_manager_default_inline_impl.hh"
-#endif /* __AKANTU_DOF_MANAGER_DEFAULT_HH__ */
+#endif /* AKANTU_DOF_MANAGER_DEFAULT_HH_ */
diff --git a/src/model/common/dof_manager/dof_manager_default_inline_impl.hh b/src/model/common/dof_manager/dof_manager_default_inline_impl.hh
index f12730dee..d473c1f68 100644
--- a/src/model/common/dof_manager/dof_manager_default_inline_impl.hh
+++ b/src/model/common/dof_manager/dof_manager_default_inline_impl.hh
@@ -1,39 +1,39 @@
/**
* @file dof_manager_default_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the DOFManagerDefault inline functions
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_HH__
-#define __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_HH__
+#ifndef AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_HH_
+#define AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_HH_
namespace akantu {} // namespace akantu
#endif /* __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_HH_ */
diff --git a/src/model/common/dof_manager/dof_manager_inline_impl.hh b/src/model/common/dof_manager/dof_manager_inline_impl.hh
index 5976447d2..22713a58d 100644
--- a/src/model/common/dof_manager/dof_manager_inline_impl.hh
+++ b/src/model/common/dof_manager/dof_manager_inline_impl.hh
@@ -1,332 +1,335 @@
/**
* @file dof_manager_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Jan 31 2018
*
* @brief inline functions of the dof manager
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
#include "element_group.hh"
#include "solver_vector.hh"
#include "sparse_matrix.hh"
#include "terms_to_assemble.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DOF_MANAGER_INLINE_IMPL_HH__
-#define __AKANTU_DOF_MANAGER_INLINE_IMPL_HH__
+#ifndef AKANTU_DOF_MANAGER_INLINE_IMPL_HH_
+#define AKANTU_DOF_MANAGER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFs(const ID & dof_id) const {
auto it = this->dofs.find(dof_id);
return it != this->dofs.end();
}
/* -------------------------------------------------------------------------- */
inline DOFManager::DOFData & DOFManager::getDOFData(const ID & dof_id) {
auto it = this->dofs.find(dof_id);
if (it == this->dofs.end()) {
AKANTU_EXCEPTION("The dof " << dof_id << " does not exists in "
<< this->id);
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
const DOFManager::DOFData & DOFManager::getDOFData(const ID & dof_id) const {
auto it = this->dofs.find(dof_id);
if (it == this->dofs.end()) {
AKANTU_EXCEPTION("The dof " << dof_id << " does not exists in "
<< this->id);
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
inline void DOFManager::extractElementEquationNumber(
const Array<Int> & equation_numbers, const Vector<UInt> & connectivity,
UInt nb_degree_of_freedom, Vector<Int> & element_equation_number) {
for (UInt i = 0, ld = 0; i < connectivity.size(); ++i) {
UInt n = connectivity(i);
for (UInt d = 0; d < nb_degree_of_freedom; ++d, ++ld) {
element_equation_number(ld) =
equation_numbers(n * nb_degree_of_freedom + d);
}
}
}
/* -------------------------------------------------------------------------- */
-template <class _DOFData>
-inline _DOFData & DOFManager::getDOFDataTyped(const ID & dof_id) {
- return aka::as_type<_DOFData>(this->getDOFData(dof_id));
+template <class DOFData_>
+inline DOFData_ & DOFManager::getDOFDataTyped(const ID & dof_id) {
+ return aka::as_type<DOFData_>(this->getDOFData(dof_id));
}
/* -------------------------------------------------------------------------- */
-template <class _DOFData>
-inline const _DOFData & DOFManager::getDOFDataTyped(const ID & dof_id) const {
- return aka::as_type<_DOFData>(this->getDOFData(dof_id));
+template <class DOFData_>
+inline const DOFData_ & DOFManager::getDOFDataTyped(const ID & dof_id) const {
+ return aka::as_type<DOFData_>(this->getDOFData(dof_id));
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFs(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).dof);
}
/* -------------------------------------------------------------------------- */
inline DOFSupportType DOFManager::getSupportType(const ID & dofs_id) const {
return this->getDOFData(dofs_id).support_type;
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getPreviousDOFs(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).previous);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasPreviousDOFs(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).previous != nullptr);
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFsIncrement(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).increment);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFsIncrement(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).increment != nullptr);
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFsDerivatives(const ID & dofs_id,
UInt order) {
if (order == 0) {
return getDOFs(dofs_id);
}
std::vector<Array<Real> *> & derivatives =
this->getDOFData(dofs_id).dof_derivatives;
- if ((order > derivatives.size()) || (derivatives[order - 1] == nullptr))
+ if ((order > derivatives.size()) || (derivatives[order - 1] == nullptr)) {
AKANTU_EXCEPTION("No derivatives of order " << order << " present in "
<< this->id << " for dof "
<< dofs_id);
+ }
return *derivatives[order - 1];
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFsDerivatives(const ID & dofs_id,
UInt order) const {
const std::vector<Array<Real> *> & derivatives =
this->getDOFData(dofs_id).dof_derivatives;
return ((order < derivatives.size()) && (derivatives[order - 1] != nullptr));
}
/* -------------------------------------------------------------------------- */
inline const Array<Real> & DOFManager::getSolution(const ID & dofs_id) const {
return this->getDOFData(dofs_id).solution;
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getSolution(const ID & dofs_id) {
return this->getDOFData(dofs_id).solution;
}
/* -------------------------------------------------------------------------- */
inline const Array<bool> &
DOFManager::getBlockedDOFs(const ID & dofs_id) const {
return *(this->getDOFData(dofs_id).blocked_dofs);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasBlockedDOFs(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).blocked_dofs != nullptr);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::isLocalOrMasterDOF(UInt dof_num) {
auto dof_flag = this->dofs_flag(dof_num);
return (dof_flag & NodeFlag::_local_master_mask) == NodeFlag::_normal;
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::isSlaveDOF(UInt dof_num) {
auto dof_flag = this->dofs_flag(dof_num);
return (dof_flag & NodeFlag::_shared_mask) == NodeFlag::_slave;
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::isPureGhostDOF(UInt dof_num) {
auto dof_flag = this->dofs_flag(dof_num);
return (dof_flag & NodeFlag::_shared_mask) == NodeFlag::_pure_ghost;
}
/* -------------------------------------------------------------------------- */
inline Int DOFManager::localToGlobalEquationNumber(Int local) const {
return this->global_equation_number(local);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasGlobalEquationNumber(Int global) const {
auto it = this->global_to_local_mapping.find(global);
return (it != this->global_to_local_mapping.end());
}
/* -------------------------------------------------------------------------- */
inline Int DOFManager::globalToLocalEquationNumber(Int global) const {
auto it = this->global_to_local_mapping.find(global);
AKANTU_DEBUG_ASSERT(it != this->global_to_local_mapping.end(),
"This global equation number "
<< global << " does not exists in " << this->id);
return it->second;
}
/* -------------------------------------------------------------------------- */
inline NodeFlag DOFManager::getDOFFlag(Int local_id) const {
return this->dofs_flag(local_id);
}
/* -------------------------------------------------------------------------- */
inline const Array<UInt> &
DOFManager::getDOFsAssociatedNodes(const ID & dof_id) const {
const auto & dof_data = this->getDOFData(dof_id);
return dof_data.associated_nodes;
}
/* -------------------------------------------------------------------------- */
const Array<Int> &
DOFManager::getLocalEquationsNumbers(const ID & dof_id) const {
return getDOFData(dof_id).local_equation_number;
}
/* -------------------------------------------------------------------------- */
template <typename Vec>
void DOFManager::assembleMatMulVectToArray_(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor) {
Vec tmp_array(aka::as_type<Vec>(*data_cache), this->id + ":tmp_array");
- tmp_array.clear();
+ tmp_array.zero();
assembleMatMulVectToGlobalArray(dof_id, A_id, x, tmp_array, scale_factor);
getArrayPerDOFs(dof_id, tmp_array, array);
}
/* -------------------------------------------------------------------------- */
template <typename Mat>
void DOFManager::assembleElementalMatricesToMatrix_(
Mat & A, const ID & dof_id, const Array<Real> & elementary_mat,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
auto & dof_data = this->getDOFData(dof_id);
AKANTU_DEBUG_ASSERT(dof_data.support_type == _dst_nodal,
"This function applies only on Nodal dofs");
const auto & equation_number = this->getLocalEquationsNumbers(dof_id);
UInt nb_element;
UInt * filter_it = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filter_it = filter_elements.storage();
} else {
if (dof_data.group_support != "__mesh__") {
const auto & group_elements =
this->mesh->getElementGroup(dof_data.group_support)
.getElements(type, ghost_type);
nb_element = group_elements.size();
filter_it = group_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
}
AKANTU_DEBUG_ASSERT(elementary_mat.size() == nb_element,
"The vector elementary_mat("
<< elementary_mat.getID()
<< ") has not the good size.");
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = dof_data.dof->getNbComponent();
const Array<UInt> & connectivity =
this->mesh->getConnectivity(type, ghost_type);
auto conn_begin = connectivity.begin(nb_nodes_per_element);
auto conn_it = conn_begin;
auto size_mat = nb_nodes_per_element * nb_degree_of_freedom;
Vector<Int> element_eq_nb(nb_degree_of_freedom * nb_nodes_per_element);
auto el_mat_it = elementary_mat.begin(size_mat, size_mat);
for (UInt e = 0; e < nb_element; ++e, ++el_mat_it) {
- if (filter_it)
+ if (filter_it) {
conn_it = conn_begin + *filter_it;
+ }
this->extractElementEquationNumber(equation_number, *conn_it,
nb_degree_of_freedom, element_eq_nb);
std::transform(element_eq_nb.begin(), element_eq_nb.end(),
element_eq_nb.begin(), [&](auto && local) {
return this->localToGlobalEquationNumber(local);
});
- if (filter_it)
+ if (filter_it) {
++filter_it;
- else
+ } else {
++conn_it;
+ }
A.addValues(element_eq_nb, element_eq_nb, *el_mat_it,
elemental_matrix_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Mat>
void DOFManager::assemblePreassembledMatrix_(Mat & A, const ID & dof_id_m,
const ID & dof_id_n,
const TermsToAssemble & terms) {
const auto & equation_number_m = this->getLocalEquationsNumbers(dof_id_m);
const auto & equation_number_n = this->getLocalEquationsNumbers(dof_id_n);
for (const auto & term : terms) {
auto gi = this->localToGlobalEquationNumber(equation_number_m(term.i()));
auto gj = this->localToGlobalEquationNumber(equation_number_n(term.j()));
A.add(gi, gj, term);
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_DOF_MANAGER_INLINE_IMPL_HH__ */
+#endif /* AKANTU_DOF_MANAGER_INLINE_IMPL_HH_ */
diff --git a/src/model/common/dof_manager/dof_manager_petsc.cc b/src/model/common/dof_manager/dof_manager_petsc.cc
index 0cbf8bfd9..4fe29e244 100644
--- a/src/model/common/dof_manager/dof_manager_petsc.cc
+++ b/src/model/common/dof_manager/dof_manager_petsc.cc
@@ -1,310 +1,305 @@
/**
* @file dof_manager_petsc.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 07 2015
* @date last modification: Tue Feb 20 2018
*
* @brief DOFManaterPETSc is the PETSc implementation of the DOFManager
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_petsc.hh"
#include "aka_iterators.hh"
#include "communicator.hh"
#include "cppargparse.hh"
#include "non_linear_solver_petsc.hh"
#include "solver_vector_petsc.hh"
#include "sparse_matrix_petsc.hh"
#include "time_step_solver_default.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <petscis.h>
#include <petscsys.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
class PETScSingleton {
private:
PETScSingleton() {
PETSc_call(PetscInitialized, &is_initialized);
- if (not is_initialized) {
+ if (is_initialized == 0U) {
cppargparse::ArgumentParser & argparser = getStaticArgumentParser();
int & argc = argparser.getArgC();
char **& argv = argparser.getArgV();
- PETSc_call(PetscInitialize, &argc, &argv, NULL, NULL);
+ PETSc_call(PetscInitialize, &argc, &argv, nullptr, nullptr);
PETSc_call(
PetscPopErrorHandler); // remove the default PETSc signal handler
- PETSc_call(PetscPushErrorHandler, PetscIgnoreErrorHandler, NULL);
+ PETSc_call(PetscPushErrorHandler, PetscIgnoreErrorHandler, nullptr);
}
}
public:
PETScSingleton(const PETScSingleton &) = delete;
PETScSingleton & operator=(const PETScSingleton &) = delete;
~PETScSingleton() {
- if (not is_initialized) {
+ if (is_initialized == 0U) {
PetscFinalize();
}
}
static PETScSingleton & getInstance() {
static PETScSingleton instance;
return instance;
}
private:
PetscBool is_initialized;
};
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFDataPETSc::DOFDataPETSc(const ID & dof_id)
: DOFData(dof_id) {}
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFManagerPETSc(const ID & id, const MemoryID & memory_id)
: DOFManager(id, memory_id) {
init();
}
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFManagerPETSc(Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: DOFManager(mesh, id, memory_id) {
init();
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::init() {
// check if the akantu types and PETSc one are consistant
static_assert(sizeof(Int) == sizeof(PetscInt),
"The integer type of Akantu does not match the one from PETSc");
static_assert(sizeof(Real) == sizeof(PetscReal),
"The integer type of Akantu does not match the one from PETSc");
#if defined(AKANTU_USE_MPI)
const auto & mpi_data =
aka::as_type<MPICommunicatorData>(communicator.getCommunicatorData());
MPI_Comm mpi_comm = mpi_data.getMPICommunicator();
this->mpi_communicator = mpi_comm;
#else
this->mpi_communicator = PETSC_COMM_SELF;
#endif
PETScSingleton & instance [[gnu::unused]] = PETScSingleton::getInstance();
}
-/* -------------------------------------------------------------------------- */
-DOFManagerPETSc::~DOFManagerPETSc() {
- // if (is_ltog_map)
- // PETSc_call(ISLocalToGlobalMappingDestroy, &is_ltog_map);
-}
-
/* -------------------------------------------------------------------------- */
auto DOFManagerPETSc::getNewDOFData(const ID & dof_id)
-> std::unique_ptr<DOFData> {
return std::make_unique<DOFDataPETSc>(dof_id);
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt, UInt>
DOFManagerPETSc::registerDOFsInternal(const ID & dof_id,
Array<Real> & dofs_array) {
dofs_ids.push_back(dof_id);
auto ret = DOFManager::registerDOFsInternal(dof_id, dofs_array);
- UInt nb_dofs, nb_pure_local_dofs;
+ UInt nb_dofs;
+ UInt nb_pure_local_dofs;
std::tie(nb_dofs, nb_pure_local_dofs, std::ignore) = ret;
auto && vector = std::make_unique<SolverVectorPETSc>(*this, id + ":solution");
- auto x = vector->getVec();
+ auto *x = vector->getVec();
PETSc_call(VecGetLocalToGlobalMapping, x, &is_ltog_map);
// redoing the indexes based on the petsc numbering
for (auto & dof_id : dofs_ids) {
auto & dof_data = this->getDOFDataTyped<DOFDataPETSc>(dof_id);
Array<PetscInt> gidx(dof_data.local_equation_number.size());
for (auto && data : zip(dof_data.local_equation_number, gidx)) {
std::get<1>(data) = localToGlobalEquationNumber(std::get<0>(data));
}
auto & lidx = dof_data.local_equation_number_petsc;
- if (is_ltog_map) {
+ if (is_ltog_map != nullptr) {
lidx.resize(gidx.size());
PetscInt n;
PETSc_call(ISGlobalToLocalMappingApply, is_ltog_map, IS_GTOLM_MASK,
gidx.size(), gidx.storage(), &n, lidx.storage());
}
}
residual = std::make_unique<SolverVectorPETSc>(*vector, id + ":residual");
data_cache = std::make_unique<SolverVectorPETSc>(*vector, id + ":data_cache");
solution = std::move(vector);
for (auto & mat : matrices) {
auto & A = this->getMatrix(mat.first);
A.resize();
}
return ret;
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assembleToGlobalArray(
const ID & dof_id, const Array<Real> & array_to_assemble,
SolverVector & global_array, Real scale_factor) {
const auto & dof_data = getDOFDataTyped<DOFDataPETSc>(dof_id);
auto & g = aka::as_type<SolverVectorPETSc>(global_array);
AKANTU_DEBUG_ASSERT(array_to_assemble.size() *
array_to_assemble.getNbComponent() ==
dof_data.local_nb_dofs,
"The array to assemble does not have the proper size");
g.addValuesLocal(dof_data.local_equation_number_petsc, array_to_assemble,
scale_factor);
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::getArrayPerDOFs(const ID & dof_id,
const SolverVector & global_array,
Array<Real> & local) {
const auto & dof_data = getDOFDataTyped<DOFDataPETSc>(dof_id);
const auto & petsc_vector = aka::as_type<SolverVectorPETSc>(global_array);
AKANTU_DEBUG_ASSERT(
local.size() * local.getNbComponent() == dof_data.local_nb_dofs,
"The array to get the values does not have the proper size");
petsc_vector.getValuesLocal(dof_data.local_equation_number_petsc, local);
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id, const Array<Real> & elementary_mat,
- const ElementType & type, const GhostType & ghost_type,
+ ElementType type, GhostType ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) {
auto & A = getMatrix(matrix_id);
DOFManager::assembleElementalMatricesToMatrix_(
A, dof_id, elementary_mat, type, ghost_type, elemental_matrix_type,
filter_elements);
A.applyModifications();
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assemblePreassembledMatrix(
const ID & dof_id_m, const ID & dof_id_n, const ID & matrix_id,
const TermsToAssemble & terms) {
auto & A = getMatrix(matrix_id);
DOFManager::assemblePreassembledMatrix_(A, dof_id_m, dof_id_n, terms);
A.applyModifications();
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assembleMatMulVectToArray(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor) {
DOFManager::assembleMatMulVectToArray_<SolverVectorPETSc>(
dof_id, A_id, x, array, scale_factor);
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::makeConsistentForPeriodicity(const ID & /*dof_id*/,
SolverVector & /*array*/) {}
/* -------------------------------------------------------------------------- */
NonLinearSolver &
DOFManagerPETSc::getNewNonLinearSolver(const ID & id,
const NonLinearSolverType & type) {
return this->registerNonLinearSolver<NonLinearSolverPETSc>(*this, id, type);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManagerPETSc::getNewTimeStepSolver(
const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, SolverCallback & callback) {
return this->registerTimeStepSolver<TimeStepSolverDefault>(
*this, id, type, non_linear_solver, callback);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerPETSc::getNewMatrix(const ID & id,
const MatrixType & matrix_type) {
return this->registerSparseMatrix<SparseMatrixPETSc>(*this, id, matrix_type);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerPETSc::getNewMatrix(const ID & id,
const ID & matrix_to_copy_id) {
return this->registerSparseMatrix<SparseMatrixPETSc>(id, matrix_to_copy_id);
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc & DOFManagerPETSc::getMatrix(const ID & id) {
auto & matrix = DOFManager::getMatrix(id);
return aka::as_type<SparseMatrixPETSc>(matrix);
}
/* -------------------------------------------------------------------------- */
SolverVector & DOFManagerPETSc::getNewLumpedMatrix(const ID & id) {
return this->registerLumpedMatrix<SolverVectorPETSc>(*this, id);
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc & DOFManagerPETSc::getSolution() {
return aka::as_type<SolverVectorPETSc>(*this->solution);
}
const SolverVectorPETSc & DOFManagerPETSc::getSolution() const {
return aka::as_type<SolverVectorPETSc>(*this->solution);
}
SolverVectorPETSc & DOFManagerPETSc::getResidual() {
return aka::as_type<SolverVectorPETSc>(*this->residual);
}
const SolverVectorPETSc & DOFManagerPETSc::getResidual() const {
return aka::as_type<SolverVectorPETSc>(*this->residual);
}
/* -------------------------------------------------------------------------- */
static bool dof_manager_is_registered [[gnu::unused]] =
DOFManagerFactory::getInstance().registerAllocator(
"petsc",
[](Mesh & mesh, const ID & id,
const MemoryID & mem_id) -> std::unique_ptr<DOFManager> {
return std::make_unique<DOFManagerPETSc>(mesh, id, mem_id);
});
} // namespace akantu
diff --git a/src/model/common/dof_manager/dof_manager_petsc.hh b/src/model/common/dof_manager/dof_manager_petsc.hh
index 77bb054e8..5f5010162 100644
--- a/src/model/common/dof_manager/dof_manager_petsc.hh
+++ b/src/model/common/dof_manager/dof_manager_petsc.hh
@@ -1,218 +1,218 @@
/**
* @file dof_manager_petsc.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Wed Jan 31 2018
*
* @brief PETSc implementation of the dof manager
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
#include <petscis.h>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DOF_MANAGER_PETSC_HH__
-#define __AKANTU_DOF_MANAGER_PETSC_HH__
+#ifndef AKANTU_DOF_MANAGER_PETSC_HH_
+#define AKANTU_DOF_MANAGER_PETSC_HH_
#define PETSc_call(func, ...) \
do { \
auto ierr = func(__VA_ARGS__); \
if (PetscUnlikely(ierr != 0)) { \
const char * desc; \
PetscErrorMessage(ierr, &desc, nullptr); \
AKANTU_EXCEPTION("Error in PETSc call to \'" << #func \
<< "\': " << desc); \
} \
} while (false)
namespace akantu {
namespace detail {
template <typename T> void PETScSetName(T t, const ID & id) {
PETSc_call(PetscObjectSetName, reinterpret_cast<PetscObject>(t),
id.c_str());
}
} // namespace detail
} // namespace akantu
namespace akantu {
class SparseMatrixPETSc;
class SolverVectorPETSc;
} // namespace akantu
namespace akantu {
class DOFManagerPETSc : public DOFManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManagerPETSc(const ID & id = "dof_manager_petsc",
const MemoryID & memory_id = 0);
DOFManagerPETSc(Mesh & mesh, const ID & id = "dof_manager_petsc",
const MemoryID & memory_id = 0);
- virtual ~DOFManagerPETSc();
+ ~DOFManagerPETSc() override = default;
protected:
void init();
struct DOFDataPETSc : public DOFData {
explicit DOFDataPETSc(const ID & dof_id);
/// petsc compressed version of local_equation_number
Array<PetscInt> local_equation_number_petsc;
- virtual Array<Int> & getLocalEquationsNumbers() {
+ Array<Int> & getLocalEquationsNumbers() override {
return local_equation_number_petsc;
}
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void assembleToLumpedMatrix(const ID & /*dof_id*/,
Array<Real> & /*array_to_assemble*/,
const ID & /*lumped_mtx*/,
- Real /*scale_factor*/ = 1.) {
+ Real /*scale_factor*/ = 1.) override {
AKANTU_TO_IMPLEMENT();
}
void assembleElementalMatricesToMatrix(
const ID & /*matrix_id*/, const ID & /*dof_id*/,
- const Array<Real> & /*elementary_mat*/, const ElementType & /*type*/,
- const GhostType & /*ghost_type*/,
+ const Array<Real> & /*elementary_mat*/, ElementType /*type*/,
+ GhostType /*ghost_type*/,
const MatrixType & /*elemental_matrix_type*/,
const Array<UInt> & /*filter_elements*/) override;
void assembleMatMulVectToArray(const ID & /*dof_id*/, const ID & /*A_id*/,
const Array<Real> & /*x*/,
Array<Real> & /*array*/,
Real /*scale_factor*/ = 1.) override;
void assembleLumpedMatMulVectToResidual(const ID & /*dof_id*/,
const ID & /*A_id*/,
const Array<Real> & /*x*/,
Real /*scale_factor*/ = 1) override {
AKANTU_TO_IMPLEMENT();
}
void assemblePreassembledMatrix(const ID & /* dof_id_m*/,
const ID & /*dof_id_n*/,
const ID & /*matrix_id*/,
const TermsToAssemble & /*terms*/) override;
protected:
void assembleToGlobalArray(const ID & dof_id,
const Array<Real> & array_to_assemble,
SolverVector & global_array,
Real scale_factor) override;
void getArrayPerDOFs(const ID & dof_id, const SolverVector & global,
Array<Real> & local) override;
void makeConsistentForPeriodicity(const ID & dof_id,
SolverVector & array) override;
std::unique_ptr<DOFData> getNewDOFData(const ID & dof_id) override;
std::tuple<UInt, UInt, UInt>
registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array) override;
void updateDOFsData(DOFDataPETSc & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local, UInt nb_node,
const std::function<UInt(UInt)> & getNode);
protected:
void getLumpedMatrixPerDOFs(const ID & /*dof_id*/, const ID & /*lumped_mtx*/,
Array<Real> & /*lumped*/) override {}
NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & non_linear_solver_type) override;
TimeStepSolver &
getNewTimeStepSolver(const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get an instance of a new SparseMatrix
SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) override;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) override;
/// Get the reference of an existing matrix
SparseMatrixPETSc & getMatrix(const ID & matrix_id);
/// Get an instance of a new lumped matrix
SolverVector & getNewLumpedMatrix(const ID & matrix_id) override;
/// Get the blocked dofs array
// AKANTU_GET_MACRO(BlockedDOFs, blocked_dofs, const Array<bool> &);
AKANTU_GET_MACRO(MPIComm, mpi_communicator, MPI_Comm);
AKANTU_GET_MACRO_NOT_CONST(ISLocalToGlobalMapping, is_ltog_map,
ISLocalToGlobalMapping &);
SolverVectorPETSc & getSolution();
const SolverVectorPETSc & getSolution() const;
SolverVectorPETSc & getResidual();
const SolverVectorPETSc & getResidual() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using PETScMatrixMap = std::map<ID, SparseMatrixPETSc *>;
using PETScLumpedMatrixMap = std::map<ID, SolverVectorPETSc *>;
/// list of matrices registered to the dof manager
PETScMatrixMap petsc_matrices;
/// list of lumped matrices registered
PETScLumpedMatrixMap petsc_lumped_matrices;
/// PETSc local to global mapping of dofs
ISLocalToGlobalMapping is_ltog_map{nullptr};
/// Communicator associated to PETSc
MPI_Comm mpi_communicator;
/// list of the dof ids to be able to always iterate in the same order
std::vector<ID> dofs_ids;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_DOF_MANAGER_PETSC_HH__ */
+#endif /* AKANTU_DOF_MANAGER_PETSC_HH_ */
diff --git a/src/model/common/integration_scheme/generalized_trapezoidal.cc b/src/model/common/integration_scheme/generalized_trapezoidal.cc
index 8ec68fabf..89f8d24b1 100644
--- a/src/model/common/integration_scheme/generalized_trapezoidal.cc
+++ b/src/model/common/integration_scheme/generalized_trapezoidal.cc
@@ -1,193 +1,193 @@
/**
* @file generalized_trapezoidal.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 23 2015
* @date last modification: Wed Jan 31 2018
*
* @brief implementation of inline functions
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "generalized_trapezoidal.hh"
#include "aka_array.hh"
#include "dof_manager.hh"
#include "mesh.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
GeneralizedTrapezoidal::GeneralizedTrapezoidal(DOFManager & dof_manager,
const ID & dof_id, Real alpha)
: IntegrationScheme1stOrder(dof_manager, dof_id), alpha(alpha) {
this->registerParam("alpha", this->alpha, alpha, _pat_parsmod,
"The alpha parameter");
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::predictor(Real delta_t, Array<Real> & u,
Array<Real> & u_dot,
const Array<bool> & blocked_dofs) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt d = 0; d < nb_degree_of_freedom; d++) {
if (!(*blocked_dofs_val)) {
*u_val += (1. - alpha) * delta_t * *u_dot_val;
}
u_val++;
u_dot_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
switch (type) {
case _temperature:
this->allCorrector<_temperature>(delta_t, u, u_dot, blocked_dofs, delta);
break;
case _temperature_rate:
this->allCorrector<_temperature_rate>(delta_t, u, u_dot, blocked_dofs,
delta);
break;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real GeneralizedTrapezoidal::getTemperatureCoefficient(
const SolutionType & type, Real delta_t) const {
switch (type) {
case _temperature:
return 1.;
case _temperature_rate:
return alpha * delta_t;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real GeneralizedTrapezoidal::getTemperatureRateCoefficient(
const SolutionType & type, Real delta_t) const {
switch (type) {
case _temperature:
return 1. / (alpha * delta_t);
case _temperature_rate:
return 1.;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
template <IntegrationScheme::SolutionType type>
void GeneralizedTrapezoidal::allCorrector(Real delta_t, Array<Real> & u,
Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real e = getTemperatureCoefficient(type, delta_t);
Real d = getTemperatureRateCoefficient(type, delta_t);
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * delta_val = delta.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt dof = 0; dof < nb_degree_of_freedom; dof++) {
if (!(*blocked_dofs_val)) {
*u_val += e * *delta_val;
*u_dot_val += d * *delta_val;
}
u_val++;
u_dot_val++;
delta_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::assembleJacobian(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & M = this->dof_manager.getMatrix("M");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
bool does_j_need_update = false;
does_j_need_update |= M.getRelease() != m_release;
does_j_need_update |= K.getRelease() != k_release;
if (!does_j_need_update) {
AKANTU_DEBUG_OUT();
return;
}
J.copyProfile(K);
- // J.clear();
+ // J.zero();
Real c = this->getTemperatureRateCoefficient(type, delta_t);
Real e = this->getTemperatureCoefficient(type, delta_t);
J.add(M, e);
J.add(K, c);
m_release = M.getRelease();
k_release = K.getRelease();
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/common/integration_scheme/generalized_trapezoidal.hh b/src/model/common/integration_scheme/generalized_trapezoidal.hh
index 2fd8da52a..556dbbcc2 100644
--- a/src/model/common/integration_scheme/generalized_trapezoidal.hh
+++ b/src/model/common/integration_scheme/generalized_trapezoidal.hh
@@ -1,161 +1,161 @@
/**
* @file generalized_trapezoidal.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 04 2011
* @date last modification: Wed Jan 31 2018
*
* @brief Generalized Trapezoidal Method. This implementation is taken from
* Méthodes numériques en mécanique des solides by Alain Curnier \note{ISBN:
* 2-88074-247-1}
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_GENERALIZED_TRAPEZOIDAL_HH__
-#define __AKANTU_GENERALIZED_TRAPEZOIDAL_HH__
+#ifndef AKANTU_GENERALIZED_TRAPEZOIDAL_HH_
+#define AKANTU_GENERALIZED_TRAPEZOIDAL_HH_
#include "integration_scheme_1st_order.hh"
namespace akantu {
/**
* The two differentiate equation (thermal and kinematic) are :
* \f{eqnarray*}{
* C\dot{u}_{n+1} + Ku_{n+1} = q_{n+1}\\
* u_{n+1} = u_{n} + (1-\alpha) \Delta t \dot{u}_{n} + \alpha \Delta t
*\dot{u}_{n+1}
* \f}
*
* To solve it :
* Predictor :
* \f{eqnarray*}{
* u^0_{n+1} &=& u_{n} + (1-\alpha) \Delta t v_{n} \\
* \dot{u}^0_{n+1} &=& \dot{u}_{n}
* \f}
*
* Solve :
* \f[ (a C + b K^i_{n+1}) w = q_{n+1} - f^i_{n+1} - C \dot{u}^i_{n+1} \f]
*
* Corrector :
* \f{eqnarray*}{
* \dot{u}^{i+1}_{n+1} &=& \dot{u}^{i}_{n+1} + a w \\
* u^{i+1}_{n+1} &=& u^{i}_{n+1} + b w
* \f}
*
* a and b depends on the resolution method : temperature (u) or temperature
*rate (\f$\dot{u}\f$)
*
* For temperature : \f$ w = \delta u, a = 1 / (\alpha \Delta t) , b = 1 \f$ @n
* For temperature rate : \f$ w = \delta \dot{u}, a = 1, b = \alpha \Delta t \f$
*/
class GeneralizedTrapezoidal : public IntegrationScheme1stOrder {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GeneralizedTrapezoidal(DOFManager & dof_manager, const ID & dof_id,
Real alpha = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs) const override;
void corrector(const SolutionType & type, Real delta_t, Array<Real> & u,
Array<Real> & u_dot, const Array<bool> & blocked_dofs,
const Array<Real> & delta) const override;
- void assembleJacobian(const SolutionType & type, Real time_step) override;
+ void assembleJacobian(const SolutionType & type, Real delta_t) override;
public:
/// the coeffichent \f$ b \f$ in the description
Real getTemperatureCoefficient(const SolutionType & type,
Real delta_t) const override;
/// the coeffichent \f$ a \f$ in the description
Real getTemperatureRateCoefficient(const SolutionType & type,
Real delta_t) const override;
private:
template <SolutionType type>
void allCorrector(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Alpha, alpha, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the \f$\alpha\f$ parameter
Real alpha;
/// last release of K matrix
UInt k_release;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/**
* Forward Euler (explicit) -> condition on delta_t
*/
class ForwardEuler : public GeneralizedTrapezoidal {
public:
ForwardEuler(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, 0.){};
std::vector<std::string> getNeededMatrixList() override { return {"M"}; }
};
/**
* Trapezoidal rule (implicit), midpoint rule or Crank-Nicolson
*/
class TrapezoidalRule1 : public GeneralizedTrapezoidal {
public:
TrapezoidalRule1(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, .5){};
};
/**
* Backward Euler (implicit)
*/
class BackwardEuler : public GeneralizedTrapezoidal {
public:
BackwardEuler(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, 1.){};
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_GENERALIZED_TRAPEZOIDAL_HH__ */
+#endif /* AKANTU_GENERALIZED_TRAPEZOIDAL_HH_ */
diff --git a/src/model/common/integration_scheme/integration_scheme.cc b/src/model/common/integration_scheme/integration_scheme.cc
index 36cbe8249..d060e9a03 100644
--- a/src/model/common/integration_scheme/integration_scheme.cc
+++ b/src/model/common/integration_scheme/integration_scheme.cc
@@ -1,90 +1,90 @@
/**
* @file integration_scheme.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Common interface to all interface schemes
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme.hh"
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
IntegrationScheme::IntegrationScheme(DOFManager & dof_manager,
const ID & dof_id, UInt order)
: Parsable(ParserType::_integration_scheme, dof_id),
dof_manager(dof_manager), dof_id(dof_id), order(order), u_store(order + 1) {}
/* -------------------------------------------------------------------------- */
/// standard input stream operator for SolutionType
std::istream & operator>>(std::istream & stream,
IntegrationScheme::SolutionType & type) {
std::string str;
stream >> str;
- if (str == "displacement")
+ if (str == "displacement") {
type = IntegrationScheme::_displacement;
- else if (str == "temperature")
+ } else if (str == "temperature") {
type = IntegrationScheme::_temperature;
- else if (str == "velocity")
+ } else if (str == "velocity") {
type = IntegrationScheme::_velocity;
- else if (str == "temperature_rate")
+ } else if (str == "temperature_rate") {
type = IntegrationScheme::_temperature_rate;
- else if (str == "acceleration")
+ } else if (str == "acceleration") {
type = IntegrationScheme::_acceleration;
- else {
+ } else {
stream.setstate(std::ios::failbit);
}
return stream;
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme::store() {
for (auto data : enumerate(u_store)) {
auto o = std::get<0>(data);
auto & u_store = std::get<1>(data);
auto & u_o = dof_manager.getDOFsDerivatives(dof_id, o);
if (not u_store) {
u_store = std::make_unique<Array<Real>>(
u_o, "integration_scheme_store:" + dof_id + ":" + std::to_string(o));
} else {
u_store->copy(u_o);
}
}
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme::restore() {
for (auto o : arange(order)) {
auto & u_o = dof_manager.getDOFsDerivatives(dof_id, o);
u_o.copy(*u_store[o]);
}
}
} // namespace akantu
diff --git a/src/model/common/integration_scheme/integration_scheme.hh b/src/model/common/integration_scheme/integration_scheme.hh
index 3fdc29299..8ffe3b8b8 100644
--- a/src/model/common/integration_scheme/integration_scheme.hh
+++ b/src/model/common/integration_scheme/integration_scheme.hh
@@ -1,122 +1,122 @@
/**
* @file integration_scheme.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief This class is just a base class for the integration schemes
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_INTEGRATION_SCHEME_HH__
-#define __AKANTU_INTEGRATION_SCHEME_HH__
+#ifndef AKANTU_INTEGRATION_SCHEME_HH_
+#define AKANTU_INTEGRATION_SCHEME_HH_
namespace akantu {
class DOFManager;
}
namespace akantu {
class IntegrationScheme : public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
enum SolutionType {
_not_defined = -1,
_displacement = 0,
_temperature = 0,
_velocity = 1,
_temperature_rate = 1,
_acceleration = 2,
};
IntegrationScheme(DOFManager & dof_manager, const ID & dof_id, UInt order);
~IntegrationScheme() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// generic interface of a predictor
virtual void predictor(Real delta_t) = 0;
/// generic interface of a corrector
virtual void corrector(const SolutionType & type, Real delta_t) = 0;
/// assemble the jacobian matrix
virtual void assembleJacobian(const SolutionType & type, Real delta_t) = 0;
/// assemble the residual
virtual void assembleResidual(bool is_lumped) = 0;
/// returns a list of needed matrices
virtual std::vector<std::string> getNeededMatrixList() = 0;
/// store dofs info (beginning of steps)
virtual void store();
/// restore dofs (solve failed)
virtual void restore();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the order of the integration scheme
UInt getOrder() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// The underlying DOFManager
DOFManager & dof_manager;
/// The id of the dof treated by this integration scheme.
ID dof_id;
/// The order of the integrator
UInt order;
/// last release of M matrix
UInt m_release{UInt(-1)};
/// stores the values at begining of solve
std::vector<std::unique_ptr<Array<Real>>> u_store;
};
/* -------------------------------------------------------------------------- */
// std::ostream & operator<<(std::ostream & stream,
// const IntegrationScheme::SolutionType & type);
std::istream & operator>>(std::istream & stream,
IntegrationScheme::SolutionType & type);
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_INTEGRATION_SCHEME_HH__ */
+#endif /* AKANTU_INTEGRATION_SCHEME_HH_ */
diff --git a/src/model/common/integration_scheme/integration_scheme_1st_order.cc b/src/model/common/integration_scheme/integration_scheme_1st_order.cc
index 85e1b3622..f8902c75e 100644
--- a/src/model/common/integration_scheme/integration_scheme_1st_order.cc
+++ b/src/model/common/integration_scheme/integration_scheme_1st_order.cc
@@ -1,95 +1,97 @@
/**
* @file integration_scheme_1st_order.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the common functions for 1st order time
* integrations
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme_1st_order.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
std::vector<std::string> IntegrationScheme1stOrder::getNeededMatrixList() {
return {"K", "M"};
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::predictor(Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->predictor(delta_t, u, u_dot, blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::corrector(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
const Array<Real> & solution = this->dof_manager.getSolution(this->dof_id);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->corrector(type, delta_t, u, u_dot, blocked_dofs, solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::assembleResidual(bool is_lumped) {
AKANTU_DEBUG_IN();
const Array<Real> & first_derivative =
dof_manager.getDOFsDerivatives(this->dof_id, 1);
if (not is_lumped) {
- if (this->dof_manager.hasMatrix("M"))
+ if (this->dof_manager.hasMatrix("M")) {
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "M",
first_derivative, -1);
+ }
} else {
- if (this->dof_manager.hasLumpedMatrix("M"))
+ if (this->dof_manager.hasLumpedMatrix("M")) {
this->dof_manager.assembleLumpedMatMulVectToResidual(
this->dof_id, "M", first_derivative, -1);
+ }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/integration_scheme/integration_scheme_1st_order.hh b/src/model/common/integration_scheme/integration_scheme_1st_order.hh
index 524bfbd3c..fbdbfce63 100644
--- a/src/model/common/integration_scheme/integration_scheme_1st_order.hh
+++ b/src/model/common/integration_scheme/integration_scheme_1st_order.hh
@@ -1,94 +1,94 @@
/**
* @file integration_scheme_1st_order.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Interface of the time integrator of first order
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH__
-#define __AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH__
+#ifndef AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH_
+#define AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH_
namespace akantu {
class IntegrationScheme1stOrder : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationScheme1stOrder(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 1){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
/// assemble the residual
void assembleResidual(bool is_lumped) override;
protected:
/// generic interface of a predictor of 1st order
virtual void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & boundary) const = 0;
/// generic interface of a corrector of 1st order
virtual void corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & boundary,
const Array<Real> & delta) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
virtual Real getTemperatureCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getTemperatureRateCoefficient(const SolutionType & type,
Real delta_t) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
std::unique_ptr<Real> u_dot_store;
};
} // namespace akantu
#include "generalized_trapezoidal.hh"
-#endif /* __AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH__ */
+#endif /* AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH_ */
diff --git a/src/model/common/integration_scheme/integration_scheme_2nd_order.hh b/src/model/common/integration_scheme/integration_scheme_2nd_order.hh
index 096fd8ce8..1ee1b7c3e 100644
--- a/src/model/common/integration_scheme/integration_scheme_2nd_order.hh
+++ b/src/model/common/integration_scheme/integration_scheme_2nd_order.hh
@@ -1,106 +1,106 @@
/**
* @file integration_scheme_2nd_order.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Interface of the integrator of second order
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__
-#define __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__
+#ifndef AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH_
+#define AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH_
namespace akantu {
class SparseMatrix;
}
namespace akantu {
class IntegrationScheme2ndOrder : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationScheme2ndOrder(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 2){};
~IntegrationScheme2ndOrder() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
void assembleResidual(bool is_lumped) override;
protected:
/// generic interface of a predictor of 2nd order
virtual void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const = 0;
/// generic interface of a corrector of 2nd order
virtual void corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
virtual Real getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getVelocityCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
#include "newmark-beta.hh"
-#endif /* __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__ */
+#endif /* AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH_ */
diff --git a/src/model/common/integration_scheme/newmark-beta.cc b/src/model/common/integration_scheme/newmark-beta.cc
index 43f952dc0..375e0a7dd 100644
--- a/src/model/common/integration_scheme/newmark-beta.cc
+++ b/src/model/common/integration_scheme/newmark-beta.cc
@@ -1,260 +1,260 @@
/**
* @file newmark-beta.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 23 2015
* @date last modification: Wed Jan 31 2018
*
* @brief implementation of the newmark-@f$\beta@f$ integration scheme. This
* implementation is taken from Méthodes numériques en mécanique des solides by
* Alain Curnier \note{ISBN: 2-88074-247-1}
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "newmark-beta.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NewmarkBeta::NewmarkBeta(DOFManager & dof_manager, const ID & dof_id,
Real alpha, Real beta)
: IntegrationScheme2ndOrder(dof_manager, dof_id), beta(beta), alpha(alpha),
k(0.), h(0.), m_release(0), k_release(0), c_release(0) {
this->registerParam("alpha", this->alpha, alpha, _pat_parsmod,
"The alpha parameter");
this->registerParam("beta", this->beta, beta, _pat_parsmod,
"The beta parameter");
}
/* -------------------------------------------------------------------------- */
/*
* @f$ \tilde{u_{n+1}} = u_{n} + \Delta t \dot{u}_n + \frac{\Delta t^2}{2}
* \ddot{u}_n @f$
* @f$ \tilde{\dot{u}_{n+1}} = \dot{u}_{n} + \Delta t \ddot{u}_{n} @f$
* @f$ \tilde{\ddot{u}_{n}} = \ddot{u}_{n} @f$
*/
void NewmarkBeta::predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * u_dot_dot_val = u_dot_dot.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt d = 0; d < nb_degree_of_freedom; d++) {
if (!(*blocked_dofs_val)) {
Real dt_a_n = delta_t * *u_dot_dot_val;
*u_val += (1 - k * alpha) * delta_t * *u_dot_val +
(.5 - h * alpha * beta) * delta_t * dt_a_n;
*u_dot_val = (1 - k) * *u_dot_val + (1 - h * beta) * dt_a_n;
*u_dot_dot_val = (1 - h) * *u_dot_dot_val;
}
u_val++;
u_dot_val++;
u_dot_dot_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NewmarkBeta::corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
switch (type) {
case _acceleration: {
this->allCorrector<_acceleration>(delta_t, u, u_dot, u_dot_dot,
blocked_dofs, delta);
break;
}
case _velocity: {
this->allCorrector<_velocity>(delta_t, u, u_dot, u_dot_dot, blocked_dofs,
delta);
break;
}
case _displacement: {
this->allCorrector<_displacement>(delta_t, u, u_dot, u_dot_dot,
blocked_dofs, delta);
break;
}
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return 1.;
case _velocity:
return 1. / (beta * delta_t);
case _displacement:
return 1. / (alpha * beta * delta_t * delta_t);
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getVelocityCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return beta * delta_t;
case _velocity:
return 1.;
case _displacement:
return 1. / (alpha * delta_t);
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return alpha * beta * delta_t * delta_t;
case _velocity:
return alpha * delta_t;
case _displacement:
return 1.;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
template <IntegrationScheme::SolutionType type>
void NewmarkBeta::allCorrector(Real delta_t, Array<Real> & u,
Array<Real> & u_dot, Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real c = getAccelerationCoefficient(type, delta_t);
Real d = getVelocityCoefficient(type, delta_t);
Real e = getDisplacementCoefficient(type, delta_t);
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * u_dot_dot_val = u_dot_dot.storage();
Real * delta_val = delta.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt dof = 0; dof < nb_degree_of_freedom; dof++) {
if (!(*blocked_dofs_val)) {
*u_val += e * *delta_val;
*u_dot_val += d * *delta_val;
*u_dot_dot_val += c * *delta_val;
}
u_val++;
u_dot_val++;
u_dot_dot_val++;
delta_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NewmarkBeta::assembleJacobian(const SolutionType & type, Real delta_t) {
AKANTU_DEBUG_IN();
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & M = this->dof_manager.getMatrix("M");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
bool does_j_need_update = false;
does_j_need_update |= M.getRelease() != m_release;
does_j_need_update |= K.getRelease() != k_release;
if (this->dof_manager.hasMatrix("C")) {
const SparseMatrix & C = this->dof_manager.getMatrix("C");
does_j_need_update |= C.getRelease() != c_release;
}
if (!does_j_need_update) {
AKANTU_DEBUG_OUT();
return;
}
J.copyProfile(K);
- // J.clear();
+ // J.zero();
Real c = this->getAccelerationCoefficient(type, delta_t);
Real e = this->getDisplacementCoefficient(type, delta_t);
if (!(e == 0.)) { // in explicit this coefficient is exactly 0.
J.add(K, e);
}
J.add(M, c);
m_release = M.getRelease();
k_release = K.getRelease();
if (this->dof_manager.hasMatrix("C")) {
Real d = this->getVelocityCoefficient(type, delta_t);
const SparseMatrix & C = this->dof_manager.getMatrix("C");
J.add(C, d);
c_release = C.getRelease();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/integration_scheme/newmark-beta.hh b/src/model/common/integration_scheme/newmark-beta.hh
index 237310f75..be7d4f4bf 100644
--- a/src/model/common/integration_scheme/newmark-beta.hh
+++ b/src/model/common/integration_scheme/newmark-beta.hh
@@ -1,194 +1,194 @@
/**
* @file newmark-beta.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 05 2010
* @date last modification: Wed Jan 31 2018
*
* @brief implementation of the newmark-@f$\beta@f$ integration scheme. This
* implementation is taken from Méthodes numériques en mécanique des solides by
* Alain Curnier \note{ISBN: 2-88074-247-1}
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme_2nd_order.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NEWMARK_BETA_HH__
-#define __AKANTU_NEWMARK_BETA_HH__
+#ifndef AKANTU_NEWMARK_BETA_HH_
+#define AKANTU_NEWMARK_BETA_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* The three differentiate equations (dynamic and cinematic) are :
* \f{eqnarray*}{
* M \ddot{u}_{n+1} + C \dot{u}_{n+1} + K u_{n+1} &=& q_{n+1} \\
* u_{n+1} &=& u_{n} + (1 - \alpha) \Delta t \dot{u}_{n} + \alpha \Delta t
*\dot{u}_{n+1} + (1/2 - \alpha) \Delta t^2 \ddot{u}_n \\
* \dot{u}_{n+1} &=& \dot{u}_{n} + (1 - \beta) \Delta t \ddot{u}_{n} + \beta
*\Delta t \ddot{u}_{n+1}
* \f}
*
* Predictor:
* \f{eqnarray*}{
* u^{0}_{n+1} &=& u_{n} + \Delta t \dot{u}_n + \frac{\Delta t^2}{2}
*\ddot{u}_n \\
* \dot{u}^{0}_{n+1} &=& \dot{u}_{n} + \Delta t \ddot{u}_{n} \\
* \ddot{u}^{0}_{n+1} &=& \ddot{u}_{n}
* \f}
*
* Solve :
* \f[ (c M + d C + e K^i_{n+1}) w = = q_{n+1} - f^i_{n+1} - C \dot{u}^i_{n+1}
*- M \ddot{u}^i_{n+1} \f]
*
* Corrector :
* \f{eqnarray*}{
* \ddot{u}^{i+1}_{n+1} &=& \ddot{u}^{i}_{n+1} + c w \\
* \dot{u}^{i+1}_{n+1} &=& \dot{u}^{i}_{n+1} + d w \\
* u^{i+1}_{n+1} &=& u^{i}_{n+1} + e w
* \f}
*
* c, d and e are parameters depending on the method used to solve the equations
*\n
* For acceleration : \f$ w = \delta \ddot{u}, e = \alpha \beta \Delta t^2, d =
*\beta \Delta t, c = 1 \f$ \n
* For velocity : \f$ w = \delta \dot{u}, e = 1/\beta \Delta t, d =
*1, c = \alpha \Delta t \f$ \n
* For displacement : \f$ w = \delta u, e = 1, d =
*1/\alpha \Delta t, c = 1/\alpha \beta \Delta t^2 \f$
*/
class NewmarkBeta : public IntegrationScheme2ndOrder {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NewmarkBeta(DOFManager & dof_manager, const ID & dof_id, Real alpha = 0.,
Real beta = 0.);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const override;
void corrector(const SolutionType & type, Real delta_t, Array<Real> & u,
Array<Real> & u_dot, Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const override;
void assembleJacobian(const SolutionType & type, Real delta_t) override;
public:
Real getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const override;
Real getVelocityCoefficient(const SolutionType & type,
Real delta_t) const override;
Real getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const override;
private:
template <SolutionType type>
void allCorrector(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot, const Array<bool> & blocked_dofs,
const Array<Real> & delta) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Beta, beta, Real);
AKANTU_GET_MACRO(Alpha, alpha, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the \f$\beta\f$ parameter
Real beta;
/// the \f$\alpha\f$ parameter
Real alpha;
Real k;
Real h;
/// last release of M matrix
UInt m_release;
/// last release of K matrix
UInt k_release;
/// last release of C matrix
UInt c_release;
};
/**
* central difference method (explicit)
* undamped stability condition :
* \f$ \Delta t = \alpha \Delta t_{crit} = \frac{2}{\omega_{max}} \leq \min_{e}
*\frac{l_e}{c_e}\f$
*
*/
class CentralDifference : public NewmarkBeta {
public:
CentralDifference(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 0., 1. / 2.){};
std::vector<std::string> getNeededMatrixList() override { return {"M", "C"}; }
};
//#include "integration_scheme/central_difference.hh"
/// undamped trapezoidal rule (implicit)
class TrapezoidalRule2 : public NewmarkBeta {
public:
TrapezoidalRule2(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 2., 1. / 2.){};
};
/// Fox-Goodwin rule (implicit)
class FoxGoodwin : public NewmarkBeta {
public:
FoxGoodwin(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 6., 1. / 2.){};
};
/// Linear acceleration (implicit)
class LinearAceleration : public NewmarkBeta {
public:
LinearAceleration(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 3., 1. / 2.){};
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_NEWMARK_BETA_HH__ */
+#endif /* AKANTU_NEWMARK_BETA_HH_ */
diff --git a/src/model/common/integration_scheme/pseudo_time.cc b/src/model/common/integration_scheme/pseudo_time.cc
index 8b86d79fc..0544e1274 100644
--- a/src/model/common/integration_scheme/pseudo_time.cc
+++ b/src/model/common/integration_scheme/pseudo_time.cc
@@ -1,82 +1,85 @@
/**
* @file pseudo_time.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 19 2016
* @date last modification: Wed Jan 31 2018
*
* @brief Implementation of a really simple integration scheme
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "pseudo_time.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
PseudoTime::PseudoTime(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 0), k_release(0) {}
/* -------------------------------------------------------------------------- */
std::vector<std::string> PseudoTime::getNeededMatrixList() { return {"K"}; }
/* -------------------------------------------------------------------------- */
-void PseudoTime::predictor(Real) {}
+void PseudoTime::predictor(Real /*delta_t*/) {}
/* -------------------------------------------------------------------------- */
-void PseudoTime::corrector(const SolutionType &, Real) {
+void PseudoTime::corrector(const SolutionType & /*type*/, Real /*delta_t*/) {
auto & us = this->dof_manager.getDOFs(this->dof_id);
const auto & deltas = this->dof_manager.getSolution(this->dof_id);
const auto & blocked_dofs = this->dof_manager.getBlockedDOFs(this->dof_id);
for (auto && tuple : zip(make_view(us), deltas, make_view(blocked_dofs))) {
auto & u = std::get<0>(tuple);
const auto & delta = std::get<1>(tuple);
const auto & bld = std::get<2>(tuple);
- if (not bld)
+ if (not bld) {
u += delta;
+ }
}
}
/* -------------------------------------------------------------------------- */
-void PseudoTime::assembleJacobian(const SolutionType &, Real) {
+void PseudoTime::assembleJacobian(const SolutionType & /*type*/,
+ Real /*delta_t*/) {
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
- if (K.getRelease() == k_release)
+ if (K.getRelease() == k_release) {
return;
+ }
J.copyProfile(K);
- // J.clear();
+ // J.zero();
J.add(K);
k_release = K.getRelease();
}
/* -------------------------------------------------------------------------- */
-void PseudoTime::assembleResidual(bool) {}
+void PseudoTime::assembleResidual(bool /*is_lumped*/) {}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/integration_scheme/pseudo_time.hh b/src/model/common/integration_scheme/pseudo_time.hh
index 095747816..201302eaf 100644
--- a/src/model/common/integration_scheme/pseudo_time.hh
+++ b/src/model/common/integration_scheme/pseudo_time.hh
@@ -1,72 +1,72 @@
/**
* @file pseudo_time.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Pseudo time integration scheme
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PSEUDO_TIME_HH__
-#define __AKANTU_PSEUDO_TIME_HH__
+#ifndef AKANTU_PSEUDO_TIME_HH_
+#define AKANTU_PSEUDO_TIME_HH_
namespace akantu {
class PseudoTime : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PseudoTime(DOFManager & dof_manager, const ID & dof_id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
/// assemble the jacobian matrix
void assembleJacobian(const SolutionType & type, Real delta_t) override;
/// assemble the residual
void assembleResidual(bool is_lumped) override;
protected:
/// last release of K matrix
UInt k_release;
};
} // namespace akantu
-#endif /* __AKANTU_PSEUDO_TIME_HH__ */
+#endif /* AKANTU_PSEUDO_TIME_HH_ */
diff --git a/src/model/common/model_solver.cc b/src/model/common/model_solver.cc
index 1f6d88cea..052b22bbc 100644
--- a/src/model/common/model_solver.cc
+++ b/src/model/common/model_solver.cc
@@ -1,369 +1,374 @@
/**
* @file model_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Wed Feb 21 2018
*
* @brief Implementation of ModelSolver
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model_solver.hh"
#include "dof_manager.hh"
#include "dof_manager_default.hh"
#include "mesh.hh"
#include "non_linear_solver.hh"
#include "time_step_solver.hh"
#if defined(AKANTU_USE_PETSC)
#include "dof_manager_petsc.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> static T getOptionToType(const std::string & opt_str) {
std::stringstream sstr(opt_str);
T opt;
sstr >> opt;
return opt;
}
/* -------------------------------------------------------------------------- */
ModelSolver::ModelSolver(Mesh & mesh, const ModelType & type, const ID & id,
UInt memory_id)
- : Parsable(ParserType::_model, id), SolverCallback(), model_type(type),
+ : Parsable(ParserType::_model, id), model_type(type),
parent_id(id), parent_memory_id(memory_id), mesh(mesh),
- dof_manager(nullptr), default_solver_id("") {}
+ dof_manager(nullptr) {}
/* -------------------------------------------------------------------------- */
ModelSolver::~ModelSolver() = default;
/* -------------------------------------------------------------------------- */
std::tuple<ParserSection, bool> ModelSolver::getParserSection() {
auto sub_sections = getStaticParser().getSubSections(ParserType::_model);
auto it = std::find_if(
sub_sections.begin(), sub_sections.end(), [&](auto && section) {
- ModelType type = getOptionToType<ModelType>(section.getName());
+ auto type = getOptionToType<ModelType>(section.getName());
// default id should be the model type if not defined
std::string name = section.getParameter("name", this->parent_id);
return type == model_type and name == this->parent_id;
});
- if (it == sub_sections.end())
+ if (it == sub_sections.end()) {
return std::make_tuple(ParserSection(), true);
+ }
return std::make_tuple(*it, false);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::initDOFManager() {
// default without external solver activated at compilation same as mumps that
// is the historical solver but with only the lumped solver
ID solver_type = "default";
#if defined(AKANTU_USE_MUMPS)
solver_type = "default";
#elif defined(AKANTU_USE_PETSC)
solver_type = "petsc";
#endif
ParserSection section;
bool is_empty;
std::tie(section, is_empty) = this->getParserSection();
if (not is_empty) {
solver_type = section.getOption(solver_type);
this->initDOFManager(section, solver_type);
} else {
this->initDOFManager(solver_type);
}
}
/* -------------------------------------------------------------------------- */
void ModelSolver::initDOFManager(const ID & solver_type) {
try {
this->dof_manager = DOFManagerFactory::getInstance().allocate(
solver_type, mesh, this->parent_id + ":dof_manager_" + solver_type,
this->parent_memory_id);
} catch (...) {
AKANTU_EXCEPTION(
"To use the solver "
<< solver_type
<< " you will have to code it. This is an unknown solver type.");
}
this->setDOFManager(*this->dof_manager);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::initDOFManager(const ParserSection & section,
const ID & solver_type) {
this->initDOFManager(solver_type);
auto sub_sections = section.getSubSections(ParserType::_time_step_solver);
// parsing the time step solvers
for (auto && section : sub_sections) {
ID type = section.getName();
ID solver_id = section.getParameter("name", type);
auto tss_type = getOptionToType<TimeStepSolverType>(type);
auto tss_options = this->getDefaultSolverOptions(tss_type);
auto sub_solvers_sect =
section.getSubSections(ParserType::_non_linear_solver);
auto nb_non_linear_solver_section =
section.getNbSubSections(ParserType::_non_linear_solver);
auto nls_type = tss_options.non_linear_solver_type;
if (nb_non_linear_solver_section == 1) {
auto && nls_section = *(sub_solvers_sect.first);
nls_type = getOptionToType<NonLinearSolverType>(nls_section.getName());
} else if (nb_non_linear_solver_section > 0) {
AKANTU_EXCEPTION("More than one non linear solver are provided for the "
"time step solver "
<< solver_id);
}
this->getNewSolver(solver_id, tss_type, nls_type);
if (nb_non_linear_solver_section == 1) {
const auto & nls_section = *(sub_solvers_sect.first);
this->dof_manager->getNonLinearSolver(solver_id).parseSection(
nls_section);
}
auto sub_integrator_sections =
section.getSubSections(ParserType::_integration_scheme);
for (auto && is_section : sub_integrator_sections) {
const auto & dof_type_str = is_section.getName();
ID dof_id;
try {
ID tmp = is_section.getParameter("name");
dof_id = tmp;
} catch (...) {
AKANTU_EXCEPTION("No degree of freedom name specified for the "
"integration scheme of type "
<< dof_type_str);
}
auto it_type = getOptionToType<IntegrationSchemeType>(dof_type_str);
IntegrationScheme::SolutionType s_type = is_section.getParameter(
"solution_type", tss_options.solution_type[dof_id]);
this->setIntegrationScheme(solver_id, dof_id, it_type, s_type);
}
for (auto & is_type : tss_options.integration_scheme_type) {
if (!this->hasIntegrationScheme(solver_id, is_type.first)) {
this->setIntegrationScheme(solver_id, is_type.first, is_type.second,
tss_options.solution_type[is_type.first]);
}
}
}
if (section.hasParameter("default_solver")) {
ID default_solver = section.getParameter("default_solver");
if (this->hasSolver(default_solver)) {
this->setDefaultSolver(default_solver);
- } else
+ } else {
AKANTU_EXCEPTION(
"The solver \""
<< default_solver
<< "\" was not created, it cannot be set as default solver");
+ }
}
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & ModelSolver::getSolver(const ID & solver_id) {
ID tmp_solver_id = solver_id;
- if (tmp_solver_id == "")
+ if (tmp_solver_id.empty()) {
tmp_solver_id = this->default_solver_id;
+ }
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(tmp_solver_id);
return tss;
}
/* -------------------------------------------------------------------------- */
const TimeStepSolver & ModelSolver::getSolver(const ID & solver_id) const {
ID tmp_solver_id = solver_id;
- if (solver_id == "")
+ if (solver_id.empty()) {
tmp_solver_id = this->default_solver_id;
+ }
const TimeStepSolver & tss =
this->dof_manager->getTimeStepSolver(tmp_solver_id);
return tss;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & ModelSolver::getTimeStepSolver(const ID & solver_id) {
return this->getSolver(solver_id);
}
/* -------------------------------------------------------------------------- */
const TimeStepSolver &
ModelSolver::getTimeStepSolver(const ID & solver_id) const {
return this->getSolver(solver_id);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & ModelSolver::getNonLinearSolver(const ID & solver_id) {
return this->getSolver(solver_id).getNonLinearSolver();
}
/* -------------------------------------------------------------------------- */
const NonLinearSolver &
ModelSolver::getNonLinearSolver(const ID & solver_id) const {
return this->getSolver(solver_id).getNonLinearSolver();
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasSolver(const ID & solver_id) const {
ID tmp_solver_id = solver_id;
- if (solver_id == "")
+ if (solver_id.empty()) {
tmp_solver_id = this->default_solver_id;
+ }
if (not this->dof_manager) {
AKANTU_EXCEPTION("No DOF manager was initialized");
}
return this->dof_manager->hasTimeStepSolver(tmp_solver_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setDefaultSolver(const ID & solver_id) {
AKANTU_DEBUG_ASSERT(
this->hasSolver(solver_id),
"Cannot set the default solver to a solver that does not exists");
this->default_solver_id = solver_id;
}
/* -------------------------------------------------------------------------- */
void ModelSolver::solveStep(SolverCallback & callback, const ID & solver_id) {
AKANTU_DEBUG_IN();
TimeStepSolver & tss = this->getSolver(solver_id);
// make one non linear solve
tss.solveStep(callback);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ModelSolver::solveStep(const ID & solver_id) {
solveStep(*this, solver_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::getNewSolver(const ID & solver_id,
TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) {
- if (this->default_solver_id == "") {
+ if (this->default_solver_id.empty()) {
this->default_solver_id = solver_id;
}
if (non_linear_solver_type == NonLinearSolverType::_auto) {
switch (time_step_solver_type) {
case TimeStepSolverType::_dynamic:
case TimeStepSolverType::_static:
non_linear_solver_type = NonLinearSolverType::_newton_raphson;
break;
case TimeStepSolverType::_dynamic_lumped:
non_linear_solver_type = NonLinearSolverType::_lumped;
break;
case TimeStepSolverType::_not_defined:
AKANTU_EXCEPTION(time_step_solver_type
<< " is not a valid time step solver type");
break;
}
}
this->initSolver(time_step_solver_type, non_linear_solver_type);
NonLinearSolver & nls = this->dof_manager->getNewNonLinearSolver(
solver_id, non_linear_solver_type);
this->dof_manager->getNewTimeStepSolver(solver_id, time_step_solver_type, nls,
*this);
}
/* -------------------------------------------------------------------------- */
Real ModelSolver::getTimeStep(const ID & solver_id) const {
const TimeStepSolver & tss = this->getSolver(solver_id);
return tss.getTimeStep();
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setTimeStep(Real time_step, const ID & solver_id) {
TimeStepSolver & tss = this->getSolver(solver_id);
return tss.setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setIntegrationScheme(
const ID & solver_id, const ID & dof_id,
const IntegrationSchemeType & integration_scheme_type,
IntegrationScheme::SolutionType solution_type) {
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(solver_id);
tss.setIntegrationScheme(dof_id, integration_scheme_type, solution_type);
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasDefaultSolver() const {
- return (this->default_solver_id != "");
+ return (not this->default_solver_id.empty());
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasIntegrationScheme(const ID & solver_id,
const ID & dof_id) const {
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(solver_id);
return tss.hasIntegrationScheme(dof_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::predictor() {}
/* -------------------------------------------------------------------------- */
void ModelSolver::corrector() {}
/* -------------------------------------------------------------------------- */
TimeStepSolverType ModelSolver::getDefaultSolverType() const {
return TimeStepSolverType::_dynamic_lumped;
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions
ModelSolver::getDefaultSolverOptions(__attribute__((unused))
const TimeStepSolverType & type) const {
ModelSolverOptions options;
options.non_linear_solver_type = NonLinearSolverType::_auto;
return options;
}
} // namespace akantu
diff --git a/src/model/common/model_solver.hh b/src/model/common/model_solver.hh
index 060d8b2d7..167132194 100644
--- a/src/model/common/model_solver.hh
+++ b/src/model/common/model_solver.hh
@@ -1,198 +1,198 @@
/**
* @file model_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Class regrouping the common solve interface to the different models
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "integration_scheme.hh"
#include "parsable.hh"
#include "solver_callback.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MODEL_SOLVER_HH__
-#define __AKANTU_MODEL_SOLVER_HH__
+#ifndef AKANTU_MODEL_SOLVER_HH_
+#define AKANTU_MODEL_SOLVER_HH_
namespace akantu {
class Mesh;
class DOFManager;
class TimeStepSolver;
class NonLinearSolver;
struct ModelSolverOptions;
} // namespace akantu
namespace akantu {
class ModelSolver : public Parsable,
public SolverCallback,
public SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ModelSolver(Mesh & mesh, const ModelType & type, const ID & id,
UInt memory_id);
~ModelSolver() override;
/// initialize the dof manager based on solver type passed in the input file
void initDOFManager();
/// initialize the dof manager based on the used chosen solver type
void initDOFManager(const ID & solver_type);
protected:
/// initialize the dof manager based on the used chosen solver type
void initDOFManager(const ParserSection & section, const ID & solver_type);
/// Callback for the model to instantiate the matricees when needed
virtual void initSolver(TimeStepSolverType /*time_step_solver_type*/,
NonLinearSolverType /*non_linear_solver_type*/) {}
/// get the section in the input file (if it exsits) corresponding to this
/// model
std::tuple<ParserSection, bool> getParserSection();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solve a step using a given pre instantiated time step solver and
/// nondynamic linear solver
virtual void solveStep(const ID & solver_id = "");
/// solve a step using a given pre instantiated time step solver and
/// non linear solver with a user defined callback instead of the
/// model itself /!\ This can mess up everything
virtual void solveStep(SolverCallback & callback, const ID & solver_id = "");
/// Initialize a time solver that can be used afterwards with its id
void getNewSolver(
const ID & solver_id, TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type = NonLinearSolverType::_auto);
/// set an integration scheme for a given dof and a given solver
void
setIntegrationScheme(const ID & solver_id, const ID & dof_id,
const IntegrationSchemeType & integration_scheme_type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
/// set an externally instantiated integration scheme
void setIntegrationScheme(const ID & solver_id, const ID & dof_id,
IntegrationScheme & integration_scheme,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
/* ------------------------------------------------------------------------ */
/* SolverCallback interface */
/* ------------------------------------------------------------------------ */
public:
/// Predictor interface for the callback
void predictor() override;
/// Corrector interface for the callback
void corrector() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Default time step solver to instantiate for this model
virtual TimeStepSolverType getDefaultSolverType() const;
/// Default configurations for a given time step solver
virtual ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const;
/// get access to the internal dof manager
DOFManager & getDOFManager() { return *this->dof_manager; }
/// get the time step of a given solver
Real getTimeStep(const ID & solver_id = "") const;
/// set the time step of a given solver
virtual void setTimeStep(Real time_step, const ID & solver_id = "");
/// set the parameter 'param' of the solver 'solver_id'
// template <typename T>
// void set(const ID & param, const T & value, const ID & solver_id = "");
/// get the parameter 'param' of the solver 'solver_id'
// const Parameter & get(const ID & param, const ID & solver_id = "") const;
/// answer to the question "does the solver exists ?"
bool hasSolver(const ID & solver_id) const;
/// changes the current default solver
void setDefaultSolver(const ID & solver_id);
/// is a default solver defined
bool hasDefaultSolver() const;
/// is an integration scheme set for a given solver and a given dof
bool hasIntegrationScheme(const ID & solver_id, const ID & dof_id) const;
TimeStepSolver & getTimeStepSolver(const ID & solver_id = "");
NonLinearSolver & getNonLinearSolver(const ID & solver_id = "");
const TimeStepSolver & getTimeStepSolver(const ID & solver_id = "") const;
const NonLinearSolver & getNonLinearSolver(const ID & solver_id = "") const;
private:
TimeStepSolver & getSolver(const ID & solver_id);
const TimeStepSolver & getSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ModelType model_type;
private:
ID parent_id;
UInt parent_memory_id;
/// Underlying mesh
Mesh & mesh;
/// Underlying dof_manager (the brain...)
std::unique_ptr<DOFManager> dof_manager;
/// Default time step solver to use
ID default_solver_id;
};
struct ModelSolverOptions {
NonLinearSolverType non_linear_solver_type;
std::map<ID, IntegrationSchemeType> integration_scheme_type;
std::map<ID, IntegrationScheme::SolutionType> solution_type;
};
} // namespace akantu
-#endif /* __AKANTU_MODEL_SOLVER_HH__ */
+#endif /* AKANTU_MODEL_SOLVER_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver.cc b/src/model/common/non_linear_solver/non_linear_solver.cc
index 0cf345361..9891039de 100644
--- a/src/model/common/non_linear_solver/non_linear_solver.cc
+++ b/src/model/common/non_linear_solver/non_linear_solver.cc
@@ -1,78 +1,78 @@
/**
* @file non_linear_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 20 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the base class NonLinearSolver
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "dof_manager.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolver::NonLinearSolver(
DOFManager & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: Memory(id, memory_id), Parsable(ParserType::_non_linear_solver, id),
_dof_manager(dof_manager),
non_linear_solver_type(non_linear_solver_type) {
this->registerParam("type", this->non_linear_solver_type, _pat_parsable,
"Non linear solver type");
}
/* -------------------------------------------------------------------------- */
NonLinearSolver::~NonLinearSolver() = default;
/* -------------------------------------------------------------------------- */
void NonLinearSolver::checkIfTypeIsSupported() {
if (this->supported_type.find(this->non_linear_solver_type) ==
this->supported_type.end() and
this->non_linear_solver_type != NonLinearSolverType::_auto) {
AKANTU_EXCEPTION("The resolution method "
<< this->non_linear_solver_type
<< " is not implemented in the non linear solver "
<< this->id << "!");
}
}
/* -------------------------------------------------------------------------- */
void NonLinearSolver::assembleResidual(SolverCallback & solver_callback) {
if (solver_callback.canSplitResidual() and
non_linear_solver_type == NonLinearSolverType::_linear) {
- this->_dof_manager.clearResidual();
+ this->_dof_manager.zeroResidual();
solver_callback.assembleResidual("external");
this->_dof_manager.assembleMatMulDOFsToResidual("K", -1.);
solver_callback.assembleResidual("inertial");
} else {
solver_callback.assembleResidual();
}
}
} // namespace akantu
diff --git a/src/model/common/non_linear_solver/non_linear_solver.hh b/src/model/common/non_linear_solver/non_linear_solver.hh
index 1fc61233e..c6011d772 100644
--- a/src/model/common/non_linear_solver/non_linear_solver.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver.hh
@@ -1,112 +1,112 @@
/**
* @file non_linear_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Non linear solver interface
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_memory.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LINEAR_SOLVER_HH__
-#define __AKANTU_NON_LINEAR_SOLVER_HH__
+#ifndef AKANTU_NON_LINEAR_SOLVER_HH_
+#define AKANTU_NON_LINEAR_SOLVER_HH_
namespace akantu {
class DOFManager;
class SolverCallback;
} // namespace akantu
namespace akantu {
class NonLinearSolver : private Memory, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolver(DOFManager & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver", UInt memory_id = 0);
~NonLinearSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solve the system described by the jacobian matrix, and rhs contained in
/// the dof manager
virtual void solve(SolverCallback & callback) = 0;
/// intercept the call to set for options
template <typename T> void set(const ID & param, T && t) {
if (has_internal_set_param) {
set_param(param, std::to_string(t));
} else {
ParameterRegistry::set(param, t);
}
}
protected:
void checkIfTypeIsSupported();
void assembleResidual(SolverCallback & callback);
/// internal set param for solvers that should intercept the parameters
virtual void set_param(const ID & /*param*/, const std::string & /*value*/) {}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
DOFManager & _dof_manager;
/// type of non linear solver
NonLinearSolverType non_linear_solver_type;
/// list of supported non linear solver types
std::set<NonLinearSolverType> supported_type;
/// specifies if the set param should be redirected
bool has_internal_set_param{false};
};
namespace debug {
class NLSNotConvergedException : public Exception {
public:
NLSNotConvergedException(Real threshold, UInt niter, Real error)
: Exception("The non linear solver did not converge."),
threshold(threshold), niter(niter), error(error) {}
Real threshold;
UInt niter;
Real error;
};
} // namespace debug
} // namespace akantu
-#endif /* __AKANTU_NON_LINEAR_SOLVER_HH__ */
+#endif /* AKANTU_NON_LINEAR_SOLVER_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_default.hh b/src/model/common/non_linear_solver/non_linear_solver_default.hh
index a43a6a622..dff69cdfd 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_default.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_default.hh
@@ -1,44 +1,44 @@
/**
* @file non_linear_solver_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Include for the default non linear solvers
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH__
-#define __AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH__
+#ifndef AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH_
+#define AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH_
#if defined(AKANTU_USE_MUMPS)
#include "non_linear_solver_linear.hh"
#include "non_linear_solver_newton_raphson.hh"
#endif
#include "non_linear_solver_lumped.hh"
-#endif /* __AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH__ */
+#endif /* AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_linear.hh b/src/model/common/non_linear_solver/non_linear_solver_linear.hh
index 743d28f10..5fb338291 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_linear.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_linear.hh
@@ -1,79 +1,79 @@
/**
* @file non_linear_solver_linear.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Default implementation of NonLinearSolver, in case no external
* library
* is there to do the job
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__
-#define __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__
+#ifndef AKANTU_NON_LINEAR_SOLVER_LINEAR_HH_
+#define AKANTU_NON_LINEAR_SOLVER_LINEAR_HH_
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class NonLinearSolverLinear : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverLinear(DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_linear",
UInt memory_id = 0);
~NonLinearSolverLinear() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
void solve(SolverCallback & solver_callback) override;
AKANTU_GET_MACRO_NOT_CONST(Solver, solver, SparseSolverMumps &);
AKANTU_GET_MACRO(Solver, solver, const SparseSolverMumps &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
DOFManagerDefault & dof_manager;
/// Sparse solver used for the linear solves
SparseSolverMumps solver;
};
} // namespace akantu
-#endif /* __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__ */
+#endif /* AKANTU_NON_LINEAR_SOLVER_LINEAR_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_lumped.cc b/src/model/common/non_linear_solver/non_linear_solver_lumped.cc
index d3182cf7a..cc200f34a 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_lumped.cc
+++ b/src/model/common/non_linear_solver/non_linear_solver_lumped.cc
@@ -1,102 +1,102 @@
/**
* @file non_linear_solver_lumped.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 16 2016
* @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the default NonLinearSolver
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_lumped.hh"
#include "communicator.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "solver_vector_default.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverLumped::NonLinearSolverLumped(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id, memory_id),
dof_manager(dof_manager) {
this->supported_type.insert(NonLinearSolverType::_lumped);
this->checkIfTypeIsSupported();
this->registerParam("b_a2x", this->alpha, 1., _pat_parsmod,
"Conversion coefficient between x and A^{-1} b");
}
/* -------------------------------------------------------------------------- */
NonLinearSolverLumped::~NonLinearSolverLumped() = default;
/* ------------------------------------------------------------------------ */
void NonLinearSolverLumped::solve(SolverCallback & solver_callback) {
solver_callback.beforeSolveStep();
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
solver_callback.assembleResidual();
auto & x = aka::as_type<SolverVectorDefault>(this->dof_manager.getSolution());
const auto & b = this->dof_manager.getResidual();
x.resize();
const auto & blocked_dofs = this->dof_manager.getBlockedDOFs();
const auto & A = this->dof_manager.getLumpedMatrix("M");
// alpha is the conversion factor from from force/mass to acceleration needed
// in model coupled with atomistic \todo find a way to define alpha per dof
// type
- this->solveLumped(A, x, b, alpha, blocked_dofs);
+ NonLinearSolverLumped::solveLumped(A, x, b, alpha, blocked_dofs);
this->dof_manager.splitSolutionPerDOFs();
solver_callback.corrector();
solver_callback.afterSolveStep(true);
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverLumped::solveLumped(const Array<Real> & A, Array<Real> & x,
const Array<Real> & b, Real alpha,
const Array<bool> & blocked_dofs) {
for (auto && data :
zip(make_view(A), make_view(x), make_view(b), make_view(blocked_dofs))) {
const auto & A = std::get<0>(data);
auto & x = std::get<1>(data);
const auto & b = std::get<2>(data);
const auto & blocked = std::get<3>(data);
if (not blocked) {
x = alpha * (b / A);
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/non_linear_solver/non_linear_solver_lumped.hh b/src/model/common/non_linear_solver/non_linear_solver_lumped.hh
index bd8473d2d..448d744d2 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_lumped.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_lumped.hh
@@ -1,80 +1,80 @@
/**
* @file non_linear_solver_lumped.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Default implementation of NonLinearSolver, in case no external
* library
* is there to do the job
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__
-#define __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__
+#ifndef AKANTU_NON_LINEAR_SOLVER_LUMPED_HH_
+#define AKANTU_NON_LINEAR_SOLVER_LUMPED_HH_
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class NonLinearSolverLumped : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverLumped(DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_lumped",
UInt memory_id = 0);
~NonLinearSolverLumped() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
void solve(SolverCallback & solver_callback) override;
static void solveLumped(const Array<Real> & A, Array<Real> & x,
const Array<Real> & b, Real alpha,
const Array<bool> & blocked_dofs);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// Coefficient to apply between x and A^{-1} b
Real alpha;
};
} // namespace akantu
-#endif /* __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__ */
+#endif /* AKANTU_NON_LINEAR_SOLVER_LUMPED_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc b/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
index 86a5b484a..12ee9e046 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
+++ b/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
@@ -1,206 +1,210 @@
/**
* @file non_linear_solver_newton_raphson.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 15 2015
* @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the default NonLinearSolver
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_newton_raphson.hh"
#include "communicator.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "solver_vector.hh"
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverNewtonRaphson::NonLinearSolverNewtonRaphson(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id, memory_id),
dof_manager(dof_manager),
solver(std::make_unique<SparseSolverMumps>(
dof_manager, "J", id + ":sparse_solver", memory_id)) {
this->supported_type.insert(NonLinearSolverType::_newton_raphson_modified);
this->supported_type.insert(NonLinearSolverType::_newton_raphson);
this->supported_type.insert(NonLinearSolverType::_linear);
this->checkIfTypeIsSupported();
this->registerParam("threshold", convergence_criteria, 1e-10, _pat_parsmod,
"Threshold to consider results as converged");
this->registerParam("convergence_type", convergence_criteria_type,
SolveConvergenceCriteria::_solution, _pat_parsmod,
"Type of convergence criteria");
this->registerParam("max_iterations", max_iterations, 10, _pat_parsmod,
"Max number of iterations");
this->registerParam("error", error, _pat_readable, "Last reached error");
this->registerParam("nb_iterations", n_iter, _pat_readable,
"Last reached number of iterations");
this->registerParam("converged", converged, _pat_readable,
"Did last solve converged");
this->registerParam("force_linear_recompute", force_linear_recompute, true,
_pat_modifiable,
"Force reassembly of the jacobian matrix");
}
/* -------------------------------------------------------------------------- */
NonLinearSolverNewtonRaphson::~NonLinearSolverNewtonRaphson() = default;
/* ------------------------------------------------------------------------ */
void NonLinearSolverNewtonRaphson::solve(SolverCallback & solver_callback) {
solver_callback.beforeSolveStep();
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
if (non_linear_solver_type == NonLinearSolverType::_linear and
- solver_callback.canSplitResidual())
+ solver_callback.canSplitResidual()) {
solver_callback.assembleMatrix("K");
+ }
this->assembleResidual(solver_callback);
if (this->non_linear_solver_type ==
NonLinearSolverType::_newton_raphson_modified ||
(this->non_linear_solver_type == NonLinearSolverType::_linear &&
this->force_linear_recompute)) {
solver_callback.assembleMatrix("J");
this->force_linear_recompute = false;
}
this->n_iter = 0;
this->converged = false;
this->convergence_criteria_normalized = this->convergence_criteria;
if (this->convergence_criteria_type == SolveConvergenceCriteria::_residual) {
this->converged = this->testConvergence(this->dof_manager.getResidual());
- if (this->converged)
+ if (this->converged) {
return;
+ }
this->convergence_criteria_normalized =
this->error * this->convergence_criteria;
}
do {
- if (this->non_linear_solver_type == NonLinearSolverType::_newton_raphson)
+ if (this->non_linear_solver_type == NonLinearSolverType::_newton_raphson) {
solver_callback.assembleMatrix("J");
+ }
this->solver->solve();
solver_callback.corrector();
// EventManager::sendEvent(NonLinearSolver::AfterSparseSolve(method));
if (this->convergence_criteria_type ==
SolveConvergenceCriteria::_residual) {
this->assembleResidual(solver_callback);
this->converged = this->testConvergence(this->dof_manager.getResidual());
} else {
this->converged = this->testConvergence(this->dof_manager.getSolution());
}
if (this->convergence_criteria_type ==
SolveConvergenceCriteria::_solution and
- not this->converged)
+ not this->converged) {
this->assembleResidual(solver_callback);
+ }
// this->dump();
this->n_iter++;
AKANTU_DEBUG_INFO(
"[" << this->convergence_criteria_type << "] Convergence iteration "
<< std::setw(std::log10(this->max_iterations)) << this->n_iter
<< ": error " << this->error << (this->converged ? " < " : " > ")
<< this->convergence_criteria);
} while (not this->converged and this->n_iter <= this->max_iterations);
// this makes sure that you have correct strains and stresses after the
// solveStep function (e.g., for dumping)
- if (this->convergence_criteria_type == SolveConvergenceCriteria::_solution)
+ if (this->convergence_criteria_type == SolveConvergenceCriteria::_solution) {
this->assembleResidual(solver_callback);
+ }
this->converged =
this->converged and not (this->n_iter > this->max_iterations);
solver_callback.afterSolveStep(this->converged);
if (not this->converged) {
AKANTU_CUSTOM_EXCEPTION(debug::NLSNotConvergedException(
this->convergence_criteria, this->n_iter, this->error));
AKANTU_DEBUG_WARNING("[" << this->convergence_criteria_type
<< "] Convergence not reached after "
<< std::setw(std::log10(this->max_iterations))
<< this->n_iter << " iteration"
<< (this->n_iter == 1 ? "" : "s") << "!");
}
- return;
}
/* -------------------------------------------------------------------------- */
bool NonLinearSolverNewtonRaphson::testConvergence(
const SolverVector & solver_vector) {
AKANTU_DEBUG_IN();
const auto & blocked_dofs = this->dof_manager.getBlockedDOFs();
const Array<Real> & array(solver_vector);
UInt nb_degree_of_freedoms = array.size();
auto arr_it = array.begin();
auto bld_it = blocked_dofs.begin();
Real norm = 0.;
for (UInt n = 0; n < nb_degree_of_freedoms; ++n, ++arr_it, ++bld_it) {
bool is_local_node = this->dof_manager.isLocalOrMasterDOF(n);
if ((!*bld_it) && is_local_node) {
norm += *arr_it * *arr_it;
}
}
dof_manager.getCommunicator().allReduce(norm, SynchronizerOperation::_sum);
norm = std::sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm),
"Something went wrong in the solve phase");
this->error = norm;
return (error < this->convergence_criteria_normalized);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.hh b/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.hh
index 609ca4142..cd6675881 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.hh
@@ -1,109 +1,109 @@
/**
* @file non_linear_solver_newton_raphson.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Default implementation of NonLinearSolver, in case no external
* library
* is there to do the job
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH__
-#define __AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH__
+#ifndef AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH_
+#define AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH_
namespace akantu {
class DOFManagerDefault;
class SparseSolverMumps;
class SolverVector;
} // namespace akantu
namespace akantu {
class NonLinearSolverNewtonRaphson : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverNewtonRaphson(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_newton_raphson", UInt memory_id = 0);
~NonLinearSolverNewtonRaphson() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
void solve(SolverCallback & solver_callback) override;
AKANTU_GET_MACRO_NOT_CONST(Solver, *solver, SparseSolverMumps &);
AKANTU_GET_MACRO(Solver, *solver, const SparseSolverMumps &);
protected:
/// test the convergence compare norm of array to convergence_criteria
- bool testConvergence(const SolverVector & array);
+ bool testConvergence(const SolverVector & solver_vector);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// Sparse solver used for the linear solves
std::unique_ptr<SparseSolverMumps> solver;
/// Type of convergence criteria
SolveConvergenceCriteria convergence_criteria_type;
/// convergence threshold
Real convergence_criteria;
/// convergence threshold
Real convergence_criteria_normalized;
/// Max number of iterations
int max_iterations;
/// Number of iterations at last solve call
int n_iter{0};
/// Convergence error at last solve call
Real error{0.};
/// Did the last call to solve reached convergence
bool converged{false};
/// Force a re-computation of the jacobian matrix
bool force_linear_recompute{true};
};
} // namespace akantu
-#endif /* __AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH__ */
+#endif /* AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_petsc.cc b/src/model/common/non_linear_solver/non_linear_solver_petsc.cc
index 99e46d2e9..629fa4a23 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_petsc.cc
+++ b/src/model/common/non_linear_solver/non_linear_solver_petsc.cc
@@ -1,221 +1,224 @@
/**
* @file non_linear_solver_petsc.cc
*
* @author Nicolas Richart
*
* @date creation Mon Dec 31 2018
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
#include "solver_callback.hh"
#include "solver_vector_petsc.hh"
#include "sparse_matrix_petsc.hh"
/* -------------------------------------------------------------------------- */
#include <petscoptions.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
NonLinearSolverPETSc::NonLinearSolverPETSc(
DOFManagerPETSc & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id, memory_id),
dof_manager(dof_manager) {
std::unordered_map<NonLinearSolverType, SNESType>
petsc_non_linear_solver_types{
{NonLinearSolverType::_newton_raphson, SNESNEWTONLS},
{NonLinearSolverType::_linear, SNESKSPONLY},
{NonLinearSolverType::_gmres, SNESNGMRES},
{NonLinearSolverType::_bfgs, SNESQN},
{NonLinearSolverType::_cg, SNESNCG}};
this->has_internal_set_param = true;
for (const auto & pair : petsc_non_linear_solver_types) {
supported_type.insert(pair.first);
}
this->checkIfTypeIsSupported();
- auto mpi_comm = dof_manager.getMPIComm();
+ auto && mpi_comm = dof_manager.getMPIComm();
PETSc_call(SNESCreate, mpi_comm, &snes);
auto it = petsc_non_linear_solver_types.find(non_linear_solver_type);
if (it != petsc_non_linear_solver_types.end()) {
PETSc_call(SNESSetType, snes, it->second);
}
SNESSetFromOptions(snes);
}
/* -------------------------------------------------------------------------- */
NonLinearSolverPETSc::~NonLinearSolverPETSc() {
PETSc_call(SNESDestroy, &snes);
}
/* -------------------------------------------------------------------------- */
class NonLinearSolverPETScCallback {
public:
NonLinearSolverPETScCallback(DOFManagerPETSc & dof_manager,
SolverVectorPETSc & x)
: dof_manager(dof_manager), x(x), x_prev(x, "previous_solution") {}
void corrector() {
auto & dx = dof_manager.getSolution();
PETSc_call(VecWAXPY, dx, -1., x_prev, x);
dof_manager.splitSolutionPerDOFs();
callback->corrector();
PETSc_call(VecCopy, x, x_prev);
}
void assembleResidual() {
corrector();
callback->assembleResidual();
}
void assembleJacobian() {
// corrector();
callback->assembleMatrix("J");
}
void setInitialSolution(SolverVectorPETSc & x) {
PETSc_call(VecCopy, x, x_prev);
}
void setCallback(SolverCallback & callback) { this->callback = &callback; }
private:
// SNES & snes;
SolverCallback * callback;
DOFManagerPETSc & dof_manager;
SolverVectorPETSc & x;
SolverVectorPETSc x_prev;
}; // namespace akantu
/* -------------------------------------------------------------------------- */
PetscErrorCode NonLinearSolverPETSc::FormFunction(SNES /*snes*/, Vec /*dx*/,
Vec /*f*/, void * ctx) {
auto * _this = reinterpret_cast<NonLinearSolverPETScCallback *>(ctx);
_this->assembleResidual();
return 0;
}
/* -------------------------------------------------------------------------- */
PetscErrorCode NonLinearSolverPETSc::FormJacobian(SNES /*snes*/, Vec /*dx*/,
Mat /*J*/, Mat /*P*/,
void * ctx) {
auto * _this = reinterpret_cast<NonLinearSolverPETScCallback *>(ctx);
_this->assembleJacobian();
return 0;
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverPETSc::solve(SolverCallback & callback) {
callback.beforeSolveStep();
this->dof_manager.updateGlobalBlockedDofs();
callback.assembleMatrix("J");
auto & global_x = dof_manager.getSolution();
- global_x.clear();
+ global_x.zero();
if (not x) {
x = std::make_unique<SolverVectorPETSc>(global_x, "temporary_solution");
}
*x = global_x;
if (not ctx) {
ctx = std::make_unique<NonLinearSolverPETScCallback>(dof_manager, *x);
}
ctx->setCallback(callback);
ctx->setInitialSolution(global_x);
auto & rhs = dof_manager.getResidual();
auto & J = dof_manager.getMatrix("J");
PETSc_call(SNESSetFunction, snes, rhs, NonLinearSolverPETSc::FormFunction,
ctx.get());
PETSc_call(SNESSetJacobian, snes, J, J, NonLinearSolverPETSc::FormJacobian,
ctx.get());
- rhs.clear();
+ rhs.zero();
callback.predictor();
callback.assembleResidual();
PETSc_call(SNESSolve, snes, nullptr, *x);
PETSc_call(SNESGetConvergedReason, snes, &reason);
PETSc_call(SNESGetIterationNumber, snes, &n_iter);
PETSc_call(VecAXPY, global_x, -1.0, *x);
dof_manager.splitSolutionPerDOFs();
callback.corrector();
bool converged = reason >= 0;
callback.afterSolveStep(converged);
if (not converged) {
- PetscReal atol, rtol, stol;
- PetscInt maxit, maxf;
+ PetscReal atol;
+ PetscReal rtol;
+ PetscReal stol;
+ PetscInt maxit;
+ PetscInt maxf;
PETSc_call(SNESGetTolerances, snes, &atol, &rtol, &stol, &maxit, &maxf);
AKANTU_CUSTOM_EXCEPTION(debug::SNESNotConvergedException(
this->reason, this->n_iter, stol, atol, rtol, maxit));
}
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverPETSc::set_param(const ID & param,
const std::string & value) {
std::map<ID, ID> akantu_to_petsc_option = {{"max_iterations", "snes_max_it"},
{"threshold", "snes_stol"}};
auto it = akantu_to_petsc_option.find(param);
auto p = it == akantu_to_petsc_option.end() ? param : it->second;
- PetscOptionsSetValue(NULL, p.c_str(), value.c_str());
+ PetscOptionsSetValue(nullptr, p.c_str(), value.c_str());
SNESSetFromOptions(snes);
- PetscOptionsClear(NULL);
+ PetscOptionsClear(nullptr);
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverPETSc::parseSection(const ParserSection & section) {
auto parameters = section.getParameters();
for (auto && param : range(parameters.first, parameters.second)) {
- PetscOptionsSetValue(NULL, param.getName().c_str(),
+ PetscOptionsSetValue(nullptr, param.getName().c_str(),
param.getValue().c_str());
}
SNESSetFromOptions(snes);
- PetscOptionsClear(NULL);
+ PetscOptionsClear(nullptr);
}
} // namespace akantu
diff --git a/src/model/common/non_linear_solver/non_linear_solver_petsc.hh b/src/model/common/non_linear_solver/non_linear_solver_petsc.hh
index e9d8112ff..15118d841 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_petsc.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_petsc.hh
@@ -1,108 +1,108 @@
/**
* @file non_linear_solver_petsc.hh
*
* @author Nicolas Richart
*
* @date creation Tue Jan 01 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#include <petscsnes.h>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LINEAR_SOLVER_PETSC_HH__
-#define __AKANTU_NON_LINEAR_SOLVER_PETSC_HH__
+#ifndef AKANTU_NON_LINEAR_SOLVER_PETSC_HH_
+#define AKANTU_NON_LINEAR_SOLVER_PETSC_HH_
namespace akantu {
class DOFManagerPETSc;
class NonLinearSolverPETScCallback;
class SolverVectorPETSc;
} // namespace akantu
namespace akantu {
class NonLinearSolverPETSc : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverPETSc(DOFManagerPETSc & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_petsc",
UInt memory_id = 0);
~NonLinearSolverPETSc() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solve the system described by the jacobian matrix, and rhs contained in
/// the dof manager
void solve(SolverCallback & callback) override;
/// parse the arguments from the input file
void parseSection(const ParserSection & section) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
static PetscErrorCode FormFunction(SNES snes, Vec dx, Vec f, void * ctx);
static PetscErrorCode FormJacobian(SNES snes, Vec dx, Mat J, Mat P,
void * ctx);
void set_param(const ID & param, const std::string & value) override;
DOFManagerPETSc & dof_manager;
/// PETSc non linear solver
SNES snes;
SNESConvergedReason reason;
SolverCallback * callback{nullptr};
std::unique_ptr<SolverVectorPETSc> x;
std::unique_ptr<NonLinearSolverPETScCallback> ctx;
Int n_iter{0};
};
namespace debug {
class SNESNotConvergedException : public NLSNotConvergedException {
public:
SNESNotConvergedException(SNESConvergedReason reason, UInt niter,
Real error, Real absolute_tolerance,
Real relative_tolerance, UInt max_iterations)
: NLSNotConvergedException(relative_tolerance, niter, error),
reason(reason), absolute_tolerance(absolute_tolerance),
max_iterations(max_iterations) {}
SNESConvergedReason reason;
Real absolute_tolerance;
UInt max_iterations;
};
} // namespace debug
} // namespace akantu
-#endif /* __AKANTU_NON_LINEAR_SOLVER_PETSC_HH__ */
+#endif /* AKANTU_NON_LINEAR_SOLVER_PETSC_HH_ */
diff --git a/src/model/common/non_local_toolbox/base_weight_function.hh b/src/model/common/non_local_toolbox/base_weight_function.hh
index 9bb0ab113..95a80e25c 100644
--- a/src/model/common/non_local_toolbox/base_weight_function.hh
+++ b/src/model/common/non_local_toolbox/base_weight_function.hh
@@ -1,168 +1,171 @@
/**
* @file base_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Fri Dec 08 2017
*
* @brief Base weight function for non local materials
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "model.hh"
#include "non_local_manager.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_BASE_WEIGHT_FUNCTION_HH__
-#define __AKANTU_BASE_WEIGHT_FUNCTION_HH__
+#ifndef AKANTU_BASE_WEIGHT_FUNCTION_HH_
+#define AKANTU_BASE_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Normal weight function */
/* -------------------------------------------------------------------------- */
class BaseWeightFunction : public Parsable, public DataAccessor<Element> {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
BaseWeightFunction(NonLocalManager & manager,
const std::string & type = "base")
: Parsable(ParserType::_weight_function, "weight_function:" + type),
manager(manager), type(type),
spatial_dimension(manager.getModel().getMesh().getSpatialDimension()) {
this->registerParam("update_rate", update_rate, UInt(1), _pat_parsmod,
"Update frequency");
}
~BaseWeightFunction() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
/// initialize the weight function
virtual inline void init();
/// update the internal parameters
virtual void updateInternals(){};
/* ------------------------------------------------------------------------ */
/// set the non-local radius
inline void setRadius(Real radius);
/* ------------------------------------------------------------------------ */
/// compute the weight for a given distance between two quadrature points
inline Real operator()(Real r, const IntegrationPoint & q1,
- const IntegrationPoint & q2);
+ const IntegrationPoint & q2) const;
/// print function
void printself(std::ostream & stream, int indent = 0) const override {
std::string space;
- for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
+ for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
+ }
stream << space << "WeightFunction " << type << " [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
}
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
/// get the radius
- Real getRadius() { return R; }
+ Real getRadius() const { return R; }
/// get the update rate
- UInt getUpdateRate() { return update_rate; }
+ UInt getUpdateRate() const { return update_rate; }
public:
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
- UInt getNbData(const Array<Element> &,
- const SynchronizationTag &) const override {
+ UInt getNbData(const Array<Element> & /*elements*/,
+ const SynchronizationTag & /*tag*/) const override {
return 0;
}
- inline void packData(CommunicationBuffer &, const Array<Element> &,
- const SynchronizationTag &) const override {}
+ inline void packData(CommunicationBuffer & /*buffer*/,
+ const Array<Element> & /*element*/,
+ const SynchronizationTag & /*tag*/) const override {}
- inline void unpackData(CommunicationBuffer &, const Array<Element> &,
- const SynchronizationTag &) override {}
+ inline void unpackData(CommunicationBuffer & /*buffer*/,
+ const Array<Element> & /*element*/,
+ const SynchronizationTag & /*tag*/) override {}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Type, type, const ID &);
protected:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// reference to the non-local manager
NonLocalManager & manager;
/// the non-local radius
Real R;
/// the non-local radius squared
Real R2;
/// the update rate
UInt update_rate;
/// name of the type of weight function
const std::string type;
/// the spatial dimension
UInt spatial_dimension;
};
inline std::ostream & operator<<(std::ostream & stream,
const BaseWeightFunction & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "base_weight_function_inline_impl.hh"
/* -------------------------------------------------------------------------- */
/* Include all other weight function types */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_DAMAGE_NON_LOCAL)
#include "damaged_weight_function.hh"
#include "remove_damaged_weight_function.hh"
#include "remove_damaged_with_damage_rate_weight_function.hh"
#include "stress_based_weight_function.hh"
#endif
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_BASE_WEIGHT_FUNCTION_HH__ */
+#endif /* AKANTU_BASE_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/common/non_local_toolbox/base_weight_function_inline_impl.hh b/src/model/common/non_local_toolbox/base_weight_function_inline_impl.hh
index 30eb53057..36533b13e 100644
--- a/src/model/common/non_local_toolbox/base_weight_function_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/base_weight_function_inline_impl.hh
@@ -1,70 +1,71 @@
/**
* @file base_weight_function_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Wed Sep 27 2017
*
* @brief Implementation of inline function of base weight function
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_HH__
-#define __AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_HH__
+#ifndef AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_HH_
+#define AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void BaseWeightFunction::init() {
/// compute R^2 for a given non-local radius
this->R2 = this->R * this->R;
}
/* -------------------------------------------------------------------------- */
inline void BaseWeightFunction::setRadius(Real radius) {
/// set the non-local radius and update R^2 accordingly
this->R = radius;
this->R2 = this->R * this->R;
}
/* -------------------------------------------------------------------------- */
-inline Real BaseWeightFunction::operator()(Real r, const IntegrationPoint &,
- const IntegrationPoint &) {
+inline Real
+BaseWeightFunction::operator()(Real r, const IntegrationPoint & /* q1 */,
+ const IntegrationPoint & /* q2 */) const {
/// initialize the weight
Real w = 0;
/// compute weight for given r
if (r <= this->R) {
Real alpha = (1. - r * r / this->R2);
w = alpha * alpha;
// *weight = 1 - sqrt(r / radius);
}
return w;
}
} // namespace akantu
-#endif /* __AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_HH__ */
+#endif /* AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/neighborhood_base.cc b/src/model/common/non_local_toolbox/neighborhood_base.cc
index 500358f29..f69b520fc 100644
--- a/src/model/common/non_local_toolbox/neighborhood_base.cc
+++ b/src/model/common/non_local_toolbox/neighborhood_base.cc
@@ -1,300 +1,304 @@
/**
* @file neighborhood_base.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Implementation of generic neighborhood base
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "grid_synchronizer.hh"
#include "mesh_accessor.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NeighborhoodBase::NeighborhoodBase(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), model(model), neighborhood_radius(0.),
spatial_grid(nullptr), is_creating_grid(false),
grid_synchronizer(nullptr), quad_coordinates(quad_coordinates),
spatial_dimension(this->model.getMesh().getSpatialDimension()) {
AKANTU_DEBUG_IN();
this->registerDataAccessor(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NeighborhoodBase::~NeighborhoodBase() = default;
/* -------------------------------------------------------------------------- */
// void NeighborhoodBase::createSynchronizerRegistry(
// DataAccessor<Element> * data_accessor) {
// this->synch_registry = new SynchronizerRegistry(*data_accessor);
// }
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::initNeighborhood() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Creating the grid");
this->createGrid();
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------- */
void NeighborhoodBase::createGrid() {
AKANTU_DEBUG_IN();
const Real safety_factor = 1.2; // for the cell grid spacing
Mesh & mesh = this->model.getMesh();
const auto & lower_bounds = mesh.getLocalLowerBounds();
const auto & upper_bounds = mesh.getLocalUpperBounds();
Vector<Real> center = 0.5 * (upper_bounds + lower_bounds);
Vector<Real> spacing(spatial_dimension,
this->neighborhood_radius * safety_factor);
spatial_grid = std::make_unique<SpatialGrid<IntegrationPoint>>(
spatial_dimension, spacing, center);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::updatePairList() {
AKANTU_DEBUG_IN();
//// loop over all quads -> all cells
for (auto && cell_id : *spatial_grid) {
AKANTU_DEBUG_INFO("Looping on next cell");
for (auto && q1 : spatial_grid->getCell(cell_id)) {
- if (q1.ghost_type == _ghost)
+ if (q1.ghost_type == _ghost) {
break;
+ }
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
auto q1_coords = Vector<Real>(coords_type_1_it[q1.global_num]);
AKANTU_DEBUG_INFO("Current quadrature point in this cell: " << q1);
auto cell_id = spatial_grid->getCellID(q1_coords);
/// loop over all the neighboring cells of the current quad
for (auto && neighbor_cell : cell_id.neighbors()) {
// loop over the quadrature point in the current neighboring cell
for (auto && q2 : spatial_grid->getCell(neighbor_cell)) {
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
auto q2_coords = Vector<Real>(coords_type_2_it[q2.global_num]);
Real distance = q1_coords.distance(q2_coords);
if (distance <= this->neighborhood_radius + Math::getTolerance() &&
(q2.ghost_type == _ghost ||
(q2.ghost_type == _not_ghost &&
q1.global_num <= q2.global_num))) { // storing only half lists
pair_list[q2.ghost_type].push_back(std::make_pair(q1, q2));
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::savePairs(const std::string & filename) const {
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
std::ofstream pout;
pout.open(sstr.str().c_str());
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
const auto & q1 = pair.first;
const auto & q2 = pair.second;
pout << q1 << " " << q2 << " " << std::endl;
}
}
pout.close();
- if (comm.getNbProc() != 1)
+ if (comm.getNbProc() != 1) {
return;
+ }
Mesh mesh_out(spatial_dimension);
MeshAccessor mesh_accessor(mesh_out);
auto & connectivity = mesh_accessor.getConnectivity(_segment_2);
auto & tag = mesh_accessor.getData<UInt>("tag_1", _segment_2);
auto & nodes = mesh_accessor.getNodes();
std::map<IntegrationPoint, UInt> quad_to_nodes;
UInt node = 0;
- IntegrationPoint q1, q2;
+ IntegrationPoint q1;
+ IntegrationPoint q2;
bool inserted;
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
std::tie(q1, q2) = pair;
auto add_node = [&](auto && q) {
std::tie(std::ignore, inserted) =
quad_to_nodes.insert(std::make_pair(q, node));
- if (not inserted)
+ if (not inserted) {
return;
+ }
auto coords_it = this->quad_coordinates(q.type, q.ghost_type)
.begin(spatial_dimension);
auto && coords = Vector<Real>(coords_it[q.global_num]);
nodes.push_back(coords);
++node;
};
add_node(q1);
add_node(q2);
}
}
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
std::tie(q1, q2) = pair;
UInt node1 = quad_to_nodes[q1];
UInt node2 = quad_to_nodes[q2];
connectivity.push_back(Vector<UInt>{node1, node2});
tag.push_back(node1 + 1);
if (node1 != node2) {
connectivity.push_back(Vector<UInt>{node2, node1});
tag.push_back(node2 + 1);
}
}
}
mesh_out.write(filename + ".msh");
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::saveNeighborCoords(const std::string & filename) const {
// this function is not optimized and only used for tests on small meshes
// @todo maybe optimize this function for better performance?
IntegrationPoint q2;
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
std::ofstream pout;
pout.open(sstr.str().c_str());
/// loop over all the quads and write the position of their neighbors
for (auto && cell_id : *spatial_grid) {
for (auto && q1 : spatial_grid->getCell(cell_id)) {
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
auto && q1_coords = Vector<Real>(coords_type_1_it[q1.global_num]);
pout << "#neighbors for quad " << q1.global_num << std::endl;
pout << q1_coords << std::endl;
for (auto && ghost_type2 : ghost_types) {
for (auto && pair : pair_list[ghost_type2]) {
if (q1 == pair.first && pair.second != q1) {
q2 = pair.second;
} else if (q1 == pair.second && pair.first != q1) {
q2 = pair.first;
} else {
continue;
}
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
auto && q2_coords = Vector<Real>(coords_type_2_it[q2.global_num]);
pout << q2_coords << std::endl;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = 0;
auto cleanPoint = [&](auto && q) {
if (new_numbering.exists(q.type, q.ghost_type)) {
UInt q_new_el = new_numbering(q.type, q.ghost_type)(q.element);
AKANTU_DEBUG_ASSERT(q_new_el != UInt(-1),
"A local quadrature_point "
<< q
<< " as been removed instead of "
"just being renumbered: " << id);
q.element = q_new_el;
nb_quad = fem.getNbIntegrationPoints(q.type, q.ghost_type);
q.global_num = nb_quad * q.element + q.num_point;
}
};
// Change the pairs in new global numbering
for (auto ghost_type : ghost_types) {
auto & pair_list = this->pair_list.at(ghost_type);
for (auto && pair : pair_list) {
if (pair.first.ghost_type == _ghost) {
cleanPoint(pair.first);
}
if (pair.second.ghost_type == _ghost) {
cleanPoint(pair.second);
}
}
}
this->grid_synchronizer->onElementsRemoved(element_list, new_numbering,
event);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/neighborhood_base.hh b/src/model/common/non_local_toolbox/neighborhood_base.hh
index b00ad49de..acbf88b23 100644
--- a/src/model/common/non_local_toolbox/neighborhood_base.hh
+++ b/src/model/common/non_local_toolbox/neighborhood_base.hh
@@ -1,152 +1,152 @@
/**
* @file neighborhood_base.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Generic neighborhood of quadrature points
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NEIGHBORHOOD_BASE_HH__
-#define __AKANTU_NEIGHBORHOOD_BASE_HH__
+#ifndef AKANTU_NEIGHBORHOOD_BASE_HH_
+#define AKANTU_NEIGHBORHOOD_BASE_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_memory.hh"
#include "data_accessor.hh"
#include "integration_point.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
template <class T> class SpatialGrid;
class GridSynchronizer;
class RemovedElementsEvent;
} // namespace akantu
namespace akantu {
class NeighborhoodBase : protected Memory,
public DataAccessor<Element>,
public SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NeighborhoodBase(Model & model,
const ElementTypeMapArray<Real> & quad_coordinates,
const ID & id = "neighborhood",
const MemoryID & memory_id = 0);
~NeighborhoodBase() override;
using PairList = std::vector<std::pair<IntegrationPoint, IntegrationPoint>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// intialize the neighborhood
virtual void initNeighborhood();
// /// create a synchronizer registry
// void createSynchronizerRegistry(DataAccessor * data_accessor);
/// initialize the material computed parameter
inline void insertIntegrationPoint(const IntegrationPoint & quad,
const Vector<Real> & coords);
/// create the pairs of quadrature points
void updatePairList();
/// save the pairs of quadrature points in a file
void savePairs(const std::string & filename) const;
/// save the coordinates of all neighbors of a quad
void saveNeighborCoords(const std::string & filename) const;
/// create grid synchronizer and exchange ghost cells
virtual void createGridSynchronizer() = 0;
virtual void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) = 0;
/// inherited function from MeshEventHandler
virtual void
onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
protected:
/// create the grid
void createGrid();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
AKANTU_GET_MACRO(Model, model, const Model &);
/// return the object handling synchronizers
- const PairList & getPairLists(const GhostType & type) {
+ const PairList & getPairLists(GhostType type) {
return pair_list[type == _not_ghost ? 0 : 1];
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the model to which the neighborhood belongs
Model & model;
/// Radius of impact: to determine if two quadrature points influence each
/// other
Real neighborhood_radius;
/**
* the pairs of quadrature points
* 0: not ghost to not ghost
* 1: not ghost to ghost
*/
std::array<PairList, 2> pair_list;
/// the regular grid to construct/update the pair lists
std::unique_ptr<SpatialGrid<IntegrationPoint>> spatial_grid;
bool is_creating_grid;
/// the grid synchronizer for parallel computations
std::unique_ptr<GridSynchronizer> grid_synchronizer;
/// the quadrature point positions
const ElementTypeMapArray<Real> & quad_coordinates;
/// the spatial dimension of the problem
const UInt spatial_dimension;
};
} // namespace akantu
#include "neighborhood_base_inline_impl.hh"
-#endif /* __AKANTU_NEIGHBORHOOD_BASE_HH__ */
+#endif /* AKANTU_NEIGHBORHOOD_BASE_HH_ */
diff --git a/src/model/common/non_local_toolbox/neighborhood_base_inline_impl.hh b/src/model/common/non_local_toolbox/neighborhood_base_inline_impl.hh
index 002e78aab..06fab302c 100644
--- a/src/model/common/non_local_toolbox/neighborhood_base_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/neighborhood_base_inline_impl.hh
@@ -1,49 +1,49 @@
/**
* @file neighborhood_base_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Jan 31 2018
*
* @brief Inline implementation of neighborhood base functions
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_grid_dynamic.hh"
#include "neighborhood_base.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_HH__
-#define __AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_HH__
+#ifndef AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_HH_
+#define AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_HH_
namespace akantu {
inline void
NeighborhoodBase::insertIntegrationPoint(const IntegrationPoint & quad,
const Vector<Real> & coords) {
this->spatial_grid->insert(quad, coords);
}
} // namespace akantu
-#endif /* __AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_HH__ */
+#endif /* AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
index fe9f7c8d2..9628dc97e 100644
--- a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
+++ b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
@@ -1,289 +1,290 @@
/**
* @file neighborhood_max_criterion.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Thu Oct 15 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of class NeighborhoodMaxCriterion
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_max_criterion.hh"
#include "grid_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NeighborhoodMaxCriterion::NeighborhoodMaxCriterion(
Model & model, const ElementTypeMapReal & quad_coordinates,
const ID & criterion_id, const ID & id, const MemoryID & memory_id)
: NeighborhoodBase(model, quad_coordinates, id, memory_id),
Parsable(ParserType::_non_local, id),
is_highest("is_highest", id, memory_id),
criterion(criterion_id, id, memory_id) {
AKANTU_DEBUG_IN();
this->registerParam("radius", neighborhood_radius, 100.,
_pat_parsable | _pat_readable, "Non local radius");
Mesh & mesh = this->model.getMesh();
/// allocate the element type map arrays for _not_ghosts: One entry per quad
GhostType ghost_type = _not_ghost;
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type)) {
UInt new_size = this->quad_coordinates(type, ghost_type).size();
this->is_highest.alloc(new_size, 1, type, ghost_type, true);
- this->criterion.alloc(new_size, 1, type, ghost_type, true);
+ this->criterion.alloc(new_size, 1, type, ghost_type, 1.);
}
/// criterion needs allocation also for ghost
ghost_type = _ghost;
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type)) {
UInt new_size = this->quad_coordinates(type, ghost_type).size();
- this->criterion.alloc(new_size, 1, type, ghost_type, true);
+ this->criterion.alloc(new_size, 1, type, ghost_type, 1.);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NeighborhoodMaxCriterion::~NeighborhoodMaxCriterion() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::initNeighborhood() {
AKANTU_DEBUG_IN();
/// parse the input parameter
const Parser & parser = getStaticParser();
const ParserSection & section_neighborhood =
*(parser.getSubSections(ParserType::_neighborhood).first);
this->parseSection(section_neighborhood);
AKANTU_DEBUG_INFO("Creating the grid");
this->createGrid();
/// insert the non-ghost quads into the grid
this->insertAllQuads(_not_ghost);
/// store the number of current ghost elements for each type in the mesh
ElementTypeMap<UInt> nb_ghost_protected;
Mesh & mesh = this->model.getMesh();
for (auto type : mesh.elementTypes(spatial_dimension, _ghost)) {
nb_ghost_protected(mesh.getNbElement(type, _ghost), type, _ghost);
}
/// create the grid synchronizer
this->createGridSynchronizer();
/// insert the ghost quads into the grid
this->insertAllQuads(_ghost);
/// create the pair lists
this->updatePairList();
/// remove the unneccessary ghosts
this->cleanupExtraGhostElements(nb_ghost_protected);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::createGridSynchronizer() {
this->is_creating_grid = true;
std::set<SynchronizationTag> tags;
tags.insert(SynchronizationTag::_nh_criterion);
std::stringstream sstr;
sstr << getID() << ":grid_synchronizer";
this->grid_synchronizer = std::make_unique<GridSynchronizer>(
this->model.getMesh(), *spatial_grid, *this, tags, sstr.str(), 0, false);
this->is_creating_grid = false;
}
/* -------------------------------------------------------------------------- */
-void NeighborhoodMaxCriterion::insertAllQuads(const GhostType & ghost_type) {
+void NeighborhoodMaxCriterion::insertAllQuads(GhostType ghost_type) {
IntegrationPoint q;
q.ghost_type = ghost_type;
Mesh & mesh = this->model.getMesh();
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type)) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_quad =
this->model.getFEEngine().getNbIntegrationPoints(type, ghost_type);
const Array<Real> & quads = this->quad_coordinates(type, ghost_type);
q.type = type;
auto quad = quads.begin(spatial_dimension);
for (UInt e = 0; e < nb_element; ++e) {
q.element = e;
for (UInt nq = 0; nq < nb_quad; ++nq) {
q.num_point = nq;
q.global_num = q.element * nb_quad + nq;
spatial_grid->insert(q, *quad);
++quad;
}
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::findMaxQuads(
std::vector<IntegrationPoint> & max_quads) {
AKANTU_DEBUG_IN();
/// clear the element type maps
- this->is_highest.clear();
- this->criterion.clear();
+ this->is_highest.zero();
+ this->criterion.zero();
/// update the values of the criterion
this->model.updateDataForNonLocalCriterion(criterion);
/// start the exchange the value of the criterion on the ghost elements
this->model.asynchronousSynchronize(SynchronizationTag::_nh_criterion);
/// compare to not-ghost neighbors
checkNeighbors(_not_ghost);
/// finish the exchange
this->model.waitEndSynchronize(SynchronizationTag::_nh_criterion);
/// compare to ghost neighbors
checkNeighbors(_ghost);
/// extract the quads with highest criterion in their neighborhood
IntegrationPoint quad;
quad.ghost_type = _not_ghost;
Mesh & mesh = this->model.getMesh();
for (auto type : mesh.elementTypes(spatial_dimension, _not_ghost)) {
quad.type = type;
UInt nb_quadrature_points =
this->model.getFEEngine().getNbIntegrationPoints(type, _not_ghost);
/// loop over is_highest for the current element type
for (auto data : enumerate(is_highest(type, _not_ghost))) {
const auto & is_highest = std::get<1>(data);
if (is_highest) {
auto q = std::get<0>(data);
/// gauss point has the highest stress in his neighbourhood
quad.element = q / nb_quadrature_points;
quad.global_num = q;
quad.num_point = q % nb_quadrature_points;
max_quads.push_back(quad);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void NeighborhoodMaxCriterion::checkNeighbors(const GhostType & ghost_type2) {
+void NeighborhoodMaxCriterion::checkNeighbors(GhostType ghost_type2) {
AKANTU_DEBUG_IN();
// Compute the weights
for (auto & pair : pair_list[ghost_type2]) {
const auto & lq1 = pair.first;
const auto & lq2 = pair.second;
Array<bool> & has_highest_eq_stress_1 =
is_highest(lq1.type, lq1.ghost_type);
const Array<Real> & criterion_1 = this->criterion(lq1.type, lq1.ghost_type);
const Array<Real> & criterion_2 = this->criterion(lq2.type, lq2.ghost_type);
- if (criterion_1(lq1.global_num) < criterion_2(lq2.global_num))
+ if (criterion_1(lq1.global_num) < criterion_2(lq2.global_num)) {
has_highest_eq_stress_1(lq1.global_num) = false;
- else if (ghost_type2 != _ghost) {
+ } else if (ghost_type2 != _ghost) {
Array<bool> & has_highest_eq_stress_2 =
is_highest(lq2.type, lq2.ghost_type);
has_highest_eq_stress_2(lq2.global_num) = false;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::cleanupExtraGhostElements(
const ElementTypeMap<UInt> & nb_ghost_protected) {
Mesh & mesh = this->model.getMesh();
/// create remove elements event
RemovedElementsEvent remove_elem(mesh);
/// create set of ghosts to keep
std::set<Element> relevant_ghost_elements;
for (auto & pair : pair_list[_ghost]) {
const auto & q2 = pair.second;
relevant_ghost_elements.insert(q2);
}
Array<Element> ghosts_to_erase(0);
Element element;
element.ghost_type = _ghost;
auto end = relevant_ghost_elements.end();
- for (auto & type : mesh.elementTypes(spatial_dimension, _ghost)) {
+ for (const auto & type : mesh.elementTypes(spatial_dimension, _ghost)) {
element.type = type;
UInt nb_ghost_elem = mesh.getNbElement(type, _ghost);
UInt nb_ghost_elem_protected = 0;
try {
nb_ghost_elem_protected = nb_ghost_protected(type, _ghost);
} catch (...) {
}
- if (!remove_elem.getNewNumbering().exists(type, _ghost))
+ if (!remove_elem.getNewNumbering().exists(type, _ghost)) {
remove_elem.getNewNumbering().alloc(nb_ghost_elem, 1, type, _ghost);
- else
+ } else {
remove_elem.getNewNumbering(type, _ghost).resize(nb_ghost_elem);
+ }
Array<UInt> & new_numbering = remove_elem.getNewNumbering(type, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
element.element = g;
if (element.element >= nb_ghost_elem_protected &&
relevant_ghost_elements.find(element) == end) {
ghosts_to_erase.push_back(element);
new_numbering(element.element) = UInt(-1);
}
}
/// renumber remaining ghosts
UInt ng = 0;
for (UInt g = 0; g < nb_ghost_elem; ++g) {
if (new_numbering(g) != UInt(-1)) {
new_numbering(g) = ng;
++ng;
}
}
}
mesh.sendEvent(remove_elem);
this->onElementsRemoved(ghosts_to_erase, remove_elem.getNewNumbering(),
remove_elem);
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
index da23be198..377e89cfb 100644
--- a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
+++ b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
@@ -1,116 +1,116 @@
/**
* @file neighborhood_max_criterion.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Neighborhood to find a maximum value in a neighborhood
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__
-#define __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__
+#ifndef AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH_
+#define AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH_
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class NeighborhoodMaxCriterion : public NeighborhoodBase, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NeighborhoodMaxCriterion(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & criterion_id,
const ID & id = "neighborhood_max_criterion",
const MemoryID & memory_id = 0);
~NeighborhoodMaxCriterion() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the neighborhood
void initNeighborhood() override;
/// create grid synchronizer and exchange ghost cells
void createGridSynchronizer() override;
/// find the quads which have the maximum criterion in their neighborhood
void findMaxQuads(std::vector<IntegrationPoint> & max_quads);
protected:
/// remove unneccessary ghost elements
void
cleanupExtraGhostElements(const ElementTypeMap<UInt> & nb_ghost_protected);
/// insert the quadrature points in the grid
- void insertAllQuads(const GhostType & ghost_type);
+ void insertAllQuads(GhostType ghost_type);
/// compare criterion with neighbors
- void checkNeighbors(const GhostType & ghost_type);
+ void checkNeighbors(GhostType ghost_type);
/* --------------------------------------------------------------------------
*/
/* DataAccessor inherited members */
/* --------------------------------------------------------------------------
*/
public:
virtual inline UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag);
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// a boolean to store the information if a quad has the max
/// criterion in the neighborhood
ElementTypeMapArray<bool> is_highest;
/// an element type map to store the flattened internal of the criterion
ElementTypeMapReal criterion;
};
} // namespace akantu
#include "neighborhood_max_criterion_inline_impl.hh"
-#endif /* __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__ */
+#endif /* AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH_ */
diff --git a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.hh b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.hh
index e4c145931..15feef9d8 100644
--- a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.hh
@@ -1,81 +1,81 @@
/**
* @file neighborhood_max_criterion_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Implementation of inline functions for class NeighborhoodMaxCriterion
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model.hh"
#include "neighborhood_max_criterion.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_HH__
-#define __AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_HH__
+#ifndef AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_HH_
+#define AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt
NeighborhoodMaxCriterion::getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
UInt nb_quadrature_points = this->model.getNbIntegrationPoints(elements);
UInt size = 0;
if (tag == SynchronizationTag::_nh_criterion) {
size += sizeof(Real) * nb_quadrature_points;
}
return size;
}
/* -------------------------------------------------------------------------- */
inline void
NeighborhoodMaxCriterion::packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
if (tag == SynchronizationTag::_nh_criterion) {
- this->packElementalDataHelper(criterion, buffer, elements, true,
- this->model.getFEEngine());
+ NeighborhoodMaxCriterion::packElementalDataHelper(
+ criterion, buffer, elements, true, this->model.getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
inline void
NeighborhoodMaxCriterion::unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
if (tag == SynchronizationTag::_nh_criterion) {
- this->unpackElementalDataHelper(criterion, buffer, elements, true,
- this->model.getFEEngine());
+ NeighborhoodMaxCriterion::unpackElementalDataHelper(
+ criterion, buffer, elements, true, this->model.getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_HH__ */
+#endif /* AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager.cc b/src/model/common/non_local_toolbox/non_local_manager.cc
index 0ba381712..925234458 100644
--- a/src/model/common/non_local_toolbox/non_local_manager.cc
+++ b/src/model/common/non_local_toolbox/non_local_manager.cc
@@ -1,641 +1,654 @@
/**
* @file non_local_manager.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Apr 13 2012
* @date last modification: Tue Jan 16 2018
*
* @brief Implementation of non-local manager
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_local_manager.hh"
#include "grid_synchronizer.hh"
#include "model.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLocalManager::NonLocalManager(Model & model,
NonLocalManagerCallback & callback,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), Parsable(ParserType::_neighborhoods, id),
spatial_dimension(model.getMesh().getSpatialDimension()), model(model),
integration_points_positions("integration_points_positions", id,
memory_id),
volumes("volumes", id, memory_id), compute_stress_calls(0),
dummy_registry(nullptr), dummy_grid(nullptr) {
/// parse the neighborhood information from the input file
const Parser & parser = getStaticParser();
/// iterate over all the non-local sections and store them in a map
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
weight_sect = parser.getSubSections(ParserType::_non_local);
Parser::const_section_iterator it = weight_sect.first;
for (; it != weight_sect.second; ++it) {
const ParserSection & section = *it;
ID name = section.getName();
this->weight_function_types[name] = section;
}
this->callback = &callback;
}
/* -------------------------------------------------------------------------- */
NonLocalManager::~NonLocalManager() = default;
/* -------------------------------------------------------------------------- */
void NonLocalManager::initialize() {
volumes.initialize(this->model.getFEEngine(),
_spatial_dimension = spatial_dimension);
AKANTU_DEBUG_ASSERT(this->callback,
"A callback should be registered prior to this call");
this->callback->insertIntegrationPointsInNeighborhoods(_not_ghost);
auto & mesh = this->model.getMesh();
mesh.registerEventHandler(*this, _ehp_non_local_manager);
/// store the number of current ghost elements for each type in the mesh
// ElementTypeMap<UInt> nb_ghost_protected;
// for (auto type : mesh.elementTypes(spatial_dimension, _ghost))
// nb_ghost_protected(mesh.getNbElement(type, _ghost), type, _ghost);
/// exchange the missing ghosts for the non-local neighborhoods
this->createNeighborhoodSynchronizers();
/// insert the ghost quadrature points of the non-local materials into the
/// non-local neighborhoods
this->callback->insertIntegrationPointsInNeighborhoods(_ghost);
FEEngine & fee = this->model.getFEEngine();
this->updatePairLists();
/// cleanup the unneccessary ghost elements
this->cleanupExtraGhostElements(); // nb_ghost_protected);
this->callback->initializeNonLocal();
this->setJacobians(fee, _ek_regular);
this->initNonLocalVariables();
this->computeWeights();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::setJacobians(const FEEngine & fe_engine,
- const ElementKind & kind) {
+ ElementKind kind) {
Mesh & mesh = this->model.getMesh();
for (auto ghost_type : ghost_types) {
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type, kind)) {
jacobians(type, ghost_type) =
&fe_engine.getIntegratorInterface().getJacobians(type, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::createNeighborhood(const ID & weight_func,
const ID & neighborhood_id) {
AKANTU_DEBUG_IN();
auto weight_func_it = this->weight_function_types.find(weight_func);
AKANTU_DEBUG_ASSERT(weight_func_it != weight_function_types.end(),
"No info found in the input file for the weight_function "
<< weight_func << " in the neighborhood "
<< neighborhood_id);
const ParserSection & section = weight_func_it->second;
const ID weight_func_type = section.getOption();
/// create new neighborhood for given ID
std::stringstream sstr;
sstr << id << ":neighborhood:" << neighborhood_id;
- if (weight_func_type == "base_wf")
+ if (weight_func_type == "base_wf") {
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<BaseWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
#if defined(AKANTU_DAMAGE_NON_LOCAL)
- else if (weight_func_type == "remove_wf")
+ } else if (weight_func_type == "remove_wf") {
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<RemoveDamagedWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
- else if (weight_func_type == "stress_wf")
+ } else if (weight_func_type == "stress_wf") {
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<StressBasedWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
- else if (weight_func_type == "damage_wf")
+ } else if (weight_func_type == "damage_wf") {
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<DamagedWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
#endif
- else
+ } else {
AKANTU_EXCEPTION("error in weight function type provided in material file");
+ }
neighborhoods[neighborhood_id]->parseSection(section);
neighborhoods[neighborhood_id]->initNeighborhood();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::createNeighborhoodSynchronizers() {
/// exchange all the neighborhood IDs, so that every proc knows how many
/// neighborhoods exist globally
/// First: Compute locally the maximum ID size
UInt max_id_size = 0;
UInt current_size = 0;
NeighborhoodMap::const_iterator it;
for (it = neighborhoods.begin(); it != neighborhoods.end(); ++it) {
current_size = it->first.size();
- if (current_size > max_id_size)
+ if (current_size > max_id_size) {
max_id_size = current_size;
+ }
}
/// get the global maximum ID size on each proc
const Communicator & static_communicator = model.getMesh().getCommunicator();
static_communicator.allReduce(max_id_size, SynchronizerOperation::_max);
/// get the rank for this proc and the total nb proc
UInt prank = static_communicator.whoAmI();
UInt psize = static_communicator.getNbProc();
/// exchange the number of neighborhoods on each proc
Array<Int> nb_neighborhoods_per_proc(psize);
nb_neighborhoods_per_proc(prank) = neighborhoods.size();
static_communicator.allGather(nb_neighborhoods_per_proc);
/// compute the total number of neighborhoods
UInt nb_neighborhoods_global = std::accumulate(
nb_neighborhoods_per_proc.begin(), nb_neighborhoods_per_proc.end(), 0);
/// allocate an array of chars to store the names of all neighborhoods
Array<char> buffer(nb_neighborhoods_global, max_id_size);
/// starting index on this proc
UInt starting_index =
std::accumulate(nb_neighborhoods_per_proc.begin(),
nb_neighborhoods_per_proc.begin() + prank, 0);
it = neighborhoods.begin();
/// store the names of local neighborhoods in the buffer
for (UInt i = 0; i < neighborhoods.size(); ++i, ++it) {
UInt c = 0;
- for (; c < it->first.size(); ++c)
+ for (; c < it->first.size(); ++c) {
buffer(i + starting_index, c) = it->first[c];
+ }
- for (; c < max_id_size; ++c)
+ for (; c < max_id_size; ++c) {
buffer(i + starting_index, c) = char(0);
+ }
}
/// store the nb of data to send in the all gather
Array<Int> buffer_size(nb_neighborhoods_per_proc);
buffer_size *= max_id_size;
/// exchange the names of all the neighborhoods with all procs
static_communicator.allGatherV(buffer, buffer_size);
for (UInt i = 0; i < nb_neighborhoods_global; ++i) {
std::stringstream neighborhood_id;
for (UInt c = 0; c < max_id_size; ++c) {
- if (buffer(i, c) == char(0))
+ if (buffer(i, c) == char(0)) {
break;
+ }
neighborhood_id << buffer(i, c);
}
global_neighborhoods.insert(neighborhood_id.str());
}
/// this proc does not know all the neighborhoods -> create dummy
/// grid so that this proc can participate in the all gather for
/// detecting the overlap of neighborhoods this proc doesn't know
Vector<Real> grid_center(this->spatial_dimension,
std::numeric_limits<Real>::max());
Vector<Real> spacing(this->spatial_dimension, 0.);
dummy_grid = std::make_unique<SpatialGrid<IntegrationPoint>>(
this->spatial_dimension, spacing, grid_center);
- for (auto & neighborhood_id : global_neighborhoods) {
+ for (const auto & neighborhood_id : global_neighborhoods) {
it = neighborhoods.find(neighborhood_id);
if (it != neighborhoods.end()) {
it->second->createGridSynchronizer();
} else {
dummy_synchronizers[neighborhood_id] = std::make_unique<GridSynchronizer>(
this->model.getMesh(), *dummy_grid,
std::string(this->id + ":" + neighborhood_id + ":grid_synchronizer"),
this->memory_id, false);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) {
- for (auto & neighborhood_id : global_neighborhoods) {
+ for (const auto & neighborhood_id : global_neighborhoods) {
auto it = neighborhoods.find(neighborhood_id);
if (it != neighborhoods.end()) {
it->second->synchronize(data_accessor, tag);
} else {
auto synchronizer_it = dummy_synchronizers.find(neighborhood_id);
- if (synchronizer_it == dummy_synchronizers.end())
+ if (synchronizer_it == dummy_synchronizers.end()) {
continue;
+ }
synchronizer_it->second->synchronizeOnce(data_accessor, tag);
}
}
}
/* -------------------------------------------------------------------------- */
-void NonLocalManager::averageInternals(const GhostType & ghost_type) {
+void NonLocalManager::averageInternals(GhostType ghost_type) {
/// update the weights of the weight function
- if (ghost_type == _not_ghost)
+ if (ghost_type == _not_ghost) {
this->computeWeights();
+ }
/// loop over all neighborhoods and compute the non-local variables
for (auto & neighborhood : neighborhoods) {
/// loop over all the non-local variables of the given neighborhood
for (auto & non_local_variable : non_local_variables) {
NonLocalVariable & non_local_var = *non_local_variable.second;
neighborhood.second->weightedAverageOnNeighbours(
non_local_var.local, non_local_var.non_local,
non_local_var.nb_component, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::computeWeights() {
AKANTU_DEBUG_IN();
this->updateWeightFunctionInternals();
- this->volumes.clear();
+ this->volumes.zero();
for (const auto & global_neighborhood : global_neighborhoods) {
auto it = neighborhoods.find(global_neighborhood);
- if (it != neighborhoods.end())
+ if (it != neighborhoods.end()) {
it->second->updateWeights();
- else {
+ } else {
dummy_synchronizers[global_neighborhood]->synchronize(
dummy_accessor, SynchronizationTag::_mnl_weight);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::updatePairLists() {
AKANTU_DEBUG_IN();
integration_points_positions.initialize(
this->model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension);
/// compute the position of the quadrature points
this->model.getFEEngine().computeIntegrationPointsCoordinates(
integration_points_positions);
- for (auto & pair : neighborhoods)
+ for (auto & pair : neighborhoods) {
pair.second->updatePairList();
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::registerNonLocalVariable(const ID & variable_name,
const ID & nl_variable_name,
UInt nb_component) {
AKANTU_DEBUG_IN();
auto non_local_variable_it = non_local_variables.find(variable_name);
- if (non_local_variable_it == non_local_variables.end())
+ if (non_local_variable_it == non_local_variables.end()) {
non_local_variables[nl_variable_name] = std::make_unique<NonLocalVariable>(
variable_name, nl_variable_name, this->id, nb_component);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementTypeMapReal &
NonLocalManager::registerWeightFunctionInternal(const ID & field_name) {
AKANTU_DEBUG_IN();
auto it = this->weight_function_internals.find(field_name);
if (it == weight_function_internals.end()) {
weight_function_internals[field_name] =
std::make_unique<ElementTypeMapReal>(field_name, this->id,
this->memory_id);
}
AKANTU_DEBUG_OUT();
return *(weight_function_internals[field_name]);
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::updateWeightFunctionInternals() {
for (auto & pair : this->weight_function_internals) {
auto & internals = *pair.second;
- internals.clear();
- for (auto ghost_type : ghost_types)
+ internals.zero();
+ for (auto ghost_type : ghost_types) {
this->callback->updateLocalInternal(internals, ghost_type, _ek_regular);
+ }
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::initNonLocalVariables() {
/// loop over all the non-local variables
for (auto & pair : non_local_variables) {
auto & variable = *pair.second;
variable.non_local.initialize(this->model.getFEEngine(),
_nb_component = variable.nb_component,
_spatial_dimension = spatial_dimension);
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::computeAllNonLocalStresses() {
/// update the flattened version of the internals
for (auto & pair : non_local_variables) {
auto & variable = *pair.second;
- variable.local.clear();
- variable.non_local.clear();
+ variable.local.zero();
+ variable.non_local.zero();
for (auto ghost_type : ghost_types) {
this->callback->updateLocalInternal(variable.local, ghost_type,
_ek_regular);
}
}
- this->volumes.clear();
+ this->volumes.zero();
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
neighborhood.asynchronousSynchronize(SynchronizationTag::_mnl_for_average);
}
this->averageInternals(_not_ghost);
AKANTU_DEBUG_INFO("Wait distant non local stresses");
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
neighborhood.waitEndSynchronize(SynchronizationTag::_mnl_for_average);
}
this->averageInternals(_ghost);
/// copy the results in the materials
for (auto & pair : non_local_variables) {
auto & variable = *pair.second;
for (auto ghost_type : ghost_types) {
this->callback->updateNonLocalInternal(variable.non_local, ghost_type,
_ek_regular);
}
}
this->callback->computeNonLocalStresses(_not_ghost);
++this->compute_stress_calls;
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::cleanupExtraGhostElements() {
// ElementTypeMap<UInt> & nb_ghost_protected) {
using ElementSet = std::set<Element>;
ElementSet relevant_ghost_elements;
/// loop over all the neighborhoods and get their protected ghosts
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
ElementSet to_keep_per_neighborhood;
neighborhood.getRelevantGhostElements(to_keep_per_neighborhood);
- relevant_ghost_elements.insert(to_keep_per_neighborhood.begin(), to_keep_per_neighborhood.end());
+ relevant_ghost_elements.insert(to_keep_per_neighborhood.begin(),
+ to_keep_per_neighborhood.end());
}
- for (auto & pair : neighborhoods) {
+ for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
neighborhood.cleanupExtraGhostElements(relevant_ghost_elements);
}
// /// remove all unneccessary ghosts from the mesh
// /// Create list of element to remove and new numbering for element to keep
// Mesh & mesh = this->model.getMesh();
// ElementSet ghost_to_erase;
// RemovedElementsEvent remove_elem(mesh);
// auto & new_numberings = remove_elem.getNewNumbering();
// Element element;
// element.ghost_type = _ghost;
// for (auto & type : mesh.elementTypes(spatial_dimension, _ghost)) {
// element.type = type;
// UInt nb_ghost_elem = mesh.getNbElement(type, _ghost);
// // UInt nb_ghost_elem_protected = 0;
// // try {
// // nb_ghost_elem_protected = nb_ghost_protected(type, _ghost);
// // } catch (...) {
// // }
// if (!new_numberings.exists(type, _ghost))
// new_numberings.alloc(nb_ghost_elem, 1, type, _ghost);
// else
// new_numberings(type, _ghost).resize(nb_ghost_elem);
// Array<UInt> & new_numbering = new_numberings(type, _ghost);
// for (UInt g = 0; g < nb_ghost_elem; ++g) {
// element.element = g;
// if (element.element >= nb_ghost_elem_protected &&
// relevant_ghost_elements.find(element) ==
// relevant_ghost_elements.end()) {
// remove_elem.getList().push_back(element);
// new_numbering(element.element) = UInt(-1);
// }
// }
// /// renumber remaining ghosts
// UInt ng = 0;
// for (UInt g = 0; g < nb_ghost_elem; ++g) {
// if (new_numbering(g) != UInt(-1)) {
// new_numbering(g) = ng;
// ++ng;
// }
// }
// }
// for (auto & type : mesh.elementTypes(spatial_dimension, _not_ghost)) {
// UInt nb_elem = mesh.getNbElement(type, _not_ghost);
// if (!new_numberings.exists(type, _not_ghost))
// new_numberings.alloc(nb_elem, 1, type, _not_ghost);
// Array<UInt> & new_numbering = new_numberings(type, _not_ghost);
// for (UInt e = 0; e < nb_elem; ++e) {
// new_numbering(e) = e;
// }
// }
// mesh.sendEvent(remove_elem);
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
FEEngine & fee = this->model.getFEEngine();
- this->removeIntegrationPointsFromMap(
+ NonLocalManager::removeIntegrationPointsFromMap(
event.getNewNumbering(), spatial_dimension, integration_points_positions,
fee, _ek_regular);
- this->removeIntegrationPointsFromMap(event.getNewNumbering(), 1, volumes, fee,
- _ek_regular);
+ NonLocalManager::removeIntegrationPointsFromMap(event.getNewNumbering(), 1,
+ volumes, fee, _ek_regular);
/// loop over all the neighborhoods and call onElementsRemoved
auto global_neighborhood_it = global_neighborhoods.begin();
NeighborhoodMap::iterator it;
for (; global_neighborhood_it != global_neighborhoods.end();
++global_neighborhood_it) {
it = neighborhoods.find(*global_neighborhood_it);
- if (it != neighborhoods.end())
+ if (it != neighborhoods.end()) {
it->second->onElementsRemoved(element_list, new_numbering, event);
- else
+ } else {
dummy_synchronizers[*global_neighborhood_it]->onElementsRemoved(
element_list, new_numbering, event);
+ }
}
}
/* -------------------------------------------------------------------------- */
-void NonLocalManager::onElementsAdded(const Array<Element> &,
- const NewElementsEvent &) {
+void NonLocalManager::onElementsAdded(const Array<Element> & /*unused*/,
+ const NewElementsEvent & /*unused*/) {
this->resizeElementTypeMap(1, volumes, model.getFEEngine());
this->resizeElementTypeMap(spatial_dimension, integration_points_positions,
model.getFEEngine());
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::resizeElementTypeMap(UInt nb_component,
ElementTypeMapReal & element_map,
const FEEngine & fee,
const ElementKind el_kind) {
Mesh & mesh = this->model.getMesh();
for (auto gt : ghost_types) {
for (auto type : mesh.elementTypes(spatial_dimension, gt, el_kind)) {
UInt nb_element = mesh.getNbElement(type, gt);
UInt nb_quads = fee.getNbIntegrationPoints(type, gt);
- if (!element_map.exists(type, gt))
+ if (!element_map.exists(type, gt)) {
element_map.alloc(nb_element * nb_quads, nb_component, type, gt);
- else
+ } else {
element_map(type, gt).resize(nb_element * nb_quads);
+ }
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::removeIntegrationPointsFromMap(
const ElementTypeMapArray<UInt> & new_numbering, UInt nb_component,
ElementTypeMapReal & element_map, const FEEngine & fee,
const ElementKind el_kind) {
for (auto gt : ghost_types) {
for (auto type : new_numbering.elementTypes(_all_dimensions, gt, el_kind)) {
if (element_map.exists(type, gt)) {
const Array<UInt> & renumbering = new_numbering(type, gt);
Array<Real> & vect = element_map(type, gt);
UInt nb_quad_per_elem = fee.getNbIntegrationPoints(type, gt);
Array<Real> tmp(renumbering.size() * nb_quad_per_elem, nb_component);
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created or disappeared in "
<< vect.getID() << "(" << vect.size() << "!=" << tmp.size()
<< ") "
"!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
memcpy(tmp.storage() + new_i * nb_component * nb_quad_per_elem,
vect.storage() + i * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem * sizeof(Real));
++new_size;
}
}
tmp.resize(new_size * nb_quad_per_elem);
vect.copy(tmp);
}
}
}
}
/* -------------------------------------------------------------------------- */
UInt NonLocalManager::getNbData(const Array<Element> & elements,
const ID & id) const {
UInt size = 0;
UInt nb_quadrature_points = this->model.getNbIntegrationPoints(elements);
auto it = non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
size += it->second->nb_component * sizeof(Real) * nb_quadrature_points;
return size;
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & id) const {
auto it = non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
DataAccessor<Element>::packElementalDataHelper<Real>(
it->second->local, buffer, elements, true, this->model.getFEEngine());
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & id) const {
auto it = non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
DataAccessor<Element>::unpackElementalDataHelper<Real>(
it->second->local, buffer, elements, true, this->model.getFEEngine());
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/non_local_manager.hh b/src/model/common/non_local_toolbox/non_local_manager.hh
index 60a3b2173..d9fbf3a7c 100644
--- a/src/model/common/non_local_toolbox/non_local_manager.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager.hh
@@ -1,284 +1,286 @@
/**
* @file non_local_manager.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Classes that manages all the non-local neighborhoods
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
#include "data_accessor.hh"
#include "mesh_events.hh"
#include "non_local_manager_callback.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LOCAL_MANAGER_HH__
-#define __AKANTU_NON_LOCAL_MANAGER_HH__
+#ifndef AKANTU_NON_LOCAL_MANAGER_HH_
+#define AKANTU_NON_LOCAL_MANAGER_HH_
namespace akantu {
class Model;
class NonLocalNeighborhoodBase;
class GridSynchronizer;
class SynchronizerRegistry;
class IntegrationPoint;
template <typename T> class SpatialGrid;
class FEEngine;
} // namespace akantu
namespace akantu {
class NonLocalManager : protected Memory,
public MeshEventHandler,
public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalManager(Model & model, NonLocalManagerCallback & callback,
const ID & id = "non_local_manager",
const MemoryID & memory_id = 0);
~NonLocalManager() override;
using NeighborhoodMap =
std::map<ID, std::unique_ptr<NonLocalNeighborhoodBase>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ----------------------------------------------------------------------- */
public:
/// register a new internal needed for the weight computations
ElementTypeMapReal & registerWeightFunctionInternal(const ID & field_name);
/// register a non-local variable
void registerNonLocalVariable(const ID & variable_name,
const ID & nl_variable_name, UInt nb_component);
/// register non-local neighborhood
inline void registerNeighborhood(const ID & neighborhood,
const ID & weight_func_id);
// void registerNonLocalManagerCallback(NonLocalManagerCallback & callback);
/// average the internals and compute the non-local stresses
virtual void computeAllNonLocalStresses();
/// initialize the non-local manager: compute pair lists and weights for all
/// neighborhoods
virtual void initialize();
/// synchronize once on a given tag using the neighborhoods synchronizer
void synchronize(DataAccessor<Element> & data_accessor,
- const SynchronizationTag &);
+ const SynchronizationTag & /*tag*/);
protected:
/// create the grid synchronizers for each neighborhood
void createNeighborhoodSynchronizers();
/// compute the weights in each neighborhood for non-local averaging
void computeWeights();
/// compute the weights in each neighborhood for non-local averaging
void updatePairLists();
/// average the non-local variables
- void averageInternals(const GhostType & ghost_type = _not_ghost);
+ void averageInternals(GhostType ghost_type = _not_ghost);
/// update the flattened version of the weight function internals
void updateWeightFunctionInternals();
protected:
/// create a new neighborhood for a given domain ID
void createNeighborhood(const ID & weight_func, const ID & neighborhood);
/// set the values of the jacobians
- void setJacobians(const FEEngine & fe_engine, const ElementKind & kind);
+ void setJacobians(const FEEngine & fe_engine, ElementKind kind);
/// allocation of eelment type maps
// void initElementTypeMap(UInt nb_component,
// ElementTypeMapReal & element_map,
// const FEEngine & fe_engine,
// const ElementKind el_kind = _ek_regular);
/// resizing of element type maps
void resizeElementTypeMap(UInt nb_component, ElementTypeMapReal & element_map,
const FEEngine & fee,
- const ElementKind el_kind = _ek_regular);
+ ElementKind el_kind = _ek_regular);
/// remove integration points from element type maps
- void removeIntegrationPointsFromMap(
+ static void removeIntegrationPointsFromMap(
const ElementTypeMapArray<UInt> & new_numbering, UInt nb_component,
ElementTypeMapReal & element_map, const FEEngine & fee,
- const ElementKind el_kind = _ek_regular);
+ ElementKind el_kind = _ek_regular);
/// allocate the non-local variables
void initNonLocalVariables();
/// cleanup unneccessary ghosts
void
cleanupExtraGhostElements(); // ElementTypeMap<UInt> & nb_ghost_protected);
/* ------------------------------------------------------------------------ */
/* DataAccessor kind of interface */
/* ------------------------------------------------------------------------ */
public:
/// get Nb data for synchronization in parallel
UInt getNbData(const Array<Element> & elements, const ID & id) const;
/// pack data for synchronization in parallel
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const ID & id) const;
/// unpack data for synchronization in parallel
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const ID & id) const;
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
AKANTU_GET_MACRO(Model, model, const Model &);
AKANTU_GET_MACRO_NOT_CONST(Model, model, Model &);
AKANTU_GET_MACRO_NOT_CONST(Volumes, volumes, ElementTypeMapReal &)
AKANTU_GET_MACRO(NbStressCalls, compute_stress_calls, UInt);
/// return the fem object associated with a provided name
inline NonLocalNeighborhoodBase & getNeighborhood(const ID & name) const;
- inline const Array<Real> & getJacobians(const ElementType & type,
- const GhostType & ghost_type) {
+ inline const Array<Real> & getJacobians(ElementType type,
+ GhostType ghost_type) {
return *jacobians(type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the spatial dimension
const UInt spatial_dimension;
protected:
/// the non-local neighborhoods present
NeighborhoodMap neighborhoods;
/// list of all the non-local materials in the model
// std::vector<ID> non_local_materials;
struct NonLocalVariable {
NonLocalVariable(const ID & variable_name, const ID & nl_variable_name,
const ID & id, UInt nb_component)
: local(variable_name, id, 0), non_local(nl_variable_name, id, 0),
nb_component(nb_component) {}
ElementTypeMapReal local;
ElementTypeMapReal non_local;
UInt nb_component;
};
/// the non-local variables associated to a certain neighborhood
std::map<ID, std::unique_ptr<NonLocalVariable>> non_local_variables;
/// reference to the model
Model & model;
/// jacobians for all the elements in the mesh
ElementTypeMap<const Array<Real> *> jacobians;
/// store the position of the quadrature points
ElementTypeMapReal integration_points_positions;
/// store the volume of each quadrature point for the non-local weight
/// normalization
ElementTypeMapReal volumes;
/// counter for computeStress calls
UInt compute_stress_calls;
/// map to store weight function types from input file
std::map<ID, ParserSection> weight_function_types;
/// map to store the internals needed by the weight functions
std::map<ID, std::unique_ptr<ElementTypeMapReal>> weight_function_internals;
/* --------------------------------------------------------------------------
*/
/// the following are members needed to make this processor participate in the
/// grid creation of neighborhoods he doesn't own as a member. For details see
/// createGridSynchronizers function
/// synchronizer registry for dummy grid synchronizers
std::unique_ptr<SynchronizerRegistry> dummy_registry;
/// map of dummy synchronizers
std::map<ID, std::unique_ptr<GridSynchronizer>> dummy_synchronizers;
/// dummy spatial grid
std::unique_ptr<SpatialGrid<IntegrationPoint>> dummy_grid;
/// create a set of all neighborhoods present in the simulation
std::set<ID> global_neighborhoods;
class DummyDataAccessor : public DataAccessor<Element> {
public:
- inline UInt getNbData(const Array<Element> &,
- const SynchronizationTag &) const override {
+ inline UInt getNbData(const Array<Element> & /*elements*/,
+ const SynchronizationTag & /*tag*/) const override {
return 0;
};
- inline void packData(CommunicationBuffer &, const Array<Element> &,
- const SynchronizationTag &) const override{};
+ inline void packData(CommunicationBuffer & /*buffer*/,
+ const Array<Element> & /*element*/,
+ const SynchronizationTag & /*tag*/) const override{};
- inline void unpackData(CommunicationBuffer &, const Array<Element> &,
- const SynchronizationTag &) override{};
+ inline void unpackData(CommunicationBuffer & /*buffer*/,
+ const Array<Element> & /*element*/,
+ const SynchronizationTag & /*tag*/) override{};
};
DummyDataAccessor dummy_accessor;
/* ------------------------------------------------------------------------ */
NonLocalManagerCallback * callback;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "non_local_manager_inline_impl.hh"
-#endif /* __AKANTU_NON_LOCAL_MANAGER_HH__ */
+#endif /* AKANTU_NON_LOCAL_MANAGER_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager_callback.hh b/src/model/common/non_local_toolbox/non_local_manager_callback.hh
index d7d36499b..ac23221b1 100644
--- a/src/model/common/non_local_toolbox/non_local_manager_callback.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager_callback.hh
@@ -1,67 +1,67 @@
/**
* @file non_local_manager_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 21 2017
* @date last modification: Tue Sep 19 2017
*
* @brief Callback functions for the non local manager
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH__
-#define __AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH__
+#ifndef AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH_
+#define AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH_
namespace akantu {
class NonLocalManager;
} // namespace akantu
namespace akantu {
class NonLocalManagerCallback {
public:
virtual void initializeNonLocal() {}
/* ------------------------------------------------------------------------ */
virtual void
- insertIntegrationPointsInNeighborhoods(const GhostType & ghost_type) = 0;
+ insertIntegrationPointsInNeighborhoods(GhostType ghost_type) = 0;
- virtual void computeNonLocalStresses(const GhostType & ghost_type) = 0;
+ virtual void computeNonLocalStresses(GhostType ghost_type) = 0;
/// update the values of the non local internal
virtual void updateLocalInternal(ElementTypeMapReal & internal_flat,
- const GhostType & ghost_type,
- const ElementKind & kind) = 0;
+ GhostType ghost_type,
+ ElementKind kind) = 0;
/// copy the results of the averaging in the materials
virtual void updateNonLocalInternal(ElementTypeMapReal & internal_flat,
- const GhostType & ghost_type,
- const ElementKind & kind) = 0;
+ GhostType ghost_type,
+ ElementKind kind) = 0;
};
} // namespace akantu
-#endif /* __AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH__ */
+#endif /* AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager_inline_impl.hh b/src/model/common/non_local_toolbox/non_local_manager_inline_impl.hh
index 8f2df49a6..df6981b35 100644
--- a/src/model/common/non_local_toolbox/non_local_manager_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager_inline_impl.hh
@@ -1,67 +1,67 @@
/**
* @file non_local_manager_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Sep 11 2017
*
* @brief inline implementation of non-local manager functions
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_HH__
-#define __AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_HH__
+#ifndef AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_HH_
+#define AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::registerNeighborhood(const ID & neighborhood,
const ID & weight_func_id) {
/// check if neighborhood has already been created
auto it = neighborhoods.find(neighborhood);
if (it == neighborhoods.end()) {
this->createNeighborhood(weight_func_id, neighborhood);
}
}
/* -------------------------------------------------------------------------- */
inline NonLocalNeighborhoodBase &
NonLocalManager::getNeighborhood(const ID & name) const {
AKANTU_DEBUG_IN();
auto it = neighborhoods.find(name);
AKANTU_DEBUG_ASSERT(it != neighborhoods.end(),
"The neighborhood " << name << " is not registered");
AKANTU_DEBUG_OUT();
return *(it->second);
}
} // namespace akantu
-#endif /* __AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_HH__ */
+#endif /* AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood.hh b/src/model/common/non_local_toolbox/non_local_neighborhood.hh
index f48817826..48ceebd66 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood.hh
@@ -1,134 +1,134 @@
/**
* @file non_local_neighborhood.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Non-local neighborhood for non-local averaging based on
* weight function
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_HH__
-#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_HH__
+#ifndef AKANTU_NON_LOCAL_NEIGHBORHOOD_HH_
+#define AKANTU_NON_LOCAL_NEIGHBORHOOD_HH_
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
#include "non_local_neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class NonLocalManager;
class BaseWeightFunction;
} // namespace akantu
namespace akantu {
template <class WeightFunction = BaseWeightFunction>
class NonLocalNeighborhood : public NonLocalNeighborhoodBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalNeighborhood(NonLocalManager & manager,
const ElementTypeMapReal & quad_coordinates,
const ID & id = "neighborhood",
const MemoryID & memory_id = 0);
~NonLocalNeighborhood() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// compute the weights for non-local averaging
void computeWeights() override;
/// save the pair of weights in a file
void saveWeights(const std::string & filename) const override;
/// compute the non-local counter part for a given element type map
// compute the non-local counter part for a given element type map
void
weightedAverageOnNeighbours(const ElementTypeMapReal & to_accumulate,
ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom,
- const GhostType & ghost_type2) const override;
+ GhostType ghost_type2) const override;
/// update the weights based on the weight function
void updateWeights() override;
/// register a new non-local variable in the neighborhood
// void registerNonLocalVariable(const ID & id);
protected:
template <class Func>
- inline void foreach_weight(const GhostType & ghost_type, Func && func);
+ inline void foreach_weight(GhostType ghost_type, Func && func);
template <class Func>
- inline void foreach_weight(const GhostType & ghost_type, Func && func) const;
+ inline void foreach_weight(GhostType ghost_type, Func && func) const;
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(NonLocalManager, non_local_manager, const NonLocalManager &);
AKANTU_GET_MACRO_NOT_CONST(NonLocalManager, non_local_manager,
NonLocalManager &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Pointer to non-local manager class
NonLocalManager & non_local_manager;
/// the weights associated to the pairs
std::array<std::unique_ptr<Array<Real>>, 2> pair_weight;
/// weight function
std::unique_ptr<WeightFunction> weight_function;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Implementation of template functions */
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_inline_impl.hh"
-#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_HH__ */
+#endif /* AKANTU_NON_LOCAL_NEIGHBORHOOD_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc b/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
index 3fc1e3cc1..a696d72db 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
@@ -1,126 +1,126 @@
/**
* @file non_local_neighborhood_base.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Fri Dec 08 2017
*
* @brief Implementation of non-local neighborhood base
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_base.hh"
#include "grid_synchronizer.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLocalNeighborhoodBase::NonLocalNeighborhoodBase(
Model & model, const ElementTypeMapReal & quad_coordinates, const ID & id,
const MemoryID & memory_id)
: NeighborhoodBase(model, quad_coordinates, id, memory_id),
Parsable(ParserType::_non_local, id) {
AKANTU_DEBUG_IN();
this->registerParam("radius", neighborhood_radius, 100.,
_pat_parsable | _pat_readable, "Non local radius");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NonLocalNeighborhoodBase::~NonLocalNeighborhoodBase() = default;
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::createGridSynchronizer() {
this->is_creating_grid = true;
this->grid_synchronizer = std::make_unique<GridSynchronizer>(
this->model.getMesh(), *spatial_grid, *this,
std::set<SynchronizationTag>{SynchronizationTag::_mnl_weight,
SynchronizationTag::_mnl_for_average},
std::string(getID() + ":grid_synchronizer"), this->memory_id, false);
this->is_creating_grid = false;
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::synchronize(
DataAccessor<Element> & data_accessor, const SynchronizationTag & tag) {
if (not grid_synchronizer) {
return;
}
grid_synchronizer->synchronizeOnce(data_accessor, tag);
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::getRelevantGhostElements(
std::set<Element> & relevant_ghost_elements) {
for (auto && ghost_type : ghost_type_t{}) {
auto & pair_list = this->pair_list.at(ghost_type);
for (auto && pair : pair_list) {
if (pair.first.ghost_type == _ghost) {
relevant_ghost_elements.insert(pair.first);
}
if (pair.second.ghost_type == _ghost) {
relevant_ghost_elements.insert(pair.second);
}
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::cleanupExtraGhostElements(
std::set<Element> & relevant_ghost_elements) {
Array<Element> ghosts_to_erase;
auto & mesh = this->model.getMesh();
auto end = relevant_ghost_elements.end();
- for (auto & type : mesh.elementTypes(_spatial_dimension = spatial_dimension,
- _ghost_type = _ghost)) {
+ for (const auto & type : mesh.elementTypes(
+ _spatial_dimension = spatial_dimension, _ghost_type = _ghost)) {
auto nb_ghost_elem = mesh.getNbElement(type, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
Element element{type, g, _ghost};
if (relevant_ghost_elements.find(element) == end) {
ghosts_to_erase.push_back(element);
}
}
}
/// remove the unneccessary ghosts from the synchronizer
mesh.eraseElements(ghosts_to_erase);
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::registerNonLocalVariable(const ID & id) {
this->non_local_variables.insert(id);
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
index ac9dfd970..5bf1dc2c7 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
@@ -1,131 +1,135 @@
/**
* @file non_local_neighborhood_base.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Non-local neighborhood base class
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__
-#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__
+#ifndef AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH_
+#define AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH_
namespace akantu {
class Model;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class NonLocalNeighborhoodBase : public NeighborhoodBase, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalNeighborhoodBase(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id = "non_local_neighborhood",
const MemoryID & memory_id = 0);
~NonLocalNeighborhoodBase() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create grid synchronizer and exchange ghost cells
void createGridSynchronizer() override;
void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) override;
/// compute weights, for instance needed for non-local damage computation
virtual void computeWeights(){};
// compute the non-local counter part for a given element type map
virtual void
weightedAverageOnNeighbours(const ElementTypeMapReal & to_accumulate,
ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom,
- const GhostType & ghost_type2) const = 0;
+ GhostType ghost_type2) const = 0;
/// update the weights for the non-local averaging
virtual void updateWeights() = 0;
/// update the weights for the non-local averaging
- virtual void saveWeights(const std::string &) const { AKANTU_TO_IMPLEMENT(); }
+ virtual void saveWeights(const std::string & /*unused*/) const {
+ AKANTU_TO_IMPLEMENT();
+ }
/// register a new non-local variable in the neighborhood
virtual void registerNonLocalVariable(const ID & id);
/// clean up the unneccessary ghosts
void cleanupExtraGhostElements(std::set<Element> & relevant_ghost_elements);
/// list releveant ghosts
void getRelevantGhostElements(std::set<Element> & relevant_ghost_elements);
protected:
/// create the grid
void createGrid();
/* --------------------------------------------------------------------------
*/
/* DataAccessor inherited members */
/* --------------------------------------------------------------------------
*/
public:
- inline UInt getNbData(const Array<Element> &,
- const SynchronizationTag &) const override {
+ inline UInt getNbData(const Array<Element> & /*elements*/,
+ const SynchronizationTag & /*tag*/) const override {
return 0;
}
- inline void packData(CommunicationBuffer &, const Array<Element> &,
- const SynchronizationTag &) const override {}
+ inline void packData(CommunicationBuffer & /*buffer*/,
+ const Array<Element> & /*element*/,
+ const SynchronizationTag & /*tag*/) const override {}
- inline void unpackData(CommunicationBuffer &, const Array<Element> &,
- const SynchronizationTag &) override {}
+ inline void unpackData(CommunicationBuffer & /*buffer*/,
+ const Array<Element> & /*element*/,
+ const SynchronizationTag & /*tag*/) override {}
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
AKANTU_GET_MACRO(NonLocalVariables, non_local_variables,
const std::set<ID> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// list of non-local variables associated to the neighborhood
std::set<ID> non_local_variables;
};
} // namespace akantu
-#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__ */
+#endif /* AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.hh
index abbdbceac..08e0b5474 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.hh
@@ -1,86 +1,86 @@
/**
* @file non_local_neighborhood_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 06 2015
* @date last modification: Thu Jul 06 2017
*
* @brief Implementation of inline functions of non-local neighborhood class
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_HH__
-#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_HH__
+#ifndef AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_HH_
+#define AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
inline UInt NonLocalNeighborhood<WeightFunction>::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
UInt size = 0;
if (tag == SynchronizationTag::_mnl_for_average) {
for (auto & variable_id : non_local_variables) {
size += this->non_local_manager.getNbData(elements, variable_id);
}
}
size += this->weight_function->getNbData(elements, tag);
return size;
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
inline void NonLocalNeighborhood<WeightFunction>::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_mnl_for_average) {
for (auto & variable_id : non_local_variables) {
this->non_local_manager.packData(buffer, elements, variable_id);
}
}
this->weight_function->packData(buffer, elements, tag);
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
inline void NonLocalNeighborhood<WeightFunction>::unpackData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == SynchronizationTag::_mnl_for_average) {
for (auto & variable_id : non_local_variables) {
this->non_local_manager.unpackData(buffer, elements, variable_id);
}
}
this->weight_function->unpackData(buffer, elements, tag);
}
} // namespace akantu
-#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_HH__ */
+#endif /* AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
index eced12942..68a76fca0 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
@@ -1,275 +1,278 @@
/**
* @file non_local_neighborhood_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 28 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of class non-local neighborhood
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "non_local_manager.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH__
-#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH__
+#ifndef AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH_
+#define AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
template <class Func>
inline void NonLocalNeighborhood<WeightFunction>::foreach_weight(
- const GhostType & ghost_type, Func && func) {
+ GhostType ghost_type, Func && func) {
auto weight_it =
pair_weight[ghost_type]->begin(pair_weight[ghost_type]->getNbComponent());
for (auto & pair : pair_list[ghost_type]) {
std::forward<decltype(func)>(func)(pair.first, pair.second, *weight_it);
++weight_it;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
template <class Func>
inline void NonLocalNeighborhood<WeightFunction>::foreach_weight(
- const GhostType & ghost_type, Func && func) const {
+ GhostType ghost_type, Func && func) const {
auto weight_it =
pair_weight[ghost_type]->begin(pair_weight[ghost_type]->getNbComponent());
for (auto & pair : pair_list[ghost_type]) {
std::forward<decltype(func)>(func)(pair.first, pair.second, *weight_it);
++weight_it;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
NonLocalNeighborhood<WeightFunction>::NonLocalNeighborhood(
NonLocalManager & manager, const ElementTypeMapReal & quad_coordinates,
const ID & id, const MemoryID & memory_id)
: NonLocalNeighborhoodBase(manager.getModel(), quad_coordinates, id,
memory_id),
non_local_manager(manager) {
AKANTU_DEBUG_IN();
this->weight_function = std::make_unique<WeightFunction>(manager);
this->registerSubSection(ParserType::_weight_function, "weight_parameter",
*weight_function);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
NonLocalNeighborhood<WeightFunction>::~NonLocalNeighborhood() = default;
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::computeWeights() {
AKANTU_DEBUG_IN();
this->weight_function->setRadius(this->neighborhood_radius);
Vector<Real> q1_coord(this->spatial_dimension);
Vector<Real> q2_coord(this->spatial_dimension);
UInt nb_weights_per_pair = 2; /// w1: q1->q2, w2: q2->q1
/// get the elementtypemap for the neighborhood volume for each quadrature
/// point
ElementTypeMapReal & quadrature_points_volumes =
this->non_local_manager.getVolumes();
/// update the internals of the weight function if applicable (not
/// all the weight functions have internals and do noting in that
/// case)
weight_function->updateInternals();
for (auto ghost_type : ghost_types) {
/// allocate the array to store the weight, if it doesn't exist already
if (!(pair_weight[ghost_type])) {
pair_weight[ghost_type] =
std::make_unique<Array<Real>>(0, nb_weights_per_pair);
}
/// resize the array to the correct size
pair_weight[ghost_type]->resize(pair_list[ghost_type].size());
/// set entries to zero
- pair_weight[ghost_type]->clear();
+ pair_weight[ghost_type]->zero();
/// loop over all pairs in the current pair list array and their
/// corresponding weights
auto first_pair = pair_list[ghost_type].begin();
auto last_pair = pair_list[ghost_type].end();
auto weight_it = pair_weight[ghost_type]->begin(nb_weights_per_pair);
// Compute the weights
for (; first_pair != last_pair; ++first_pair, ++weight_it) {
Vector<Real> & weight = *weight_it;
const IntegrationPoint & q1 = first_pair->first;
const IntegrationPoint & q2 = first_pair->second;
/// get the coordinates for the given pair of quads
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(this->spatial_dimension);
q1_coord = coords_type_1_it[q1.global_num];
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(this->spatial_dimension);
q2_coord = coords_type_2_it[q2.global_num];
Array<Real> & quad_volumes_1 =
quadrature_points_volumes(q1.type, q1.ghost_type);
const Array<Real> & jacobians_2 =
this->non_local_manager.getJacobians(q2.type, q2.ghost_type);
const Real & q2_wJ = jacobians_2(q2.global_num);
/// compute distance between the two quadrature points
Real r = q1_coord.distance(q2_coord);
/// compute the weight for averaging on q1 based on the distance
Real w1 = this->weight_function->operator()(r, q1, q2);
weight(0) = q2_wJ * w1;
quad_volumes_1(q1.global_num) += weight(0);
if (q2.ghost_type != _ghost && q1.global_num != q2.global_num) {
const Array<Real> & jacobians_1 =
this->non_local_manager.getJacobians(q1.type, q1.ghost_type);
Array<Real> & quad_volumes_2 =
quadrature_points_volumes(q2.type, q2.ghost_type);
/// compute the weight for averaging on q2
const Real & q1_wJ = jacobians_1(q1.global_num);
Real w2 = this->weight_function->operator()(r, q2, q1);
weight(1) = q1_wJ * w2;
quad_volumes_2(q2.global_num) += weight(1);
- } else
+ } else {
weight(1) = 0.;
+ }
}
}
/// normalize the weights
for (auto ghost_type : ghost_types) {
foreach_weight(ghost_type, [&](const auto & q1, const auto & q2,
auto & weight) {
auto & quad_volumes_1 = quadrature_points_volumes(q1.type, q1.ghost_type);
auto & quad_volumes_2 = quadrature_points_volumes(q2.type, q2.ghost_type);
Real q1_volume = quad_volumes_1(q1.global_num);
auto ghost_type2 = q2.ghost_type;
weight(0) *= 1. / q1_volume;
if (ghost_type2 != _ghost) {
Real q2_volume = quad_volumes_2(q2.global_num);
weight(1) *= 1. / q2_volume;
}
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::saveWeights(
const std::string & filename) const {
std::ofstream pout;
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
pout.open(sstr.str().c_str());
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
auto ghost_type = (GhostType)gt;
AKANTU_DEBUG_ASSERT((pair_weight[ghost_type]),
"the weights have not been computed yet");
Array<Real> & weights = *(pair_weight[ghost_type]);
auto weights_it = weights.begin(2);
- for (UInt i = 0; i < weights.size(); ++i, ++weights_it)
+ for (UInt i = 0; i < weights.size(); ++i, ++weights_it) {
pout << "w1: " << (*weights_it)(0) << " w2: " << (*weights_it)(1)
<< std::endl;
+ }
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::weightedAverageOnNeighbours(
const ElementTypeMapReal & to_accumulate, ElementTypeMapReal & accumulated,
- UInt nb_degree_of_freedom, const GhostType & ghost_type2) const {
+ UInt nb_degree_of_freedom, GhostType ghost_type2) const {
auto it = non_local_variables.find(accumulated.getName());
// do averaging only for variables registered in the neighborhood
- if (it == non_local_variables.end())
+ if (it == non_local_variables.end()) {
return;
+ }
foreach_weight(
ghost_type2,
[ghost_type2, nb_degree_of_freedom, &to_accumulate,
&accumulated](const auto & q1, const auto & q2, auto & weight) {
const Vector<Real> to_acc_1 =
to_accumulate(q1.type, q1.ghost_type)
.begin(nb_degree_of_freedom)[q1.global_num];
const Vector<Real> to_acc_2 =
to_accumulate(q2.type, q2.ghost_type)
.begin(nb_degree_of_freedom)[q2.global_num];
Vector<Real> acc_1 = accumulated(q1.type, q1.ghost_type)
.begin(nb_degree_of_freedom)[q1.global_num];
Vector<Real> acc_2 = accumulated(q2.type, q2.ghost_type)
.begin(nb_degree_of_freedom)[q2.global_num];
acc_1 += weight(0) * to_acc_2;
if (ghost_type2 != _ghost) {
acc_2 += weight(1) * to_acc_1;
}
});
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::updateWeights() {
// Update the weights for the non local variable averaging
if (this->weight_function->getUpdateRate() &&
(this->non_local_manager.getNbStressCalls() %
this->weight_function->getUpdateRate() ==
0)) {
SynchronizerRegistry::synchronize(SynchronizationTag::_mnl_weight);
this->computeWeights();
}
}
} // namespace akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL__ */
diff --git a/src/model/common/solver_callback.hh b/src/model/common/solver_callback.hh
index 696041da4..7d72cdcd7 100644
--- a/src/model/common/solver_callback.hh
+++ b/src/model/common/solver_callback.hh
@@ -1,108 +1,108 @@
/**
* @file solver_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Class defining the interface for non_linear_solver callbacks
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLVER_CALLBACK_HH__
-#define __AKANTU_SOLVER_CALLBACK_HH__
+#ifndef AKANTU_SOLVER_CALLBACK_HH_
+#define AKANTU_SOLVER_CALLBACK_HH_
namespace akantu {
class DOFManager;
}
namespace akantu {
class SolverCallback {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit SolverCallback(DOFManager & dof_manager);
explicit SolverCallback();
/* ------------------------------------------------------------------------ */
virtual ~SolverCallback();
protected:
void setDOFManager(DOFManager & dof_manager);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the type of matrix needed
virtual MatrixType getMatrixType(const ID &) = 0;
/// callback to assemble a Matrix
virtual void assembleMatrix(const ID &) = 0;
/// callback to assemble a lumped Matrix
virtual void assembleLumpedMatrix(const ID &) = 0;
/// callback to assemble the residual (rhs)
virtual void assembleResidual() = 0;
/// callback to assemble the rhs parts, (e.g. internal_forces +
/// external_forces)
virtual void assembleResidual(const ID & /*residual_part*/) {}
/* ------------------------------------------------------------------------ */
/* Dynamic simulations part */
/* ------------------------------------------------------------------------ */
/// callback for the predictor (in case of dynamic simulation)
virtual void predictor() {}
/// callback for the corrector (in case of dynamic simulation)
virtual void corrector() {}
/// tells if the residual can be computed in separated parts
virtual bool canSplitResidual() { return false; }
/* ------------------------------------------------------------------------ */
/* management callbacks */
/* ------------------------------------------------------------------------ */
virtual void beforeSolveStep(){};
virtual void afterSolveStep(bool /*converged*/ = true){};
protected:
/// DOFManager prefixed to avoid collision in multiple inheritance cases
DOFManager * sc_dof_manager{nullptr};
};
namespace debug {
class SolverCallbackResidualPartUnknown : public Exception {
public:
SolverCallbackResidualPartUnknown(const ID & residual_part)
: Exception(residual_part + " is not known here.") {}
};
} // namespace debug
} // namespace akantu
-#endif /* __AKANTU_SOLVER_CALLBACK_HH__ */
+#endif /* AKANTU_SOLVER_CALLBACK_HH_ */
diff --git a/src/model/common/time_step_solvers/time_step_solver.cc b/src/model/common/time_step_solvers/time_step_solver.cc
index ec365d701..69a57e356 100644
--- a/src/model/common/time_step_solvers/time_step_solver.cc
+++ b/src/model/common/time_step_solvers/time_step_solver.cc
@@ -1,192 +1,198 @@
/**
* @file time_step_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Wed Feb 21 2018
*
* @brief Implementation of common part of TimeStepSolvers
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "time_step_solver.hh"
#include "dof_manager.hh"
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
TimeStepSolver::TimeStepSolver(DOFManager & dof_manager,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback, const ID & id,
UInt memory_id)
: Memory(id, memory_id), SolverCallback(dof_manager),
_dof_manager(dof_manager), type(type), time_step(0.),
solver_callback(&solver_callback), non_linear_solver(non_linear_solver) {
this->registerSubRegistry("non_linear_solver", non_linear_solver);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver::~TimeStepSolver() = default;
/* -------------------------------------------------------------------------- */
void TimeStepSolver::setIntegrationScheme(
const ID & dof_id, const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type) {
this->setIntegrationSchemeInternal(dof_id, type, solution_type);
for (auto & pair : needed_matrices) {
auto & mat_type = pair.second;
const auto & name = pair.first;
if (mat_type == _mt_not_defined) {
mat_type = this->solver_callback->getMatrixType(name);
}
- if (mat_type == _mt_not_defined)
+ if (mat_type == _mt_not_defined) {
continue;
+ }
- if (not _dof_manager.hasMatrix(name))
+ if (not _dof_manager.hasMatrix(name)) {
_dof_manager.getNewMatrix(name, mat_type);
+ }
}
}
/* -------------------------------------------------------------------------- */
MatrixType TimeStepSolver::getCommonMatrixType() {
MatrixType common_type = _mt_not_defined;
for (auto & pair : needed_matrices) {
auto & type = pair.second;
common_type = std::min(common_type, type);
}
AKANTU_DEBUG_ASSERT(common_type != _mt_not_defined,
"No type defined for the matrices");
return common_type;
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::predictor() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->predictor();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::corrector() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->corrector();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::beforeSolveStep() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->beforeSolveStep();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::afterSolveStep(bool converged) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->afterSolveStep(converged);
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleLumpedMatrix(const ID & matrix_id) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
- if (not _dof_manager.hasLumpedMatrix(matrix_id))
+ if (not _dof_manager.hasLumpedMatrix(matrix_id)) {
_dof_manager.getNewLumpedMatrix(matrix_id);
+ }
this->solver_callback->assembleLumpedMatrix(matrix_id);
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleMatrix(const ID & matrix_id) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
auto common_type = this->getCommonMatrixType();
if (matrix_id != "J") {
auto type = needed_matrices[matrix_id];
- if (type == _mt_not_defined)
+ if (type == _mt_not_defined) {
return;
+ }
if (not _dof_manager.hasMatrix(matrix_id)) {
_dof_manager.getNewMatrix(matrix_id, type);
}
this->solver_callback->assembleMatrix(matrix_id);
return;
}
- if (not _dof_manager.hasMatrix("J"))
+ if (not _dof_manager.hasMatrix("J")) {
_dof_manager.getNewMatrix("J", common_type);
+ }
MatrixType type;
ID name;
for (auto & pair : needed_matrices) {
std::tie(name, type) = pair;
- if (type == _mt_not_defined)
+ if (type == _mt_not_defined) {
continue;
+ }
this->solver_callback->assembleMatrix(name);
}
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleResidual() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
- this->_dof_manager.clearResidual();
+ this->_dof_manager.zeroResidual();
this->solver_callback->assembleResidual();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->assembleResidual(residual_part);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/time_step_solvers/time_step_solver.hh b/src/model/common/time_step_solvers/time_step_solver.hh
index 6e61f1d97..ff8c4c86c 100644
--- a/src/model/common/time_step_solvers/time_step_solver.hh
+++ b/src/model/common/time_step_solvers/time_step_solver.hh
@@ -1,153 +1,155 @@
/**
* @file time_step_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Feb 21 2018
*
* @brief This corresponding to the time step evolution solver
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_memory.hh"
#include "integration_scheme.hh"
#include "parameter_registry.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TIME_STEP_SOLVER_HH__
-#define __AKANTU_TIME_STEP_SOLVER_HH__
+#ifndef AKANTU_TIME_STEP_SOLVER_HH_
+#define AKANTU_TIME_STEP_SOLVER_HH_
namespace akantu {
class DOFManager;
class NonLinearSolver;
} // namespace akantu
namespace akantu {
class TimeStepSolver : public Memory,
public ParameterRegistry,
public SolverCallback {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolver(DOFManager & dof_manager, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback, const ID & id,
UInt memory_id);
~TimeStepSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solves on step
virtual void solveStep(SolverCallback & solver_callback) = 0;
/// register an integration scheme for a given dof
void setIntegrationScheme(const ID & dof_id,
const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
protected:
/// register an integration scheme for a given dof
virtual void
setIntegrationSchemeInternal(const ID & dof_id,
const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined) = 0;
public:
/// replies if a integration scheme has been set
virtual bool hasIntegrationScheme(const ID & dof_id) const = 0;
/* ------------------------------------------------------------------------ */
/* Solver Callback interface */
/* ------------------------------------------------------------------------ */
public:
/// implementation of the SolverCallback::getMatrixType()
- MatrixType getMatrixType(const ID &) final { return _mt_not_defined; }
+ MatrixType getMatrixType(const ID & /*unused*/) final {
+ return _mt_not_defined;
+ }
/// implementation of the SolverCallback::predictor()
void predictor() override;
/// implementation of the SolverCallback::corrector()
void corrector() override;
/// implementation of the SolverCallback::assembleJacobian()
void assembleMatrix(const ID & matrix_id) override;
/// implementation of the SolverCallback::assembleJacobian()
void assembleLumpedMatrix(const ID & matrix_id) override;
/// implementation of the SolverCallback::assembleResidual()
void assembleResidual() override;
/// implementation of the SolverCallback::assembleResidual()
void assembleResidual(const ID & residual_part) override;
void beforeSolveStep() override;
void afterSolveStep(bool converged = true) override;
bool canSplitResidual() override {
return solver_callback->canSplitResidual();
}
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(TimeStep, time_step, Real);
AKANTU_SET_MACRO(TimeStep, time_step, Real);
AKANTU_GET_MACRO(NonLinearSolver, non_linear_solver, const NonLinearSolver &);
AKANTU_GET_MACRO_NOT_CONST(NonLinearSolver, non_linear_solver,
NonLinearSolver &);
protected:
MatrixType getCommonMatrixType();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Underlying dof manager containing the dof to treat
DOFManager & _dof_manager;
/// Type of solver
TimeStepSolverType type;
/// The time step for this solver
Real time_step;
/// Temporary storage for solver callback
SolverCallback * solver_callback;
/// NonLinearSolver used by this tome step solver
NonLinearSolver & non_linear_solver;
/// List of required matrices
std::map<std::string, MatrixType> needed_matrices;
/// specifies if the solvers gives to full solution or just the increment of
/// solution
bool is_solution_increment{true};
};
} // namespace akantu
-#endif /* __AKANTU_TIME_STEP_SOLVER_HH__ */
+#endif /* AKANTU_TIME_STEP_SOLVER_HH_ */
diff --git a/src/model/common/time_step_solvers/time_step_solver_default.cc b/src/model/common/time_step_solvers/time_step_solver_default.cc
index 081856893..993ccb7d0 100644
--- a/src/model/common/time_step_solvers/time_step_solver_default.cc
+++ b/src/model/common/time_step_solvers/time_step_solver_default.cc
@@ -1,331 +1,333 @@
/**
* @file time_step_solver_default.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 15 2015
* @date last modification: Wed Feb 21 2018
*
* @brief Default implementation of the time step solver
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "time_step_solver_default.hh"
#include "dof_manager_default.hh"
#include "integration_scheme_1st_order.hh"
#include "integration_scheme_2nd_order.hh"
#include "mesh.hh"
#include "non_linear_solver.hh"
#include "pseudo_time.hh"
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
TimeStepSolverDefault::TimeStepSolverDefault(
DOFManager & dof_manager, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, SolverCallback & solver_callback,
const ID & id, UInt memory_id)
: TimeStepSolver(dof_manager, type, non_linear_solver, solver_callback, id,
memory_id) {
switch (type) {
case TimeStepSolverType::_dynamic:
break;
case TimeStepSolverType::_dynamic_lumped:
this->is_mass_lumped = true;
break;
case TimeStepSolverType::_static:
/// initialize a static time solver for callback dofs
break;
default:
AKANTU_TO_IMPLEMENT();
}
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::setIntegrationSchemeInternal(
const ID & dof_id, const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type) {
if (this->integration_schemes.find(dof_id) !=
this->integration_schemes.end()) {
AKANTU_EXCEPTION("Their DOFs "
<< dof_id
<< " have already an integration scheme associated");
}
std::unique_ptr<IntegrationScheme> integration_scheme;
if (this->is_mass_lumped) {
switch (type) {
case IntegrationSchemeType::_forward_euler: {
integration_scheme = std::make_unique<ForwardEuler>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_central_difference: {
integration_scheme =
std::make_unique<CentralDifference>(_dof_manager, dof_id);
break;
}
default:
AKANTU_EXCEPTION(
"This integration scheme cannot be used in lumped dynamic");
}
} else {
switch (type) {
case IntegrationSchemeType::_pseudo_time: {
integration_scheme = std::make_unique<PseudoTime>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_forward_euler: {
integration_scheme = std::make_unique<ForwardEuler>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_trapezoidal_rule_1: {
integration_scheme =
std::make_unique<TrapezoidalRule1>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_backward_euler: {
integration_scheme =
std::make_unique<BackwardEuler>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_central_difference: {
integration_scheme =
std::make_unique<CentralDifference>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_fox_goodwin: {
integration_scheme = std::make_unique<FoxGoodwin>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_trapezoidal_rule_2: {
integration_scheme =
std::make_unique<TrapezoidalRule2>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_linear_acceleration: {
integration_scheme =
std::make_unique<LinearAceleration>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_generalized_trapezoidal: {
integration_scheme =
std::make_unique<GeneralizedTrapezoidal>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_newmark_beta:
integration_scheme = std::make_unique<NewmarkBeta>(_dof_manager, dof_id);
break;
}
}
AKANTU_DEBUG_ASSERT(integration_scheme,
"No integration scheme was found for the provided types");
auto && matrices_names = integration_scheme->getNeededMatrixList();
for (auto && name : matrices_names) {
needed_matrices.insert({name, _mt_not_defined});
}
this->integration_schemes[dof_id] = std::move(integration_scheme);
this->solution_types[dof_id] = solution_type;
this->integration_schemes_owner.insert(dof_id);
}
/* -------------------------------------------------------------------------- */
bool TimeStepSolverDefault::hasIntegrationScheme(const ID & dof_id) const {
return this->integration_schemes.find(dof_id) !=
this->integration_schemes.end();
}
/* -------------------------------------------------------------------------- */
TimeStepSolverDefault::~TimeStepSolverDefault() = default;
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::solveStep(SolverCallback & solver_callback) {
this->solver_callback = &solver_callback;
this->non_linear_solver.solve(*this);
this->solver_callback = nullptr;
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::predictor() {
TimeStepSolver::predictor();
for (auto && pair : this->integration_schemes) {
const auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
if (this->_dof_manager.hasPreviousDOFs(dof_id)) {
this->_dof_manager.savePreviousDOFs(dof_id);
}
/// integrator predictor
integration_scheme->predictor(this->time_step);
}
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::corrector() {
AKANTU_DEBUG_IN();
TimeStepSolver::corrector();
for (auto & pair : this->integration_schemes) {
- auto & dof_id = pair.first;
+ const auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
const auto & solution_type = this->solution_types[dof_id];
integration_scheme->corrector(solution_type, this->time_step);
/// computing the increment of dof if needed
if (this->_dof_manager.hasDOFsIncrement(dof_id)) {
if (not this->_dof_manager.hasPreviousDOFs(dof_id)) {
AKANTU_DEBUG_WARNING("In order to compute the increment of "
<< dof_id << " a 'previous' has to be registered");
continue;
}
auto & increment = this->_dof_manager.getDOFsIncrement(dof_id);
auto & previous = this->_dof_manager.getPreviousDOFs(dof_id);
auto dof_array_comp = this->_dof_manager.getDOFs(dof_id).getNbComponent();
increment.copy(this->_dof_manager.getDOFs(dof_id));
for (auto && data : zip(make_view(increment, dof_array_comp),
make_view(previous, dof_array_comp))) {
std::get<0>(data) -= std::get<1>(data);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleMatrix(const ID & matrix_id) {
AKANTU_DEBUG_IN();
TimeStepSolver::assembleMatrix(matrix_id);
- if (matrix_id != "J")
+ if (matrix_id != "J") {
return;
+ }
for_each_integrator([&](auto && dof_id, auto && integration_scheme) {
const auto & solution_type = this->solution_types[dof_id];
integration_scheme.assembleJacobian(solution_type, this->time_step);
});
this->_dof_manager.applyBoundary("J");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void TimeStepSolverDefault::assembleLumpedMatrix(const ID & matrix_id) {
// AKANTU_DEBUG_IN();
// TimeStepSolver::assembleLumpedMatrix(matrix_id);
// if (matrix_id != "J")
// return;
// for (auto & pair : this->integration_schemes) {
// auto & dof_id = pair.first;
// auto & integration_scheme = pair.second;
// const auto & solution_type = this->solution_types[dof_id];
// integration_scheme->assembleJacobianLumped(solution_type,
// this->time_step);
// }
// this->_dof_manager.applyBoundaryLumped("J");
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleResidual() {
if (this->needed_matrices.find("M") != needed_matrices.end()) {
if (this->is_mass_lumped) {
this->assembleLumpedMatrix("M");
} else {
this->assembleMatrix("M");
}
}
TimeStepSolver::assembleResidual();
- for_each_integrator([&](auto &&, auto && integration_scheme) {
+ for_each_integrator([&](auto && /*unused*/, auto && integration_scheme) {
integration_scheme.assembleResidual(this->is_mass_lumped);
});
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_IN();
if (this->needed_matrices.find("M") != needed_matrices.end()) {
if (this->is_mass_lumped) {
this->assembleLumpedMatrix("M");
} else {
this->assembleMatrix("M");
}
}
if (residual_part != "inertial") {
TimeStepSolver::assembleResidual(residual_part);
}
if (residual_part == "inertial") {
- for_each_integrator([&](auto &&, auto && integration_scheme) {
+ for_each_integrator([&](auto && /*unused*/, auto && integration_scheme) {
integration_scheme.assembleResidual(this->is_mass_lumped);
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::beforeSolveStep() {
TimeStepSolver::beforeSolveStep();
- for_each_integrator(
- [&](auto &&, auto && integration_scheme) { integration_scheme.store(); });
+ for_each_integrator([&](auto && /*unused*/, auto && integration_scheme) {
+ integration_scheme.store();
+ });
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::afterSolveStep(bool converged) {
if (not converged) {
- for_each_integrator([&](auto &&, auto && integration_scheme) {
+ for_each_integrator([&](auto && /*unused*/, auto && integration_scheme) {
integration_scheme.restore();
});
}
TimeStepSolver::afterSolveStep(converged);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/time_step_solvers/time_step_solver_default.hh b/src/model/common/time_step_solvers/time_step_solver_default.hh
index a622fea05..09531eae7 100644
--- a/src/model/common/time_step_solvers/time_step_solver_default.hh
+++ b/src/model/common/time_step_solvers/time_step_solver_default.hh
@@ -1,129 +1,129 @@
/**
* @file time_step_solver_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Default implementation for the time stepper
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__
-#define __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__
+#ifndef AKANTU_TIME_STEP_SOLVER_DEFAULT_HH_
+#define AKANTU_TIME_STEP_SOLVER_DEFAULT_HH_
namespace akantu {
class DOFManager;
}
namespace akantu {
class TimeStepSolverDefault : public TimeStepSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolverDefault(DOFManager & dof_manager,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback, const ID & id,
UInt memory_id);
~TimeStepSolverDefault() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// registers an integration scheme for a given dof
void
setIntegrationSchemeInternal(const ID & dof_id,
const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined) override;
public:
bool hasIntegrationScheme(const ID & dof_id) const override;
/// implementation of the TimeStepSolver::predictor()
void predictor() override;
/// implementation of the TimeStepSolver::corrector()
void corrector() override;
/// implementation of the TimeStepSolver::assembleMatrix()
void assembleMatrix(const ID & matrix_id) override;
// void assembleLumpedMatrix(const ID & matrix_id) override;
/// implementation of the TimeStepSolver::assembleResidual()
void assembleResidual() override;
void assembleResidual(const ID & residual_part) override;
void beforeSolveStep() override;
void afterSolveStep(bool converged = true) override;
/// implementation of the generic TimeStepSolver::solveStep()
void solveStep(SolverCallback & solver_callback) override;
private:
template<class Func>
void for_each_integrator(Func && function) {
for (auto & pair : this->integration_schemes) {
- auto & dof_id = pair.first;
+ const auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
function(dof_id, *integration_scheme);
}
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using DOFsIntegrationSchemes =
std::map<ID, std::unique_ptr<IntegrationScheme>>;
using DOFsIntegrationSchemesSolutionTypes =
std::map<ID, IntegrationScheme::SolutionType>;
using DOFsIntegrationSchemesOwner = std::set<ID>;
/// Underlying integration scheme per dof, \todo check what happens in dynamic
/// in case of coupled equations
DOFsIntegrationSchemes integration_schemes;
/// defines if the solver is owner of the memory or not
DOFsIntegrationSchemesOwner integration_schemes_owner;
/// Type of corrector to use
DOFsIntegrationSchemesSolutionTypes solution_types;
/// define if the mass matrix is lumped or not
bool is_mass_lumped{false};
};
} // namespace akantu
-#endif /* __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__ */
+#endif /* AKANTU_TIME_STEP_SOLVER_DEFAULT_HH_ */
diff --git a/src/model/common/time_step_solvers/time_step_solver_default_explicit.hh b/src/model/common/time_step_solvers/time_step_solver_default_explicit.hh
index 98c28c8ac..c339454ce 100644
--- a/src/model/common/time_step_solvers/time_step_solver_default_explicit.hh
+++ b/src/model/common/time_step_solvers/time_step_solver_default_explicit.hh
@@ -1,77 +1,77 @@
/**
* @file time_step_solver_default_explicit.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Default solver for explicit resolution
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH__
-#define __AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH__
+#ifndef AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH_
+#define AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH_
namespace akantu {
class TimeStepSolverDefaultExplicit : public TimeStepSolverDefault {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolverDefaultExplicit();
virtual ~TimeStepSolverDefaultExplicit();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void solveStep();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const TimeStepSolverDefaultExplicit & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
//#include "time_step_solver_default_explicit_inline_impl.hh"
-#endif /* __AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH__ */
+#endif /* AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH_ */
diff --git a/src/model/heat_transfer/heat_transfer_model.cc b/src/model/heat_transfer/heat_transfer_model.cc
index bfd46e200..29b8e416c 100644
--- a/src/model/heat_transfer/heat_transfer_model.cc
+++ b/src/model/heat_transfer/heat_transfer_model.cc
@@ -1,943 +1,958 @@
/**
* @file heat_transfer_model.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Rui Wang <rui.wang@epfl.ch>
*
* @date creation: Sun May 01 2011
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of HeatTransferModel class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model.hh"
#include "dumpable_inline_impl.hh"
#include "element_synchronizer.hh"
#include "fe_engine_template.hh"
#include "generalized_trapezoidal.hh"
#include "group_manager_inline_impl.hh"
#include "integrator_gauss.hh"
#include "mesh.hh"
#include "parser.hh"
#include "shape_lagrange.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_element_partition.hh"
#include "dumper_elemental_field.hh"
#include "dumper_internal_material_field.hh"
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace heat_transfer {
namespace details {
class ComputeRhoFunctor {
public:
ComputeRhoFunctor(const HeatTransferModel & model) : model(model){};
- void operator()(Matrix<Real> & rho, const Element &) {
+ void operator()(Matrix<Real> & rho, const Element & /*unused*/) {
rho.set(model.getCapacity() * model.getDensity());
}
private:
const HeatTransferModel & model;
};
} // namespace details
} // namespace heat_transfer
/* -------------------------------------------------------------------------- */
HeatTransferModel::HeatTransferModel(Mesh & mesh, UInt dim, const ID & id,
const MemoryID & memory_id)
: Model(mesh, ModelType::_heat_transfer_model, dim, id, memory_id),
temperature_gradient("temperature_gradient", id),
temperature_on_qpoints("temperature_on_qpoints", id),
conductivity_on_qpoints("conductivity_on_qpoints", id),
k_gradt_on_qpoints("k_gradt_on_qpoints", id) {
AKANTU_DEBUG_IN();
conductivity = Matrix<Real>(this->spatial_dimension, this->spatial_dimension);
this->initDOFManager();
this->registerDataAccessor(*this);
if (this->mesh.isDistributed()) {
auto & synchronizer = this->mesh.getElementSynchronizer();
this->registerSynchronizer(synchronizer,
SynchronizationTag::_htm_temperature);
this->registerSynchronizer(synchronizer,
SynchronizationTag::_htm_gradient_temperature);
}
registerFEEngineObject<FEEngineType>(id + ":fem", mesh, spatial_dimension);
#ifdef AKANTU_USE_IOHELPER
this->mesh.registerDumper<DumperParaview>("heat_transfer", id, true);
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
#endif
this->registerParam("conductivity", conductivity, _pat_parsmod);
this->registerParam("conductivity_variation", conductivity_variation, 0.,
_pat_parsmod);
this->registerParam("temperature_reference", T_ref, 0., _pat_parsmod);
this->registerParam("capacity", capacity, _pat_parsmod);
this->registerParam("density", density, _pat_parsmod);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initModel() {
auto & fem = this->getFEEngine();
fem.initShapeFunctions(_not_ghost);
fem.initShapeFunctions(_ghost);
temperature_on_qpoints.initialize(fem, _nb_component = 1);
temperature_gradient.initialize(fem, _nb_component = spatial_dimension);
conductivity_on_qpoints.initialize(fem, _nb_component = spatial_dimension *
spatial_dimension);
k_gradt_on_qpoints.initialize(fem, _nb_component = spatial_dimension);
}
/* -------------------------------------------------------------------------- */
FEEngine & HeatTransferModel::getFEEngineBoundary(const ID & name) {
return aka::as_type<FEEngine>(getFEEngineClassBoundary<FEEngineType>(name));
}
/* -------------------------------------------------------------------------- */
template <typename T>
void HeatTransferModel::allocNodalField(Array<T> *& array, const ID & name) {
if (array == nullptr) {
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_disp;
sstr_disp << id << ":" << name;
array = &(alloc<T>(sstr_disp.str(), nb_nodes, 1, T()));
}
}
/* -------------------------------------------------------------------------- */
HeatTransferModel::~HeatTransferModel() = default;
/* -------------------------------------------------------------------------- */
-void HeatTransferModel::assembleCapacityLumped(const GhostType & ghost_type) {
+void HeatTransferModel::assembleCapacityLumped(GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<FEEngineType>();
heat_transfer::details::ComputeRhoFunctor compute_rho(*this);
- for (auto & type :
+ for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
fem.assembleFieldLumped(compute_rho, "M", "temperature",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MatrixType HeatTransferModel::getMatrixType(const ID & matrix_id) {
if (matrix_id == "K" or matrix_id == "M") {
return _symmetric;
}
return _mt_not_defined;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleConductivityMatrix();
} else if (matrix_id == "M" and need_to_reassemble_capacity) {
this->assembleCapacity();
}
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleLumpedMatrix(const ID & matrix_id) {
if (matrix_id == "M" and need_to_reassemble_capacity) {
this->assembleCapacityLumped();
}
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleResidual() {
AKANTU_DEBUG_IN();
this->assembleInternalHeatRate();
this->getDOFManager().assembleToResidual("temperature",
*this->external_heat_rate, 1);
this->getDOFManager().assembleToResidual("temperature",
*this->internal_heat_rate, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::predictor() { ++temperature_release; }
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacityLumped() {
AKANTU_DEBUG_IN();
if (!this->getDOFManager().hasLumpedMatrix("M")) {
this->getDOFManager().getNewLumpedMatrix("M");
}
- this->getDOFManager().clearLumpedMatrix("M");
+ this->getDOFManager().zeroLumpedMatrix("M");
assembleCapacityLumped(_not_ghost);
assembleCapacityLumped(_ghost);
need_to_reassemble_capacity_lumped = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initSolver(TimeStepSolverType time_step_solver_type,
- NonLinearSolverType) {
+ NonLinearSolverType /*unused*/) {
DOFManager & dof_manager = this->getDOFManager();
this->allocNodalField(this->temperature, "temperature");
this->allocNodalField(this->external_heat_rate, "external_heat_rate");
this->allocNodalField(this->internal_heat_rate, "internal_heat_rate");
this->allocNodalField(this->blocked_dofs, "blocked_dofs");
if (!dof_manager.hasDOFs("temperature")) {
dof_manager.registerDOFs("temperature", *this->temperature, _dst_nodal);
dof_manager.registerBlockedDOFs("temperature", *this->blocked_dofs);
}
if (time_step_solver_type == TimeStepSolverType::_dynamic ||
time_step_solver_type == TimeStepSolverType::_dynamic_lumped) {
this->allocNodalField(this->temperature_rate, "temperature_rate");
if (!dof_manager.hasDOFsDerivatives("temperature", 1)) {
dof_manager.registerDOFsDerivative("temperature", 1,
*this->temperature_rate);
}
}
}
/* -------------------------------------------------------------------------- */
std::tuple<ID, TimeStepSolverType>
HeatTransferModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _explicit_lumped_mass: {
return std::make_tuple("explicit_lumped",
TimeStepSolverType::_dynamic_lumped);
}
case _static: {
return std::make_tuple("static", TimeStepSolverType::_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
}
default:
return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
}
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions HeatTransferModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case TimeStepSolverType::_dynamic_lumped: {
options.non_linear_solver_type = NonLinearSolverType::_lumped;
options.integration_scheme_type["temperature"] =
IntegrationSchemeType::_forward_euler;
options.solution_type["temperature"] = IntegrationScheme::_temperature_rate;
break;
}
case TimeStepSolverType::_static: {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["temperature"] =
IntegrationSchemeType::_pseudo_time;
options.solution_type["temperature"] = IntegrationScheme::_not_defined;
break;
}
case TimeStepSolverType::_dynamic: {
if (this->method == _explicit_consistent_mass) {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["temperature"] =
IntegrationSchemeType::_forward_euler;
options.solution_type["temperature"] =
IntegrationScheme::_temperature_rate;
} else {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["temperature"] =
IntegrationSchemeType::_backward_euler;
options.solution_type["temperature"] = IntegrationScheme::_temperature;
}
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleConductivityMatrix() {
AKANTU_DEBUG_IN();
this->computeConductivityOnQuadPoints(_not_ghost);
-
- if (conductivity_release[_not_ghost] == conductivity_matrix_release)
+
+ if (conductivity_release[_not_ghost] == conductivity_matrix_release) {
return;
+ }
AKANTU_DEBUG_ASSERT(this->getDOFManager().hasMatrix("K"),
"The K matrix has not been initialized yet.");
- this->getDOFManager().clearMatrix("K");
+ this->getDOFManager().zeroMatrix("K");
auto & fem = this->getFEEngine();
for (auto && type : mesh.elementTypes(spatial_dimension)) {
auto nb_element = mesh.getNbElement(type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type);
auto bt_d_b = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points,
nb_nodes_per_element * nb_nodes_per_element, "B^t*D*B");
fem.computeBtDB(conductivity_on_qpoints(type), *bt_d_b, 2, type);
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto K_e = std::make_unique<Array<Real>>(
nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_e");
fem.integrate(*bt_d_b, *K_e, nb_nodes_per_element * nb_nodes_per_element,
type);
this->getDOFManager().assembleElementalMatricesToMatrix(
"K", "temperature", *K_e, type, _not_ghost, _symmetric);
}
conductivity_matrix_release = conductivity_release[_not_ghost];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void HeatTransferModel::computeConductivityOnQuadPoints(
- const GhostType & ghost_type) {
+void HeatTransferModel::computeConductivityOnQuadPoints(GhostType ghost_type) {
// if already computed once check if need to compute
if (not initial_conductivity[ghost_type]) {
// if temperature did not change, conductivity will not vary
- if (temperature_release == conductivity_release[ghost_type])
+ if (temperature_release == conductivity_release[ghost_type]) {
return;
-
+ }
// if conductivity_variation is 0 no need to recompute
- if (conductivity_variation == 0.)
+ if (conductivity_variation == 0.) {
return;
+ }
}
- for (auto & type :
+ for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
auto & temperature_interpolated = temperature_on_qpoints(type, ghost_type);
// compute the temperature on quadrature points
this->getFEEngine().interpolateOnIntegrationPoints(
*temperature, temperature_interpolated, 1, type, ghost_type);
auto & cond = conductivity_on_qpoints(type, ghost_type);
for (auto && tuple :
zip(make_view(cond, spatial_dimension, spatial_dimension),
temperature_interpolated)) {
auto & C = std::get<0>(tuple);
auto & T = std::get<1>(tuple);
C = conductivity;
Matrix<Real> variation(spatial_dimension, spatial_dimension,
conductivity_variation * (T - T_ref));
// @TODO: Guillaume are you sure ? why due you compute variation then ?
C += conductivity_variation;
}
}
conductivity_release[ghost_type] = temperature_release;
initial_conductivity[ghost_type] = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void HeatTransferModel::computeKgradT(const GhostType & ghost_type) {
+void HeatTransferModel::computeKgradT(GhostType ghost_type) {
computeConductivityOnQuadPoints(ghost_type);
- for (auto & type :
+ for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
auto & gradient = temperature_gradient(type, ghost_type);
this->getFEEngine().gradientOnIntegrationPoints(*temperature, gradient, 1,
type, ghost_type);
for (auto && values :
zip(make_view(conductivity_on_qpoints(type, ghost_type),
spatial_dimension, spatial_dimension),
make_view(gradient, spatial_dimension),
make_view(k_gradt_on_qpoints(type, ghost_type),
spatial_dimension))) {
const auto & C = std::get<0>(values);
const auto & BT = std::get<1>(values);
auto & k_BT = std::get<2>(values);
k_BT.mul<false>(C, BT);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleInternalHeatRate() {
AKANTU_DEBUG_IN();
- this->internal_heat_rate->clear();
+ this->internal_heat_rate->zero();
this->synchronize(SynchronizationTag::_htm_temperature);
auto & fem = this->getFEEngine();
for (auto ghost_type : ghost_types) {
// compute k \grad T
computeKgradT(ghost_type);
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto & k_gradt_on_qpoints_vect = k_gradt_on_qpoints(type, ghost_type);
UInt nb_quad_points = k_gradt_on_qpoints_vect.size();
Array<Real> bt_k_gT(nb_quad_points, nb_nodes_per_element);
fem.computeBtD(k_gradt_on_qpoints_vect, bt_k_gT, type, ghost_type);
UInt nb_elements = mesh.getNbElement(type, ghost_type);
Array<Real> int_bt_k_gT(nb_elements, nb_nodes_per_element);
fem.integrate(bt_k_gT, int_bt_k_gT, nb_nodes_per_element, type,
ghost_type);
this->getDOFManager().assembleElementalArrayLocalArray(
int_bt_k_gT, *this->internal_heat_rate, type, ghost_type, -1);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real el_size;
Real min_el_size = std::numeric_limits<Real>::max();
Real conductivitymax = conductivity(0, 0);
// get the biggest parameter from k11 until k33//
- for (UInt i = 0; i < spatial_dimension; i++)
- for (UInt j = 0; j < spatial_dimension; j++)
+ for (UInt i = 0; i < spatial_dimension; i++) {
+ for (UInt j = 0; j < spatial_dimension; j++) {
conductivitymax = std::max(conductivity(i, j), conductivitymax);
-
- for (auto & type :
+ }
+ }
+ for (auto && type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> coord(0, nb_nodes_per_element * spatial_dimension);
FEEngine::extractNodalToElementField(mesh, mesh.getNodes(), coord, type,
_not_ghost);
auto el_coord = coord.begin(spatial_dimension, nb_nodes_per_element);
UInt nb_element = mesh.getNbElement(type);
for (UInt el = 0; el < nb_element; ++el, ++el_coord) {
el_size = getFEEngine().getElementInradius(*el_coord, type);
min_el_size = std::min(min_el_size, el_size);
}
AKANTU_DEBUG_INFO("The minimum element size : "
<< min_el_size
<< " and the max conductivity is : " << conductivitymax);
}
Real min_dt = 2. * min_el_size * min_el_size / 4. * density * capacity /
conductivitymax;
mesh.getCommunicator().allReduce(min_dt, SynchronizerOperation::_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::setTimeStep(Real time_step, const ID & solver_id) {
Model::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper("heat_transfer").setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::readMaterials() {
auto sect = this->getParserSection();
if (not std::get<1>(sect)) {
const auto & section = std::get<0>(sect);
this->parseSection(section);
}
conductivity_on_qpoints.set(conductivity);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initFullImpl(const ModelOptions & options) {
Model::initFullImpl(options);
readMaterials();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacity() {
AKANTU_DEBUG_IN();
auto ghost_type = _not_ghost;
- this->getDOFManager().clearMatrix("M");
+ this->getDOFManager().zeroMatrix("M");
auto & fem = getFEEngineClass<FEEngineType>();
heat_transfer::details::ComputeRhoFunctor rho_functor(*this);
for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
fem.assembleFieldMatrix(rho_functor, "M", "temperature",
this->getDOFManager(), type, ghost_type);
}
need_to_reassemble_capacity = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeRho(Array<Real> & rho, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->getFEEngine();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
rho.resize(nb_element * nb_quadrature_points);
rho.set(this->capacity);
// Real * rho_1_val = rho.storage();
// /// compute @f$ rho @f$ for each nodes of each element
// for (UInt el = 0; el < nb_element; ++el) {
// for (UInt n = 0; n < nb_quadrature_points; ++n) {
// *rho_1_val++ = this->capacity;
// }
// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::computeThermalEnergyByNode() {
AKANTU_DEBUG_IN();
Real ethermal = 0.;
for (auto && pair : enumerate(make_view(
*internal_heat_rate, internal_heat_rate->getNbComponent()))) {
auto n = std::get<0>(pair);
auto & heat_rate = std::get<1>(pair);
Real heat = 0.;
bool is_local_node = mesh.isLocalOrMasterNode(n);
bool count_node = is_local_node;
for (UInt i = 0; i < heat_rate.size(); ++i) {
- if (count_node)
+ if (count_node) {
heat += heat_rate[i] * time_step;
+ }
}
ethermal += heat;
}
mesh.getCommunicator().allReduce(ethermal, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return ethermal;
}
/* -------------------------------------------------------------------------- */
template <class iterator>
void HeatTransferModel::getThermalEnergy(
iterator Eth, Array<Real>::const_iterator<Real> T_it,
- Array<Real>::const_iterator<Real> T_end) const {
+ const Array<Real>::const_iterator<Real> & T_end) const {
for (; T_it != T_end; ++T_it, ++Eth) {
*Eth = capacity * density * *T_it;
}
}
/* -------------------------------------------------------------------------- */
-Real HeatTransferModel::getThermalEnergy(const ElementType & type, UInt index) {
+Real HeatTransferModel::getThermalEnergy(ElementType type, UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
Vector<Real> Eth_on_quarature_points(nb_quadrature_points);
auto T_it = this->temperature_on_qpoints(type).begin();
T_it += index * nb_quadrature_points;
auto T_end = T_it + nb_quadrature_points;
getThermalEnergy(Eth_on_quarature_points.storage(), T_it, T_end);
return getFEEngine().integrate(Eth_on_quarature_points, type, index);
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getThermalEnergy() {
Real Eth = 0;
auto & fem = getFEEngine();
for (auto && type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
auto nb_element = mesh.getNbElement(type, _not_ghost);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type, _not_ghost);
Array<Real> Eth_per_quad(nb_element * nb_quadrature_points, 1);
auto & temperature_interpolated = temperature_on_qpoints(type);
// compute the temperature on quadrature points
this->getFEEngine().interpolateOnIntegrationPoints(
*temperature, temperature_interpolated, 1, type);
auto T_it = temperature_interpolated.begin();
auto T_end = temperature_interpolated.end();
getThermalEnergy(Eth_per_quad.begin(), T_it, T_end);
Eth += fem.integrate(Eth_per_quad, type);
}
return Eth;
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getEnergy(const std::string & id) {
AKANTU_DEBUG_IN();
Real energy = 0;
- if (id == "thermal")
+ if (id == "thermal") {
energy = getThermalEnergy();
-
+ }
// reduction sum over all processors
mesh.getCommunicator().allReduce(energy, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
-Real HeatTransferModel::getEnergy(const std::string & id,
- const ElementType & type, UInt index) {
+Real HeatTransferModel::getEnergy(const std::string & id, ElementType type,
+ UInt index) {
AKANTU_DEBUG_IN();
Real energy = 0.;
- if (id == "thermal")
+ if (id == "thermal") {
energy = getThermalEnergy(type, index);
+ }
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
std::shared_ptr<dumpers::Field> HeatTransferModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs;
auto field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> HeatTransferModel::createNodalFieldReal(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
if (field_name == "capacity_lumped") {
AKANTU_EXCEPTION(
"Capacity lumped is a nodal field now stored in the DOF manager."
"Therefore it cannot be used by a dumper anymore");
}
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["temperature"] = temperature;
real_nodal_fields["temperature_rate"] = temperature_rate;
real_nodal_fields["external_heat_rate"] = external_heat_rate;
real_nodal_fields["internal_heat_rate"] = internal_heat_rate;
real_nodal_fields["increment"] = increment;
std::shared_ptr<dumpers::Field> field =
mesh.createNodalField(real_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> HeatTransferModel::createElementalField(
const std::string & field_name, const std::string & group_name,
- __attribute__((unused)) bool padding_flag,
- __attribute__((unused)) const UInt & spatial_dimension,
- const ElementKind & element_kind) {
+ bool /*padding_flag*/, UInt /*spatial_dimension*/,
+ ElementKind element_kind) {
std::shared_ptr<dumpers::Field> field;
- if (field_name == "partitions")
+ if (field_name == "partitions") {
field = mesh.createElementalField<UInt, dumpers::ElementPartitionField>(
mesh.getConnectivities(), group_name, this->spatial_dimension,
element_kind);
- else if (field_name == "temperature_gradient") {
+ } else if (field_name == "temperature_gradient") {
ElementTypeMap<UInt> nb_data_per_elem =
this->mesh.getNbDataPerElem(temperature_gradient);
field = mesh.createElementalField<Real, dumpers::InternalMaterialField>(
temperature_gradient, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
} else if (field_name == "conductivity") {
ElementTypeMap<UInt> nb_data_per_elem =
this->mesh.getNbDataPerElem(conductivity_on_qpoints);
field = mesh.createElementalField<Real, dumpers::InternalMaterialField>(
conductivity_on_qpoints, group_name, this->spatial_dimension,
element_kind, nb_data_per_elem);
}
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> HeatTransferModel::createElementalField(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag,
- __attribute__((unused)) const ElementKind & element_kind) {
+ __attribute__((unused)) ElementKind element_kind) {
return nullptr;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> HeatTransferModel::createNodalFieldBool(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return nullptr;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> HeatTransferModel::createNodalFieldReal(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return nullptr;
}
#endif
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump(const std::string & dumper_name) {
mesh.dump(dumper_name);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump(const std::string & dumper_name, UInt step) {
mesh.dump(dumper_name, step);
}
/* ------------------------------------------------------------------------- */
void HeatTransferModel::dump(const std::string & dumper_name, Real time,
UInt step) {
mesh.dump(dumper_name, time, step);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump() { mesh.dump(); }
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump(UInt step) { mesh.dump(step); }
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump(Real time, UInt step) { mesh.dump(time, step); }
/* -------------------------------------------------------------------------- */
inline UInt HeatTransferModel::getNbData(const Array<UInt> & indexes,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes = indexes.size();
switch (tag) {
case SynchronizationTag::_htm_temperature: {
size += nb_nodes * sizeof(Real);
break;
}
- default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
+ default: {
+ AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
+ }
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::packData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
for (auto index : indexes) {
switch (tag) {
case SynchronizationTag::_htm_temperature: {
buffer << (*temperature)(index);
break;
}
- default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
+ default: {
+ AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
+ }
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::unpackData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
for (auto index : indexes) {
switch (tag) {
case SynchronizationTag::_htm_temperature: {
buffer >> (*temperature)(index);
break;
}
- default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
+ default: {
+ AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
+ }
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline UInt HeatTransferModel::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes_per_element = 0;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
const Element & el = *it;
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
switch (tag) {
case SynchronizationTag::_htm_temperature: {
size += nb_nodes_per_element * sizeof(Real); // temperature
break;
}
case SynchronizationTag::_htm_gradient_temperature: {
// temperature gradient
size += getNbIntegrationPoints(elements) * spatial_dimension * sizeof(Real);
size += nb_nodes_per_element * sizeof(Real); // nodal temperatures
break;
}
- default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
+ default: {
+ AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
+ }
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
switch (tag) {
case SynchronizationTag::_htm_temperature: {
packNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
case SynchronizationTag::_htm_gradient_temperature: {
packElementalDataHelper(temperature_gradient, buffer, elements, true,
getFEEngine());
packNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
- default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
+ default: {
+ AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
+ }
}
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
switch (tag) {
case SynchronizationTag::_htm_temperature: {
unpackNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
case SynchronizationTag::_htm_gradient_temperature: {
unpackElementalDataHelper(temperature_gradient, buffer, elements, true,
getFEEngine());
unpackNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
- default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
+ default: {
+ AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
+ }
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/heat_transfer/heat_transfer_model.hh b/src/model/heat_transfer/heat_transfer_model.hh
index 2ffa48a19..df063fb5c 100644
--- a/src/model/heat_transfer/heat_transfer_model.hh
+++ b/src/model/heat_transfer/heat_transfer_model.hh
@@ -1,335 +1,334 @@
/**
* @file heat_transfer_model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Rui Wang <rui.wang@epfl.ch>
*
* @date creation: Sun May 01 2011
* @date last modification: Mon Feb 05 2018
*
* @brief Model of Heat Transfer
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <array>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_HEAT_TRANSFER_MODEL_HH__
-#define __AKANTU_HEAT_TRANSFER_MODEL_HH__
+#ifndef AKANTU_HEAT_TRANSFER_MODEL_HH_
+#define AKANTU_HEAT_TRANSFER_MODEL_HH_
namespace akantu {
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
} // namespace akantu
namespace akantu {
class HeatTransferModel : public Model,
public DataAccessor<Element>,
public DataAccessor<UInt> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using FEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
- HeatTransferModel(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
+ HeatTransferModel(Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "heat_transfer_model",
const MemoryID & memory_id = 0);
- virtual ~HeatTransferModel();
+ ~HeatTransferModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// generic function to initialize everything ready for explicit dynamics
void initFullImpl(const ModelOptions & options) override;
/// read one material file to instantiate all the materials
void readMaterials();
/// allocate all vectors
- void initSolver(TimeStepSolverType, NonLinearSolverType) override;
+ void initSolver(TimeStepSolverType time_step_solver_type,
+ NonLinearSolverType non_linear_solver_type) override;
/// initialize the model
void initModel() override;
void predictor() override;
/// compute the heat flux
void assembleResidual() override;
/// get the type of matrix needed
- MatrixType getMatrixType(const ID &) override;
+ MatrixType getMatrixType(const ID & matrix_id) override;
/// callback to assemble a Matrix
- void assembleMatrix(const ID &) override;
+ void assembleMatrix(const ID & matrix_id) override;
/// callback to assemble a lumped Matrix
- void assembleLumpedMatrix(const ID &) override;
+ void assembleLumpedMatrix(const ID & matrix_id) override;
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
/* ------------------------------------------------------------------------ */
/* Methods for explicit */
/* ------------------------------------------------------------------------ */
public:
/// compute and get the stable time step
Real getStableTimeStep();
/// set the stable timestep
void setTimeStep(Real time_step, const ID & solver_id = "") override;
// temporary protection to prevent bad usage: should check for bug
protected:
/// compute the internal heat flux \todo Need code review: currently not
/// public method
void assembleInternalHeatRate();
public:
/// calculate the lumped capacity vector for heat transfer problem
void assembleCapacityLumped();
public:
/// assemble the conductivity matrix
void assembleConductivityMatrix();
/// assemble the conductivity matrix
void assembleCapacity();
/// compute the capacity on quadrature points
void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);
private:
/// calculate the lumped capacity vector for heat transfer problem (w
/// ghost type)
- void assembleCapacityLumped(const GhostType & ghost_type);
+ void assembleCapacityLumped(GhostType ghost_type);
/// compute the conductivity tensor for each quadrature point in an array
- void computeConductivityOnQuadPoints(const GhostType & ghost_type);
+ void computeConductivityOnQuadPoints(GhostType ghost_type);
/// compute vector \f[k \grad T\f] for each quadrature point
- void computeKgradT(const GhostType & ghost_type);
+ void computeKgradT(GhostType ghost_type);
/// compute the thermal energy
Real computeThermalEnergyByNode();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
inline UInt getNbData(const Array<UInt> & indexes,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
- const UInt & spatial_dimension,
- const ElementKind & kind) override;
+ UInt spatial_dimension, ElementKind kind) override;
virtual void dump(const std::string & dumper_name);
virtual void dump(const std::string & dumper_name, UInt step);
virtual void dump(const std::string & dumper_name, Real time, UInt step);
void dump() override;
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Density, density, Real);
AKANTU_GET_MACRO(Capacity, capacity, Real);
/// get the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the current value of the time step
AKANTU_GET_MACRO(TimeStep, time_step, Real);
/// get the assembled heat flux
AKANTU_GET_MACRO(InternalHeatRate, *internal_heat_rate, Array<Real> &);
/// get the boundary vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool> &);
/// get the external heat rate vector
AKANTU_GET_MACRO(ExternalHeatRate, *external_heat_rate, Array<Real> &);
/// get the temperature gradient
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(TemperatureGradient,
temperature_gradient, Real);
/// get the conductivity on q points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ConductivityOnQpoints,
conductivity_on_qpoints, Real);
/// get the conductivity on q points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(TemperatureOnQpoints,
temperature_on_qpoints, Real);
/// internal variables
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(KgradT, k_gradt_on_qpoints, Real);
/// get the temperature
AKANTU_GET_MACRO(Temperature, *temperature, Array<Real> &);
/// get the temperature derivative
AKANTU_GET_MACRO(TemperatureRate, *temperature_rate, Array<Real> &);
/// get the energy denominated by thermal
- Real getEnergy(const std::string & energy_id, const ElementType & type,
- UInt index);
+ Real getEnergy(const std::string & energy_id, ElementType type, UInt index);
/// get the energy denominated by thermal
Real getEnergy(const std::string & energy_id);
/// get the thermal energy for a given element
- Real getThermalEnergy(const ElementType & type, UInt index);
+ Real getThermalEnergy(ElementType type, UInt index);
/// get the thermal energy for a given element
Real getThermalEnergy();
protected:
/* ------------------------------------------------------------------------ */
FEEngine & getFEEngineBoundary(const ID & name = "") override;
/* ----------------------------------------------------------------------- */
template <class iterator>
void getThermalEnergy(iterator Eth, Array<Real>::const_iterator<Real> T_it,
- Array<Real>::const_iterator<Real> T_end) const;
+ const Array<Real>::const_iterator<Real> & T_end) const;
template <typename T>
void allocNodalField(Array<T> *& array, const ID & name);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// number of iterations
- //UInt n_iter;
+ // UInt n_iter;
/// time step
Real time_step;
/// temperatures array
Array<Real> * temperature{nullptr};
/// temperatures derivatives array
Array<Real> * temperature_rate{nullptr};
/// increment array (@f$\delta \dot T@f$ or @f$\delta T@f$)
Array<Real> * increment{nullptr};
/// the density
Real density;
/// the speed of the changing temperature
ElementTypeMapArray<Real> temperature_gradient;
/// temperature field on quadrature points
ElementTypeMapArray<Real> temperature_on_qpoints;
/// conductivity tensor on quadrature points
ElementTypeMapArray<Real> conductivity_on_qpoints;
/// vector \f[k \grad T\f] on quad points
ElementTypeMapArray<Real> k_gradt_on_qpoints;
/// external flux vector
Array<Real> * external_heat_rate{nullptr};
/// residuals array
Array<Real> * internal_heat_rate{nullptr};
/// boundary vector
Array<bool> * blocked_dofs{nullptr};
// realtime
- //Real time;
+ // Real time;
/// capacity
Real capacity;
// conductivity matrix
Matrix<Real> conductivity;
// linear variation of the conductivity (for temperature dependent
// conductivity)
Real conductivity_variation;
// reference temperature for the interpretation of temperature variation
Real T_ref;
// the biggest parameter of conductivity matrix
- //Real conductivitymax;
+ // Real conductivitymax;
bool need_to_reassemble_capacity{true};
bool need_to_reassemble_capacity_lumped{true};
UInt temperature_release{0};
UInt conductivity_matrix_release{UInt(-1)};
std::unordered_map<GhostType, bool> initial_conductivity{{_not_ghost, true},
{_ghost, true}};
std::unordered_map<GhostType, UInt> conductivity_release{{_not_ghost, 0},
{_ghost, 0}};
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model_inline_impl.hh"
-#endif /* __AKANTU_HEAT_TRANSFER_MODEL_HH__ */
+#endif /* AKANTU_HEAT_TRANSFER_MODEL_HH_ */
diff --git a/src/model/heat_transfer/heat_transfer_model_inline_impl.hh b/src/model/heat_transfer/heat_transfer_model_inline_impl.hh
index ebb534002..672e0551d 100644
--- a/src/model/heat_transfer/heat_transfer_model_inline_impl.hh
+++ b/src/model/heat_transfer/heat_transfer_model_inline_impl.hh
@@ -1,41 +1,41 @@
/**
* @file heat_transfer_model_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Aug 20 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the inline functions of the HeatTransferModel class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_HH__
-#define __AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_HH__
+#ifndef AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_HH_
+#define AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_HH__ */
+#endif /* AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_HH_ */
diff --git a/src/model/model.cc b/src/model/model.cc
index 32fcffe96..8071891b8 100644
--- a/src/model/model.cc
+++ b/src/model/model.cc
@@ -1,333 +1,339 @@
/**
* @file model.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Oct 03 2011
* @date last modification: Tue Feb 20 2018
*
* @brief implementation of model common parts
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model.hh"
#include "communicator.hh"
#include "data_accessor.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Model::Model(Mesh & mesh, const ModelType & type, UInt dim, const ID & id,
const MemoryID & memory_id)
: Memory(id, memory_id), ModelSolver(mesh, type, id, memory_id), mesh(mesh),
spatial_dimension(dim == _all_dimensions ? mesh.getSpatialDimension()
: dim),
parser(getStaticParser()) {
AKANTU_DEBUG_IN();
this->mesh.registerEventHandler(*this, _ehp_model);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Model::~Model() = default;
/* -------------------------------------------------------------------------- */
void Model::initFullImpl(const ModelOptions & options) {
AKANTU_DEBUG_IN();
method = options.analysis_method;
if (!this->hasDefaultSolver()) {
this->initNewSolver(this->method);
}
initModel();
initFEEngineBoundary();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Model::initNewSolver(const AnalysisMethod & method) {
ID solver_name;
TimeStepSolverType tss_type;
std::tie(solver_name, tss_type) = this->getDefaultSolverID(method);
if (not this->hasSolver(solver_name)) {
ModelSolverOptions options = this->getDefaultSolverOptions(tss_type);
this->getNewSolver(solver_name, tss_type, options.non_linear_solver_type);
for (auto && is_type : options.integration_scheme_type) {
if (!this->hasIntegrationScheme(solver_name, is_type.first)) {
this->setIntegrationScheme(solver_name, is_type.first, is_type.second,
options.solution_type[is_type.first]);
}
}
}
this->method = method;
this->setDefaultSolver(solver_name);
}
/* -------------------------------------------------------------------------- */
void Model::initFEEngineBoundary() {
FEEngine & fem_boundary = getFEEngineBoundary();
fem_boundary.initShapeFunctions(_not_ghost);
fem_boundary.initShapeFunctions(_ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_not_ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_ghost);
}
/* -------------------------------------------------------------------------- */
void Model::dumpGroup(const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.dump();
}
/* -------------------------------------------------------------------------- */
void Model::dumpGroup(const std::string & group_name,
const std::string & dumper_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.dump(dumper_name);
}
/* -------------------------------------------------------------------------- */
void Model::dumpGroup() {
for (auto & group : mesh.iterateElementGroups()) {
group.dump();
}
}
/* -------------------------------------------------------------------------- */
void Model::setGroupDirectory(const std::string & directory) {
for (auto & group : mesh.iterateElementGroups()) {
group.setDirectory(directory);
}
}
/* -------------------------------------------------------------------------- */
void Model::setGroupDirectory(const std::string & directory,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Model::setGroupBaseName(const std::string & basename,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.setBaseName(basename);
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Model::getGroupDumper(const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
return group.getDumper();
}
/* -------------------------------------------------------------------------- */
// DUMPER stuff
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & field_id,
std::shared_ptr<dumpers::Field> field,
DumperIOHelper & dumper) {
#ifdef AKANTU_USE_IOHELPER
- dumper.registerField(field_id, field);
+ dumper.registerField(field_id, std::move(field));
#endif
}
/* -------------------------------------------------------------------------- */
void Model::addDumpField(const std::string & field_id) {
this->addDumpFieldToDumper(mesh.getDefaultDumperName(), field_id);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldVector(const std::string & field_id) {
this->addDumpFieldVectorToDumper(mesh.getDefaultDumperName(), field_id);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldTensor(const std::string & field_id) {
this->addDumpFieldTensorToDumper(mesh.getDefaultDumperName(), field_id);
}
/* -------------------------------------------------------------------------- */
void Model::setBaseName(const std::string & field_id) {
mesh.setBaseName(field_id);
}
/* -------------------------------------------------------------------------- */
void Model::setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
mesh.setBaseNameToDumper(dumper_name, basename);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, "all", _ek_regular,
false);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupField(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->addDumpGroupFieldToDumper(group.getDefaultDumperName(), field_id,
group_name, _ek_regular, false);
}
/* -------------------------------------------------------------------------- */
void Model::removeDumpGroupField(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->removeDumpGroupFieldFromDumper(group.getDefaultDumperName(), field_id,
group_name);
}
/* -------------------------------------------------------------------------- */
void Model::removeDumpGroupFieldFromDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.removeDumpFieldFromDumper(dumper_name, field_id);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, "all", _ek_regular,
true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldVector(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->addDumpGroupFieldVectorToDumper(group.getDefaultDumperName(), field_id,
group_name);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
_ek_regular, true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, "all", _ek_regular,
true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
- const ElementKind & element_kind,
+ ElementKind element_kind,
bool padding_flag) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
this->spatial_dimension, element_kind,
padding_flag);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
UInt spatial_dimension,
- const ElementKind & element_kind,
+ ElementKind element_kind,
bool padding_flag) {
#ifdef AKANTU_USE_IOHELPER
std::shared_ptr<dumpers::Field> field;
- if (!field)
+ if (!field) {
field = this->createNodalFieldReal(field_id, group_name, padding_flag);
- if (!field)
+ }
+ if (!field) {
field = this->createNodalFieldUInt(field_id, group_name, padding_flag);
- if (!field)
+ }
+ if (!field) {
field = this->createNodalFieldBool(field_id, group_name, padding_flag);
- if (!field)
+ }
+ if (!field) {
field = this->createElementalField(field_id, group_name, padding_flag,
spatial_dimension, element_kind);
- if (!field)
+ }
+ if (!field) {
field = this->mesh.createFieldFromAttachedData<UInt>(field_id, group_name,
element_kind);
- if (!field)
+ }
+ if (!field) {
field = this->mesh.createFieldFromAttachedData<Real>(field_id, group_name,
element_kind);
+ }
#ifndef AKANTU_NDEBUG
if (!field) {
AKANTU_DEBUG_WARNING("No field could be found based on name: " << field_id);
}
#endif
if (field) {
DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name, group_name);
this->addDumpGroupFieldToDumper(field_id, field, dumper);
}
#endif
}
/* -------------------------------------------------------------------------- */
void Model::dump() { mesh.dump(); }
/* -------------------------------------------------------------------------- */
void Model::setDirectory(const std::string & directory) {
mesh.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Model::setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
mesh.setDirectoryToDumper(dumper_name, directory);
}
/* -------------------------------------------------------------------------- */
void Model::setTextModeToDumper() { mesh.setTextModeToDumper(); }
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/model.hh b/src/model/model.hh
index df108b1c1..08d099325 100644
--- a/src/model/model.hh
+++ b/src/model/model.hh
@@ -1,348 +1,349 @@
/**
* @file model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Interface of a model
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_memory.hh"
#include "aka_named_argument.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "model_options.hh"
#include "model_solver.hh"
/* -------------------------------------------------------------------------- */
#include <typeindex>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MODEL_HH__
-#define __AKANTU_MODEL_HH__
+#ifndef AKANTU_MODEL_HH_
+#define AKANTU_MODEL_HH_
namespace akantu {
class SynchronizerRegistry;
class Parser;
class DumperIOHelper;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model : public Memory, public ModelSolver, public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- Model(Mesh & mesh, const ModelType & type,
- UInt spatial_dimension = _all_dimensions, const ID & id = "model",
- const MemoryID & memory_id = 0);
+ Model(Mesh & mesh, const ModelType & type, UInt dim = _all_dimensions,
+ const ID & id = "model", const MemoryID & memory_id = 0);
~Model() override;
using FEEngineMap = std::map<std::string, std::unique_ptr<FEEngine>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
virtual void initFullImpl(const ModelOptions & options);
public:
template <typename... pack>
std::enable_if_t<are_named_argument<pack...>::value>
initFull(pack &&... _pack) {
switch (this->model_type) {
#ifdef AKANTU_SOLID_MECHANICS
case ModelType::_solid_mechanics_model:
this->initFullImpl(SolidMechanicsModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_COHESIVE_ELEMENT
case ModelType::_solid_mechanics_model_cohesive:
this->initFullImpl(SolidMechanicsModelCohesiveOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_HEAT_TRANSFER
case ModelType::_heat_transfer_model:
this->initFullImpl(HeatTransferModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_EMBEDDED
case ModelType::_embedded_model:
this->initFullImpl(EmbeddedInterfaceModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
default:
this->initFullImpl(ModelOptions{use_named_args,
std::forward<decltype(_pack)>(_pack)...});
}
}
template <typename... pack>
std::enable_if_t<not are_named_argument<pack...>::value>
initFull(pack &&... _pack) {
this->initFullImpl(std::forward<decltype(_pack)>(_pack)...);
}
/// initialize a new solver if needed
void initNewSolver(const AnalysisMethod & method);
protected:
/// get some default values for derived classes
virtual std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) = 0;
virtual void initModel() = 0;
virtual void initFEEngineBoundary();
/// function to print the containt of the class
- void printself(std::ostream &, int = 0) const override{};
+ void printself(std::ostream & /*stream*/,
+ int /*indent*/ = 0) const override{};
public:
/* ------------------------------------------------------------------------ */
/* Access to the dumpable interface of the boundaries */
/* ------------------------------------------------------------------------ */
/// Dump the data for a given group
void dumpGroup(const std::string & group_name);
void dumpGroup(const std::string & group_name,
const std::string & dumper_name);
/// Dump the data for all boundaries
void dumpGroup();
/// Set the directory for a given group
void setGroupDirectory(const std::string & directory,
const std::string & group_name);
/// Set the directory for all boundaries
void setGroupDirectory(const std::string & directory);
/// Set the base name for a given group
void setGroupBaseName(const std::string & basename,
const std::string & group_name);
/// Get the internal dumper of a given group
DumperIOHelper & getGroupDumper(const std::string & group_name);
/* ------------------------------------------------------------------------ */
/* Function for non local capabilities */
/* ------------------------------------------------------------------------ */
virtual void updateDataForNonLocalCriterion(__attribute__((unused))
ElementTypeMapReal & criterion) {
AKANTU_TO_IMPLEMENT();
}
protected:
template <typename T>
void allocNodalField(Array<T> *& array, UInt nb_component,
const ID & name);
template <typename T>
void allocNodalField(std::unique_ptr<Array<T>> & array, UInt nb_component,
const ID & name) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get id of model
- AKANTU_GET_MACRO(ID, id, const ID)
+ AKANTU_GET_MACRO(ID, id, const ID &)
/// get the number of surfaces
AKANTU_GET_MACRO(Mesh, mesh, Mesh &)
/// synchronize the boundary in case of parallel run
virtual void synchronizeBoundaries(){};
/// return the fem object associated with a provided name
inline FEEngine & getFEEngine(const ID & name = "") const;
/// return the fem boundary object associated with a provided name
virtual FEEngine & getFEEngineBoundary(const ID & name = "");
/// register a fem object associated with name
template <typename FEEngineClass>
inline void registerFEEngineObject(const std::string & name, Mesh & mesh,
UInt spatial_dimension);
/// unregister a fem object associated with name
inline void unRegisterFEEngineObject(const std::string & name);
/// return the synchronizer registry
SynchronizerRegistry & getSynchronizerRegistry();
/// return the fem object associated with a provided name
template <typename FEEngineClass>
inline FEEngineClass & getFEEngineClass(std::string name = "") const;
/// return the fem boundary object associated with a provided name
template <typename FEEngineClass>
inline FEEngineClass & getFEEngineClassBoundary(std::string name = "");
/// Get the type of analysis method used
AKANTU_GET_MACRO(AnalysisMethod, method, AnalysisMethod);
/* ------------------------------------------------------------------------ */
/* Pack and unpack helper functions */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbIntegrationPoints(const Array<Element> & elements,
const ID & fem_id = ID()) const;
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
void setTextModeToDumper();
virtual void addDumpGroupFieldToDumper(const std::string & field_id,
std::shared_ptr<dumpers::Field> field,
DumperIOHelper & dumper);
virtual void addDumpField(const std::string & field_id);
virtual void addDumpFieldVector(const std::string & field_id);
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensor(const std::string & field_id);
- virtual void setBaseName(const std::string & basename);
+ virtual void setBaseName(const std::string & field_id);
virtual void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename);
virtual void addDumpGroupField(const std::string & field_id,
const std::string & group_name);
virtual void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
- const ElementKind & element_kind,
+ ElementKind element_kind,
bool padding_flag);
virtual void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
UInt spatial_dimension,
- const ElementKind & element_kind,
+ ElementKind element_kind,
bool padding_flag);
virtual void removeDumpGroupField(const std::string & field_id,
const std::string & group_name);
virtual void removeDumpGroupFieldFromDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name);
virtual void addDumpGroupFieldVector(const std::string & field_id,
const std::string & group_name);
virtual void addDumpGroupFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name);
virtual std::shared_ptr<dumpers::Field>
- createNodalFieldReal(__attribute__((unused)) const std::string & field_name,
- __attribute__((unused)) const std::string & group_name,
- __attribute__((unused)) bool padding_flag) {
+ createNodalFieldReal(const std::string & /*field_name*/,
+ const std::string & /*group_name*/,
+ bool /*padding_flag*/) {
return nullptr;
}
virtual std::shared_ptr<dumpers::Field>
- createNodalFieldUInt(__attribute__((unused)) const std::string & field_name,
- __attribute__((unused)) const std::string & group_name,
- __attribute__((unused)) bool padding_flag) {
+ createNodalFieldUInt(const std::string & /*field_name*/,
+ const std::string & /*group_name*/,
+ bool /*padding_flag*/) {
return nullptr;
}
virtual std::shared_ptr<dumpers::Field>
- createNodalFieldBool(__attribute__((unused)) const std::string & field_name,
- __attribute__((unused)) const std::string & group_name,
- __attribute__((unused)) bool padding_flag) {
+ createNodalFieldBool(const std::string & /*field_name*/,
+ const std::string & /*group_name*/,
+ bool /*padding_flag*/) {
return nullptr;
}
virtual std::shared_ptr<dumpers::Field>
- createElementalField(__attribute__((unused)) const std::string & field_name,
- __attribute__((unused)) const std::string & group_name,
- __attribute__((unused)) bool padding_flag,
- __attribute__((unused)) const UInt & spatial_dimension,
- __attribute__((unused)) const ElementKind & kind) {
+ createElementalField(const std::string & /*field_name*/,
+ const std::string & /*group_name*/,
+ bool /*padding_flag*/,
+ UInt /*spatial_dimension*/,
+ ElementKind /*kind*/) {
return nullptr;
}
void setDirectory(const std::string & directory);
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory);
virtual void dump();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
- friend std::ostream & operator<<(std::ostream &, const Model &);
+ friend std::ostream & operator<<(std::ostream & /*stream*/,
+ const Model & /*_this*/);
/// analysis method check the list in akantu::AnalysisMethod
AnalysisMethod method;
/// Mesh
Mesh & mesh;
/// Spatial dimension of the problem
UInt spatial_dimension;
/// the main fem object present in all models
FEEngineMap fems;
/// the fem object present in all models for boundaries
FEEngineMap fems_boundary;
/// default fem object
std::string default_fem;
/// parser to the pointer to use
Parser & parser;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Model & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "model_inline_impl.hh"
-#endif /* __AKANTU_MODEL_HH__ */
+#endif /* AKANTU_MODEL_HH_ */
diff --git a/src/model/model_inline_impl.hh b/src/model/model_inline_impl.hh
index d1a67bd98..48135af3f 100644
--- a/src/model/model_inline_impl.hh
+++ b/src/model/model_inline_impl.hh
@@ -1,175 +1,181 @@
/**
* @file model_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 25 2010
* @date last modification: Wed Nov 08 2017
*
* @brief inline implementation of the model class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MODEL_INLINE_IMPL_HH__
-#define __AKANTU_MODEL_INLINE_IMPL_HH__
+#ifndef AKANTU_MODEL_INLINE_IMPL_HH_
+#define AKANTU_MODEL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline FEEngineClass & Model::getFEEngineClassBoundary(std::string name) {
- if (name == "")
+ if (name.empty()) {
name = default_fem;
+ }
auto it_boun = fems_boundary.find(name);
if (it_boun == fems_boundary.end()) {
AKANTU_DEBUG_INFO("Creating FEEngine boundary " << name);
auto it = fems.find(name);
if (it == fems.end()) {
AKANTU_EXCEPTION("The FEEngine " << name << " is not registered");
}
auto spatial_dimension = it->second->getElementDimension();
fems_boundary[name] = std::make_unique<FEEngineClass>(
it->second->getMesh(), spatial_dimension - 1,
id + ":fem_boundary:" + name, memory_id);
}
return aka::as_type<FEEngineClass>(*fems_boundary[name]);
}
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline FEEngineClass & Model::getFEEngineClass(std::string name) const {
- if (name == "")
+ if (name.empty()) {
name = default_fem;
+ }
auto it = fems.find(name);
if (it == fems.end()) {
AKANTU_EXCEPTION("The FEEngine " << name << " is not registered");
}
return aka::as_type<FEEngineClass>(*(it->second));
}
/* -------------------------------------------------------------------------- */
inline void Model::unRegisterFEEngineObject(const std::string & name) {
auto it = fems.find(name);
if (it == fems.end()) {
AKANTU_EXCEPTION("FEEngine object with name " << name << " was not found");
}
fems.erase(it);
- if (not fems.empty() and default_fem == name)
+ if (not fems.empty() and default_fem == name) {
default_fem = (*fems.begin()).first;
+ }
}
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline void Model::registerFEEngineObject(const std::string & name, Mesh & mesh,
UInt spatial_dimension) {
- if (fems.size() == 0)
+ if (fems.empty()) {
default_fem = name;
+ }
auto it = fems.find(name);
if (it != fems.end()) {
AKANTU_EXCEPTION("FEEngine object with name " << name
<< " was already created");
}
fems[name] = std::make_unique<FEEngineClass>(
mesh, spatial_dimension, id + ":fem:" + name + std::to_string(memory_id),
memory_id);
}
/* -------------------------------------------------------------------------- */
inline FEEngine & Model::getFEEngine(const ID & name) const {
- ID tmp_name = (name == "") ? default_fem : name;
+ ID tmp_name = (name.empty()) ? default_fem : name;
auto it = fems.find(tmp_name);
if (it == fems.end()) {
AKANTU_EXCEPTION("The FEEngine " << tmp_name << " is not registered");
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
inline FEEngine & Model::getFEEngineBoundary(const ID & name) {
- ID tmp_name = (name == "") ? default_fem : name;
+ ID tmp_name = (name.empty()) ? default_fem : name;
auto it = fems_boundary.find(tmp_name);
if (it == fems_boundary.end()) {
AKANTU_EXCEPTION("The FEEngine boundary " << tmp_name
<< " is not registered");
}
AKANTU_DEBUG_ASSERT(it->second != nullptr, "The FEEngine boundary "
<< tmp_name
<< " was not created");
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Model::allocNodalField(Array<T> *& array, UInt nb_component,
const ID & name) {
- if (array)
+ if (array) {
return;
+ }
UInt nb_nodes = mesh.getNbNodes();
array = &(alloc<T>(id + ":" + name, nb_nodes, nb_component, T()));
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Model::allocNodalField(std::unique_ptr<Array<T>> & array,
UInt nb_component, const ID & name) const {
- if (array)
+ if (array) {
return;
+ }
UInt nb_nodes = mesh.getNbNodes();
array =
std::make_unique<Array<T>>(nb_nodes, nb_component, T(), id + ":" + name);
}
/* -------------------------------------------------------------------------- */
inline UInt Model::getNbIntegrationPoints(const Array<Element> & elements,
const ID & fem_id) const {
UInt nb_quad = 0;
for (auto && el : elements) {
nb_quad +=
getFEEngine(fem_id).getNbIntegrationPoints(el.type, el.ghost_type);
}
return nb_quad;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_MODEL_INLINE_IMPL_HH__ */
+#endif /* AKANTU_MODEL_INLINE_IMPL_HH_ */
diff --git a/src/model/model_options.hh b/src/model/model_options.hh
index b0aa1e058..b4ce6d8d1 100644
--- a/src/model/model_options.hh
+++ b/src/model/model_options.hh
@@ -1,138 +1,139 @@
/**
* @file model_options.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 04 2017
* @date last modification: Wed Jan 31 2018
*
* @brief A Documented file.
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_named_argument.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MODEL_OPTIONS_HH__
-#define __AKANTU_MODEL_OPTIONS_HH__
+#ifndef AKANTU_MODEL_OPTIONS_HH_
+#define AKANTU_MODEL_OPTIONS_HH_
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(analysis_method);
}
struct ModelOptions {
explicit ModelOptions(AnalysisMethod analysis_method = _static)
: analysis_method(analysis_method) {}
template <typename... pack>
- ModelOptions(use_named_args_t, pack &&... _pack)
+ ModelOptions(use_named_args_t /*unused*/, pack &&... _pack)
: ModelOptions(OPTIONAL_NAMED_ARG(analysis_method, _static)) {}
virtual ~ModelOptions() = default;
AnalysisMethod analysis_method;
};
#ifdef AKANTU_SOLID_MECHANICS
/* -------------------------------------------------------------------------- */
struct SolidMechanicsModelOptions : public ModelOptions {
explicit SolidMechanicsModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass)
: ModelOptions(analysis_method) {}
template <typename... pack>
- SolidMechanicsModelOptions(use_named_args_t, pack &&... _pack)
+ SolidMechanicsModelOptions(use_named_args_t /*unused*/, pack &&... _pack)
: SolidMechanicsModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass)) {}
};
#endif
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_COHESIVE_ELEMENT
namespace {
DECLARE_NAMED_ARGUMENT(is_extrinsic);
}
/* -------------------------------------------------------------------------- */
struct SolidMechanicsModelCohesiveOptions : public SolidMechanicsModelOptions {
SolidMechanicsModelCohesiveOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass,
bool extrinsic = false)
: SolidMechanicsModelOptions(analysis_method), is_extrinsic(extrinsic) {}
template <typename... pack>
- SolidMechanicsModelCohesiveOptions(use_named_args_t, pack &&... _pack)
+ SolidMechanicsModelCohesiveOptions(use_named_args_t /*unused*/,
+ pack &&... _pack)
: SolidMechanicsModelCohesiveOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass),
OPTIONAL_NAMED_ARG(is_extrinsic, false)) {}
bool is_extrinsic{false};
};
#endif
#ifdef AKANTU_HEAT_TRANSFER
/* -------------------------------------------------------------------------- */
struct HeatTransferModelOptions : public ModelOptions {
explicit HeatTransferModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass)
: ModelOptions(analysis_method) {}
template <typename... pack>
- HeatTransferModelOptions(use_named_args_t, pack &&... _pack)
+ HeatTransferModelOptions(use_named_args_t /*unused*/, pack &&... _pack)
: HeatTransferModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass)) {}
};
#endif
#ifdef AKANTU_EMBEDDED
namespace {
DECLARE_NAMED_ARGUMENT(init_intersections);
}
/* -------------------------------------------------------------------------- */
struct EmbeddedInterfaceModelOptions : SolidMechanicsModelOptions {
/**
* @brief Constructor for EmbeddedInterfaceModelOptions
* @param analysis_method see SolidMechanicsModelOptions
* @param init_intersections compute intersections
*/
EmbeddedInterfaceModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass,
bool init_intersections = true)
: SolidMechanicsModelOptions(analysis_method),
has_intersections(init_intersections) {}
template <typename... pack>
- EmbeddedInterfaceModelOptions(use_named_args_t, pack &&... _pack)
+ EmbeddedInterfaceModelOptions(use_named_args_t /*unused*/, pack &&... _pack)
: EmbeddedInterfaceModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass),
OPTIONAL_NAMED_ARG(init_intersections, true)) {}
/// Should consider reinforcements
bool has_intersections;
};
#endif
} // namespace akantu
-#endif /* __AKANTU_MODEL_OPTIONS_HH__ */
+#endif /* AKANTU_MODEL_OPTIONS_HH_ */
diff --git a/src/model/solid_mechanics/material.cc b/src/model/solid_mechanics/material.cc
index e4726a1ec..9004c7f2a 100644
--- a/src/model/solid_mechanics/material.cc
+++ b/src/model/solid_mechanics/material.cc
@@ -1,1363 +1,1384 @@
/**
* @file material.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the common part of the material class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Material::Material(SolidMechanicsModel & model, const ID & id)
: Memory(id, model.getMemoryID()), Parsable(ParserType::_material, id),
is_init(false), fem(model.getFEEngine()), finite_deformation(false),
- name(""), model(model),
- spatial_dimension(this->model.getSpatialDimension()),
+ model(model), spatial_dimension(this->model.getSpatialDimension()),
element_filter("element_filter", id, this->memory_id),
stress("stress", *this), eigengradu("eigen_grad_u", *this),
gradu("grad_u", *this), green_strain("green_strain", *this),
piola_kirchhoff_2("piola_kirchhoff_2", *this),
potential_energy("potential_energy", *this), is_non_local(false),
use_previous_stress(false), use_previous_gradu(false),
interpolation_inverse_coordinates("interpolation inverse coordinates",
*this),
interpolation_points_matrices("interpolation points matrices", *this),
eigen_grad_u(model.getSpatialDimension(), model.getSpatialDimension(),
0.) {
AKANTU_DEBUG_IN();
this->registerParam("eigen_grad_u", eigen_grad_u, _pat_parsable,
"EigenGradU");
/// for each connectivity types allocate the element filer array of the
/// material
element_filter.initialize(model.getMesh(),
_spatial_dimension = spatial_dimension,
_element_kind = _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: Memory(id, model.getMemoryID()), Parsable(ParserType::_material, id),
- is_init(false), fem(fe_engine), finite_deformation(false), name(""),
- model(model), spatial_dimension(dim),
+ is_init(false), fem(fe_engine), finite_deformation(false), model(model),
+ spatial_dimension(dim),
element_filter("element_filter", id, this->memory_id),
stress("stress", *this, dim, fe_engine, this->element_filter),
eigengradu("eigen_grad_u", *this, dim, fe_engine, this->element_filter),
gradu("gradu", *this, dim, fe_engine, this->element_filter),
green_strain("green_strain", *this, dim, fe_engine, this->element_filter),
piola_kirchhoff_2("piola_kirchhoff_2", *this, dim, fe_engine,
this->element_filter),
potential_energy("potential_energy", *this, dim, fe_engine,
this->element_filter),
is_non_local(false), use_previous_stress(false),
use_previous_gradu(false),
interpolation_inverse_coordinates("interpolation inverse_coordinates",
*this, dim, fe_engine,
this->element_filter),
interpolation_points_matrices("interpolation points matrices", *this, dim,
fe_engine, this->element_filter) {
AKANTU_DEBUG_IN();
element_filter.initialize(mesh, _spatial_dimension = spatial_dimension,
_element_kind = _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::~Material() = default;
/* -------------------------------------------------------------------------- */
void Material::initialize() {
registerParam("rho", rho, Real(0.), _pat_parsable | _pat_modifiable,
"Density");
registerParam("name", name, std::string(), _pat_parsable | _pat_readable);
registerParam("finite_deformation", finite_deformation, false,
_pat_parsable | _pat_readable, "Is finite deformation");
registerParam("inelastic_deformation", inelastic_deformation, false,
_pat_internal, "Is inelastic deformation");
/// allocate gradu stress for local elements
eigengradu.initialize(spatial_dimension * spatial_dimension);
gradu.initialize(spatial_dimension * spatial_dimension);
stress.initialize(spatial_dimension * spatial_dimension);
potential_energy.initialize(1);
this->model.registerEventHandler(*this);
}
/* -------------------------------------------------------------------------- */
void Material::initMaterial() {
AKANTU_DEBUG_IN();
if (finite_deformation) {
this->piola_kirchhoff_2.initialize(spatial_dimension * spatial_dimension);
- if (use_previous_stress)
+ if (use_previous_stress) {
this->piola_kirchhoff_2.initializeHistory();
+ }
this->green_strain.initialize(spatial_dimension * spatial_dimension);
}
- if (use_previous_stress)
+ if (use_previous_stress) {
this->stress.initializeHistory();
- if (use_previous_gradu)
+ }
+ if (use_previous_gradu) {
this->gradu.initializeHistory();
+ }
this->resizeInternals();
auto dim = model.getSpatialDimension();
for(const auto & type : element_filter.elementTypes()) {
for(auto eigen_gradu : make_view(eigengradu(type), dim, dim)) {
eigen_gradu = eigen_grad_u;
}
}
is_init = true;
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::savePreviousState() {
AKANTU_DEBUG_IN();
- for (auto pair : internal_vectors_real)
- if (pair.second->hasHistory())
+ for (auto pair : internal_vectors_real) {
+ if (pair.second->hasHistory()) {
pair.second->saveCurrentValues();
+ }
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::restorePreviousState() {
AKANTU_DEBUG_IN();
- for (auto pair : internal_vectors_real)
- if (pair.second->hasHistory())
+ for (auto pair : internal_vectors_real) {
+ if (pair.second->hasHistory()) {
pair.second->restorePreviousValues();
+ }
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the internal forces by assembling @f$\int_{e} \sigma_e \frac{\partial
* \varphi}{\partial X} dX @f$
*
* @param[in] ghost_type compute the internal forces for _ghost or _not_ghost
* element
*/
void Material::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
if (!finite_deformation) {
auto & internal_force = const_cast<Array<Real> &>(model.getInternalForce());
// Mesh & mesh = fem.getMesh();
for (auto && type :
element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
- if (nb_element == 0)
+ if (nb_element == 0) {
continue;
+ }
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
/// compute @f$\sigma \frac{\partial \varphi}{\partial X}@f$ by
/// @f$\mathbf{B}^t \mathbf{\sigma}_q@f$
- Array<Real> * sigma_dphi_dx =
+ auto * sigma_dphi_dx =
new Array<Real>(nb_element * nb_quadrature_points,
size_of_shapes_derivatives, "sigma_x_dphi_/_dX");
fem.computeBtD(stress(type, ghost_type), *sigma_dphi_dx, type, ghost_type,
elem_filter);
/**
* compute @f$\int \sigma * \frac{\partial \varphi}{\partial X}dX@f$ by
* @f$ \sum_q \mathbf{B}^t
* \mathbf{\sigma}_q \overline w_q J_q@f$
*/
- Array<Real> * int_sigma_dphi_dx =
+ auto * int_sigma_dphi_dx =
new Array<Real>(nb_element, nb_nodes_per_element * spatial_dimension,
"int_sigma_x_dphi_/_dX");
fem.integrate(*sigma_dphi_dx, *int_sigma_dphi_dx,
size_of_shapes_derivatives, type, ghost_type, elem_filter);
delete sigma_dphi_dx;
/// assemble
model.getDOFManager().assembleElementalArrayLocalArray(
*int_sigma_dphi_dx, internal_force, type, ghost_type, -1,
elem_filter);
delete int_sigma_dphi_dx;
}
} else {
switch (spatial_dimension) {
case 1:
this->assembleInternalForces<1>(ghost_type);
break;
case 2:
this->assembleInternalForces<2>(ghost_type);
break;
case 3:
this->assembleInternalForces<3>(ghost_type);
break;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stress from the gradu
*
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void Material::computeAllStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (const auto & type :
element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
- if (elem_filter.size() == 0)
+ if (elem_filter.empty()) {
continue;
+ }
Array<Real> & gradu_vect = gradu(type, ghost_type);
/// compute @f$\nabla u@f$
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect,
spatial_dimension, type, ghost_type,
elem_filter);
gradu_vect -= eigengradu(type, ghost_type);
/// compute @f$\mathbf{\sigma}_q@f$ from @f$\nabla u@f$
computeStress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computeAllCauchyStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(finite_deformation, "The Cauchy stress can only be "
"computed if you are working in "
"finite deformation.");
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
switch (spatial_dimension) {
case 1:
this->StoCauchy<1>(type, ghost_type);
break;
case 2:
this->StoCauchy<2>(type, ghost_type);
break;
case 3:
this->StoCauchy<3>(type, ghost_type);
break;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::StoCauchy(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto gradu_it = this->gradu(el_type, ghost_type).begin(dim, dim);
auto gradu_end = this->gradu(el_type, ghost_type).end(dim, dim);
auto piola_it = this->piola_kirchhoff_2(el_type, ghost_type).begin(dim, dim);
auto stress_it = this->stress(el_type, ghost_type).begin(dim, dim);
for (; gradu_it != gradu_end; ++gradu_it, ++piola_it, ++stress_it) {
Matrix<Real> & grad_u = *gradu_it;
Matrix<Real> & piola = *piola_it;
Matrix<Real> & sigma = *stress_it;
auto F_tensor = gradUToF<dim>(grad_u);
this->StoCauchy<dim>(F_tensor, piola, sigma);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::setToSteadyState(GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & displacement = model.getDisplacement();
// resizeInternalArray(gradu);
UInt spatial_dimension = model.getSpatialDimension();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
/// compute @f$\nabla u@f$
fem.gradientOnIntegrationPoints(displacement, gradu_vect, spatial_dimension,
type, ghost_type, elem_filter);
setToSteadyState(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stiffness matrix by assembling @f$\int_{\omega} B^t \times D
* \times B d\omega @f$
*
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void Material::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
if (finite_deformation) {
switch (spatial_dimension) {
case 1: {
assembleStiffnessMatrixNL<1>(type, ghost_type);
assembleStiffnessMatrixL2<1>(type, ghost_type);
break;
}
case 2: {
assembleStiffnessMatrixNL<2>(type, ghost_type);
assembleStiffnessMatrixL2<2>(type, ghost_type);
break;
}
case 3: {
assembleStiffnessMatrixNL<3>(type, ghost_type);
assembleStiffnessMatrixL2<3>(type, ghost_type);
break;
}
}
} else {
switch (spatial_dimension) {
case 1: {
assembleStiffnessMatrix<1>(type, ghost_type);
break;
}
case 2: {
assembleStiffnessMatrix<2>(type, ghost_type);
break;
}
case 3: {
assembleStiffnessMatrix<3>(type, ghost_type);
break;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
-void Material::assembleStiffnessMatrix(const ElementType & type,
- GhostType ghost_type) {
+void Material::assembleStiffnessMatrix(ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> & elem_filter = element_filter(type, ghost_type);
- if (elem_filter.size() == 0) {
+ if (elem_filter.empty()) {
AKANTU_DEBUG_OUT();
return;
}
// const Array<Real> & shapes_derivatives =
// fem.getShapesDerivatives(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect, dim,
type, ghost_type, elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
- Array<Real> * tangent_stiffness_matrix =
+ auto * tangent_stiffness_matrix =
new Array<Real>(nb_element * nb_quadrature_points,
tangent_size * tangent_size, "tangent_stiffness_matrix");
- tangent_stiffness_matrix->clear();
+ tangent_stiffness_matrix->zero();
computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = dim * nb_nodes_per_element;
- Array<Real> * bt_d_b = new Array<Real>(nb_element * nb_quadrature_points,
- bt_d_b_size * bt_d_b_size, "B^t*D*B");
+ auto * bt_d_b = new Array<Real>(nb_element * nb_quadrature_points,
+ bt_d_b_size * bt_d_b_size, "B^t*D*B");
fem.computeBtDB(*tangent_stiffness_matrix, *bt_d_b, 4, type, ghost_type,
elem_filter);
delete tangent_stiffness_matrix;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
- Array<Real> * K_e =
- new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
+ auto * K_e = new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
fem.integrate(*bt_d_b, *K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
elem_filter);
delete bt_d_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
-void Material::assembleStiffnessMatrixNL(const ElementType & type,
+void Material::assembleStiffnessMatrixNL(ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
// Array<Real> & gradu_vect = delta_gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
- Array<Real> * shapes_derivatives_filtered = new Array<Real>(
+ auto * shapes_derivatives_filtered = new Array<Real>(
nb_element * nb_quadrature_points, dim * nb_nodes_per_element,
"shapes derivatives filtered");
- fem.filterElementalData(fem.getMesh(), shapes_derivatives,
- *shapes_derivatives_filtered, type, ghost_type,
- elem_filter);
+ FEEngine::filterElementalData(fem.getMesh(), shapes_derivatives,
+ *shapes_derivatives_filtered, type, ghost_type,
+ elem_filter);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_s_b_size = dim * nb_nodes_per_element;
- Array<Real> * bt_s_b = new Array<Real>(nb_element * nb_quadrature_points,
- bt_s_b_size * bt_s_b_size, "B^t*D*B");
+ auto * bt_s_b = new Array<Real>(nb_element * nb_quadrature_points,
+ bt_s_b_size * bt_s_b_size, "B^t*D*B");
UInt piola_matrix_size = getCauchyStressMatrixSize(dim);
Matrix<Real> B(piola_matrix_size, bt_s_b_size);
Matrix<Real> Bt_S(bt_s_b_size, piola_matrix_size);
Matrix<Real> S(piola_matrix_size, piola_matrix_size);
auto shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
spatial_dimension, nb_nodes_per_element);
auto Bt_S_B_it = bt_s_b->begin(bt_s_b_size, bt_s_b_size);
auto Bt_S_B_end = bt_s_b->end(bt_s_b_size, bt_s_b_size);
auto piola_it = piola_kirchhoff_2(type, ghost_type).begin(dim, dim);
for (; Bt_S_B_it != Bt_S_B_end;
++Bt_S_B_it, ++shapes_derivatives_filtered_it, ++piola_it) {
auto & Bt_S_B = *Bt_S_B_it;
const auto & Piola_kirchhoff_matrix = *piola_it;
setCauchyStressMatrix<dim>(Piola_kirchhoff_matrix, S);
VoigtHelper<dim>::transferBMatrixToBNL(*shapes_derivatives_filtered_it, B,
nb_nodes_per_element);
Bt_S.template mul<true, false>(B, S);
Bt_S_B.template mul<false, false>(Bt_S, B);
}
delete shapes_derivatives_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
- Array<Real> * K_e =
- new Array<Real>(nb_element, bt_s_b_size * bt_s_b_size, "K_e");
+ auto * K_e = new Array<Real>(nb_element, bt_s_b_size * bt_s_b_size, "K_e");
fem.integrate(*bt_s_b, *K_e, bt_s_b_size * bt_s_b_size, type, ghost_type,
elem_filter);
delete bt_s_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
-void Material::assembleStiffnessMatrixL2(const ElementType & type,
+void Material::assembleStiffnessMatrixL2(ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect, dim,
type, ghost_type, elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
- Array<Real> * tangent_stiffness_matrix =
+ auto * tangent_stiffness_matrix =
new Array<Real>(nb_element * nb_quadrature_points,
tangent_size * tangent_size, "tangent_stiffness_matrix");
- tangent_stiffness_matrix->clear();
+ tangent_stiffness_matrix->zero();
computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);
- Array<Real> * shapes_derivatives_filtered = new Array<Real>(
+ auto * shapes_derivatives_filtered = new Array<Real>(
nb_element * nb_quadrature_points, dim * nb_nodes_per_element,
"shapes derivatives filtered");
- fem.filterElementalData(fem.getMesh(), shapes_derivatives,
- *shapes_derivatives_filtered, type, ghost_type,
- elem_filter);
+ FEEngine::filterElementalData(fem.getMesh(), shapes_derivatives,
+ *shapes_derivatives_filtered, type, ghost_type,
+ elem_filter);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = dim * nb_nodes_per_element;
- Array<Real> * bt_d_b = new Array<Real>(nb_element * nb_quadrature_points,
- bt_d_b_size * bt_d_b_size, "B^t*D*B");
+ auto * bt_d_b = new Array<Real>(nb_element * nb_quadrature_points,
+ bt_d_b_size * bt_d_b_size, "B^t*D*B");
Matrix<Real> B(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> B2(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> Bt_D(dim * nb_nodes_per_element, tangent_size);
auto shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
spatial_dimension, nb_nodes_per_element);
auto Bt_D_B_it = bt_d_b->begin(bt_d_b_size, bt_d_b_size);
auto grad_u_it = gradu_vect.begin(dim, dim);
auto D_it = tangent_stiffness_matrix->begin(tangent_size, tangent_size);
auto D_end = tangent_stiffness_matrix->end(tangent_size, tangent_size);
for (; D_it != D_end;
++D_it, ++Bt_D_B_it, ++shapes_derivatives_filtered_it, ++grad_u_it) {
const auto & grad_u = *grad_u_it;
const auto & D = *D_it;
auto & Bt_D_B = *Bt_D_B_it;
// transferBMatrixToBL1<dim > (*shapes_derivatives_filtered_it, B,
// nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToBL2(*shapes_derivatives_filtered_it,
grad_u, B2, nb_nodes_per_element);
B += B2;
Bt_D.template mul<true, false>(B, D);
Bt_D_B.template mul<false, false>(Bt_D, B);
}
delete tangent_stiffness_matrix;
delete shapes_derivatives_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
- Array<Real> * K_e =
- new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
+ auto * K_e = new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
fem.integrate(*bt_d_b, *K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
elem_filter);
delete bt_d_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & internal_force = model.getInternalForce();
Mesh & mesh = fem.getMesh();
for (auto type : element_filter.elementTypes(_ghost_type = ghost_type)) {
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
- if (elem_filter.size() == 0)
+ if (elem_filter.empty()) {
continue;
+ }
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
- Array<Real> * shapesd_filtered = new Array<Real>(
+ auto * shapesd_filtered = new Array<Real>(
nb_element, size_of_shapes_derivatives, "filtered shapesd");
- fem.filterElementalData(mesh, shapes_derivatives, *shapesd_filtered, type,
- ghost_type, elem_filter);
+ FEEngine::filterElementalData(mesh, shapes_derivatives, *shapesd_filtered,
+ type, ghost_type, elem_filter);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
// Set stress vectors
UInt stress_size = getTangentStiffnessVoigtSize(dim);
// Set matrices B and BNL*
UInt bt_s_size = dim * nb_nodes_per_element;
auto * bt_s =
new Array<Real>(nb_element * nb_quadrature_points, bt_s_size, "B^t*S");
auto grad_u_it = this->gradu(type, ghost_type).begin(dim, dim);
auto grad_u_end = this->gradu(type, ghost_type).end(dim, dim);
auto stress_it = this->piola_kirchhoff_2(type, ghost_type).begin(dim, dim);
shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator bt_s_it = bt_s->begin(bt_s_size, 1);
Matrix<Real> B_tensor(stress_size, bt_s_size);
Matrix<Real> B2_tensor(stress_size, bt_s_size);
for (; grad_u_it != grad_u_end; ++grad_u_it, ++stress_it,
++shapes_derivatives_filtered_it,
++bt_s_it) {
auto & grad_u = *grad_u_it;
auto & r = *bt_s_it;
auto & S = *stress_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B_tensor, nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToBL2(*shapes_derivatives_filtered_it,
grad_u, B2_tensor,
nb_nodes_per_element);
B_tensor += B2_tensor;
auto S_vect = Material::stressToVoigt<dim>(S);
Matrix<Real> S_voigt(S_vect.storage(), stress_size, 1);
r.template mul<true, false>(B_tensor, S_voigt);
}
delete shapesd_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
- Array<Real> * r_e = new Array<Real>(nb_element, bt_s_size, "r_e");
+ auto * r_e = new Array<Real>(nb_element, bt_s_size, "r_e");
fem.integrate(*bt_s, *r_e, bt_s_size, type, ghost_type, elem_filter);
delete bt_s;
model.getDOFManager().assembleElementalArrayLocalArray(
*r_e, internal_force, type, ghost_type, -1., elem_filter);
delete r_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computePotentialEnergyByElements() {
AKANTU_DEBUG_IN();
for (auto type : element_filter.elementTypes(spatial_dimension, _not_ghost)) {
computePotentialEnergy(type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void Material::computePotentialEnergy(ElementType) {
+void Material::computePotentialEnergy(ElementType /*unused*/) {
AKANTU_DEBUG_IN();
AKANTU_TO_IMPLEMENT();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real Material::getPotentialEnergy() {
AKANTU_DEBUG_IN();
Real epot = 0.;
computePotentialEnergyByElements();
/// integrate the potential energy for each type of elements
for (auto type : element_filter.elementTypes(spatial_dimension, _not_ghost)) {
epot += fem.integrate(potential_energy(type, _not_ghost), type, _not_ghost,
element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
Real Material::getPotentialEnergy(ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
Real epot = 0.;
Vector<Real> epot_on_quad_points(fem.getNbIntegrationPoints(type));
computePotentialEnergyByElement(type, index, epot_on_quad_points);
epot = fem.integrate(epot_on_quad_points, type, element_filter(type)(index));
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(const std::string & type) {
AKANTU_DEBUG_IN();
- if (type == "potential")
+ if (type == "potential") {
return getPotentialEnergy();
+ }
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(const std::string & energy_id, ElementType type,
UInt index) {
AKANTU_DEBUG_IN();
- if (energy_id == "potential")
+ if (energy_id == "potential") {
return getPotentialEnergy(type, index);
+ }
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
void Material::initElementalFieldInterpolation(
const ElementTypeMapArray<Real> & interpolation_points_coordinates) {
AKANTU_DEBUG_IN();
this->fem.initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates, this->interpolation_points_matrices,
this->interpolation_inverse_coordinates, &(this->element_filter));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStress(ElementTypeMapArray<Real> & result,
const GhostType ghost_type) {
this->fem.interpolateElementalFieldFromIntegrationPoints(
this->stress, this->interpolation_points_matrices,
this->interpolation_inverse_coordinates, result, ghost_type,
&(this->element_filter));
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStressOnFacets(
ElementTypeMapArray<Real> & result,
ElementTypeMapArray<Real> & by_elem_result, const GhostType ghost_type) {
interpolateStress(by_elem_result, ghost_type);
UInt stress_size = this->stress.getNbComponent();
const Mesh & mesh = this->model.getMesh();
const Mesh & mesh_facets = mesh.getMeshFacets();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_fil = element_filter(type, ghost_type);
Array<Real> & by_elem_res = by_elem_result(type, ghost_type);
UInt nb_element = elem_fil.size();
UInt nb_element_full = this->model.getMesh().getNbElement(type, ghost_type);
UInt nb_interpolation_points_per_elem =
by_elem_res.size() / nb_element_full;
const Array<Element> & facet_to_element =
mesh_facets.getSubelementToElement(type, ghost_type);
ElementType type_facet = Mesh::getFacetType(type);
UInt nb_facet_per_elem = facet_to_element.getNbComponent();
UInt nb_quad_per_facet =
nb_interpolation_points_per_elem / nb_facet_per_elem;
Element element_for_comparison{type, 0, ghost_type};
const Array<std::vector<Element>> * element_to_facet = nullptr;
GhostType current_ghost_type = _casper;
Array<Real> * result_vec = nullptr;
Array<Real>::const_matrix_iterator result_it =
by_elem_res.begin_reinterpret(
stress_size, nb_interpolation_points_per_elem, nb_element_full);
for (UInt el = 0; el < nb_element; ++el) {
UInt global_el = elem_fil(el);
element_for_comparison.element = global_el;
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
Element facet_elem = facet_to_element(global_el, f);
UInt global_facet = facet_elem.element;
if (facet_elem.ghost_type != current_ghost_type) {
current_ghost_type = facet_elem.ghost_type;
element_to_facet = &mesh_facets.getElementToSubelement(
type_facet, current_ghost_type);
result_vec = &result(type_facet, current_ghost_type);
}
bool is_second_element =
(*element_to_facet)(global_facet)[0] != element_for_comparison;
for (UInt q = 0; q < nb_quad_per_facet; ++q) {
Vector<Real> result_local(result_vec->storage() +
(global_facet * nb_quad_per_facet + q) *
result_vec->getNbComponent() +
- is_second_element * stress_size,
+ static_cast<UInt>(is_second_element) *
+ stress_size,
stress_size);
const Matrix<Real> & result_tmp(result_it[global_el]);
result_local = result_tmp(f * nb_quad_per_facet + q);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
const Array<T> & Material::getArray(const ID & /*vect_id*/,
- const ElementType & /*type*/,
- const GhostType & /*ghost_type*/) const {
+ ElementType /*type*/,
+ GhostType /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <typename T>
-Array<T> & Material::getArray(const ID & /*vect_id*/,
- const ElementType & /*type*/,
- const GhostType & /*ghost_type*/) {
+Array<T> & Material::getArray(const ID & /*vect_id*/, ElementType /*type*/,
+ GhostType /*ghost_type*/) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
-const Array<Real> & Material::getArray(const ID & vect_id,
- const ElementType & type,
- const GhostType & ghost_type) const {
+const Array<Real> & Material::getArray(const ID & vect_id, ElementType type,
+ GhostType ghost_type) const {
std::stringstream sstr;
- std::string ghost_id = "";
- if (ghost_type == _ghost)
+ std::string ghost_id;
+ if (ghost_type == _ghost) {
ghost_id = ":ghost";
+ }
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<Real>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << " (" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <>
-Array<Real> & Material::getArray(const ID & vect_id, const ElementType & type,
- const GhostType & ghost_type) {
+Array<Real> & Material::getArray(const ID & vect_id, ElementType type,
+ GhostType ghost_type) {
std::stringstream sstr;
- std::string ghost_id = "";
- if (ghost_type == _ghost)
+ std::string ghost_id;
+ if (ghost_type == _ghost) {
ghost_id = ":ghost";
+ }
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<Real>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << " (" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <>
-const Array<UInt> & Material::getArray(const ID & vect_id,
- const ElementType & type,
- const GhostType & ghost_type) const {
+const Array<UInt> & Material::getArray(const ID & vect_id, ElementType type,
+ GhostType ghost_type) const {
std::stringstream sstr;
- std::string ghost_id = "";
- if (ghost_type == _ghost)
+ std::string ghost_id;
+ if (ghost_type == _ghost) {
ghost_id = ":ghost";
+ }
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<UInt>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << " (" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <>
-Array<UInt> & Material::getArray(const ID & vect_id, const ElementType & type,
- const GhostType & ghost_type) {
+Array<UInt> & Material::getArray(const ID & vect_id, ElementType type,
+ GhostType ghost_type) {
std::stringstream sstr;
- std::string ghost_id = "";
- if (ghost_type == _ghost)
+ std::string ghost_id;
+ if (ghost_type == _ghost) {
ghost_id = ":ghost";
+ }
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<UInt>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << "(" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
const InternalField<T> &
Material::getInternal([[gnu::unused]] const ID & int_id) const {
AKANTU_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T> & Material::getInternal([[gnu::unused]] const ID & int_id) {
AKANTU_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <>
const InternalField<Real> & Material::getInternal(const ID & int_id) const {
auto it = internal_vectors_real.find(getID() + ":" + int_id);
if (it == internal_vectors_real.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <> InternalField<Real> & Material::getInternal(const ID & int_id) {
auto it = internal_vectors_real.find(getID() + ":" + int_id);
if (it == internal_vectors_real.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <>
const InternalField<UInt> & Material::getInternal(const ID & int_id) const {
auto it = internal_vectors_uint.find(getID() + ":" + int_id);
if (it == internal_vectors_uint.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <> InternalField<UInt> & Material::getInternal(const ID & int_id) {
auto it = internal_vectors_uint.find(getID() + ":" + int_id);
if (it == internal_vectors_uint.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
void Material::addElements(const Array<Element> & elements_to_add) {
AKANTU_DEBUG_IN();
UInt mat_id = model.getInternalIndexFromID(getID());
Array<Element>::const_iterator<Element> el_begin = elements_to_add.begin();
Array<Element>::const_iterator<Element> el_end = elements_to_add.end();
for (; el_begin != el_end; ++el_begin) {
const Element & element = *el_begin;
Array<UInt> & mat_indexes =
model.getMaterialByElement(element.type, element.ghost_type);
Array<UInt> & mat_loc_num =
model.getMaterialLocalNumbering(element.type, element.ghost_type);
UInt index =
this->addElement(element.type, element.element, element.ghost_type);
mat_indexes(element.element) = mat_id;
mat_loc_num(element.element) = index;
}
this->resizeInternals();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::removeElements(const Array<Element> & elements_to_remove) {
AKANTU_DEBUG_IN();
Array<Element>::const_iterator<Element> el_begin = elements_to_remove.begin();
Array<Element>::const_iterator<Element> el_end = elements_to_remove.end();
- if (el_begin == el_end)
+ if (el_begin == el_end) {
return;
+ }
ElementTypeMapArray<UInt> material_local_new_numbering(
"remove mat filter elem", getID(), getMemoryID());
Element element;
for (auto ghost_type : ghost_types) {
element.ghost_type = ghost_type;
- for (auto & type : element_filter.elementTypes(_ghost_type = ghost_type,
- _element_kind = _ek_not_defined)) {
+ for (const auto & type : element_filter.elementTypes(
+ _ghost_type = ghost_type, _element_kind = _ek_not_defined)) {
element.type = type;
Array<UInt> & elem_filter = this->element_filter(type, ghost_type);
Array<UInt> & mat_loc_num =
this->model.getMaterialLocalNumbering(type, ghost_type);
- if (!material_local_new_numbering.exists(type, ghost_type))
+ if (!material_local_new_numbering.exists(type, ghost_type)) {
material_local_new_numbering.alloc(elem_filter.size(), 1, type,
ghost_type);
+ }
Array<UInt> & mat_renumbering =
material_local_new_numbering(type, ghost_type);
UInt nb_element = elem_filter.size();
Array<UInt> elem_filter_tmp;
UInt new_id = 0;
for (UInt el = 0; el < nb_element; ++el) {
element.element = elem_filter(el);
if (std::find(el_begin, el_end, element) == el_end) {
elem_filter_tmp.push_back(element.element);
mat_renumbering(el) = new_id;
mat_loc_num(element.element) = new_id;
++new_id;
} else {
mat_renumbering(el) = UInt(-1);
}
}
elem_filter.resize(elem_filter_tmp.size());
elem_filter.copy(elem_filter_tmp);
}
}
for (auto it = internal_vectors_real.begin();
- it != internal_vectors_real.end(); ++it)
+ it != internal_vectors_real.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
+ }
for (auto it = internal_vectors_uint.begin();
- it != internal_vectors_uint.end(); ++it)
+ it != internal_vectors_uint.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
+ }
for (auto it = internal_vectors_bool.begin();
- it != internal_vectors_bool.end(); ++it)
+ it != internal_vectors_bool.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::resizeInternals() {
AKANTU_DEBUG_IN();
for (auto it = internal_vectors_real.begin();
- it != internal_vectors_real.end(); ++it)
+ it != internal_vectors_real.end(); ++it) {
it->second->resize();
+ }
for (auto it = internal_vectors_uint.begin();
- it != internal_vectors_uint.end(); ++it)
+ it != internal_vectors_uint.end(); ++it) {
it->second->resize();
+ }
for (auto it = internal_vectors_bool.begin();
- it != internal_vectors_bool.end(); ++it)
+ it != internal_vectors_bool.end(); ++it) {
it->second->resize();
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void Material::onElementsAdded(const Array<Element> &,
- const NewElementsEvent &) {
+void Material::onElementsAdded(const Array<Element> & /*unused*/,
+ const NewElementsEvent & /*unused*/) {
this->resizeInternals();
}
/* -------------------------------------------------------------------------- */
void Material::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
[[gnu::unused]] const RemovedElementsEvent & event) {
UInt my_num = model.getInternalIndexFromID(getID());
ElementTypeMapArray<UInt> material_local_new_numbering(
"remove mat filter elem", getID(), getMemoryID());
auto el_begin = element_list.begin();
auto el_end = element_list.end();
for (auto && gt : ghost_types) {
for (auto && type :
new_numbering.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
if (not element_filter.exists(type, gt) ||
- element_filter(type, gt).size() == 0)
+ element_filter(type, gt).empty()) {
continue;
+ }
auto & elem_filter = element_filter(type, gt);
auto & mat_indexes = this->model.getMaterialByElement(type, gt);
auto & mat_loc_num = this->model.getMaterialLocalNumbering(type, gt);
auto nb_element = this->model.getMesh().getNbElement(type, gt);
// all materials will resize of the same size...
mat_indexes.resize(nb_element);
mat_loc_num.resize(nb_element);
- if (!material_local_new_numbering.exists(type, gt))
+ if (!material_local_new_numbering.exists(type, gt)) {
material_local_new_numbering.alloc(elem_filter.size(), 1, type, gt);
+ }
auto & mat_renumbering = material_local_new_numbering(type, gt);
const auto & renumbering = new_numbering(type, gt);
Array<UInt> elem_filter_tmp;
UInt ni = 0;
Element el{type, 0, gt};
for (UInt i = 0; i < elem_filter.size(); ++i) {
el.element = elem_filter(i);
if (std::find(el_begin, el_end, el) == el_end) {
UInt new_el = renumbering(el.element);
AKANTU_DEBUG_ASSERT(new_el != UInt(-1),
"A not removed element as been badly renumbered");
elem_filter_tmp.push_back(new_el);
mat_renumbering(i) = ni;
mat_indexes(new_el) = my_num;
mat_loc_num(new_el) = ni;
++ni;
} else {
mat_renumbering(i) = UInt(-1);
}
}
elem_filter.resize(elem_filter_tmp.size());
elem_filter.copy(elem_filter_tmp);
}
}
for (auto it = internal_vectors_real.begin();
- it != internal_vectors_real.end(); ++it)
+ it != internal_vectors_real.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
+ }
for (auto it = internal_vectors_uint.begin();
- it != internal_vectors_uint.end(); ++it)
+ it != internal_vectors_uint.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
+ }
for (auto it = internal_vectors_bool.begin();
- it != internal_vectors_bool.end(); ++it)
+ it != internal_vectors_bool.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
+ }
}
/* -------------------------------------------------------------------------- */
void Material::beforeSolveStep() { this->savePreviousState(); }
/* -------------------------------------------------------------------------- */
void Material::afterSolveStep(bool converged) {
if (not converged) {
this->restorePreviousState();
return;
}
- for (auto & type : element_filter.elementTypes(_all_dimensions, _not_ghost,
- _ek_not_defined)) {
+ for (const auto & type : element_filter.elementTypes(
+ _all_dimensions, _not_ghost, _ek_not_defined)) {
this->updateEnergies(type);
}
}
/* -------------------------------------------------------------------------- */
void Material::onDamageIteration() { this->savePreviousState(); }
/* -------------------------------------------------------------------------- */
void Material::onDamageUpdate() {
- for (auto & type : element_filter.elementTypes(_all_dimensions, _not_ghost,
- _ek_not_defined)) {
+ for (const auto & type : element_filter.elementTypes(
+ _all_dimensions, _not_ghost, _ek_not_defined)) {
this->updateEnergiesAfterDamage(type);
}
}
/* -------------------------------------------------------------------------- */
void Material::onDump() {
- if (this->isFiniteDeformation())
+ if (this->isFiniteDeformation()) {
this->computeAllCauchyStresses(_not_ghost);
+ }
}
/* -------------------------------------------------------------------------- */
void Material::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
std::string type = getID().substr(getID().find_last_of(':') + 1);
stream << space << "Material " << type << " [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/// extrapolate internal values
void Material::extrapolateInternal(const ID & id, const Element & element,
[[gnu::unused]] const Matrix<Real> & point,
Matrix<Real> & extrapolated) {
if (this->isInternal<Real>(id, element.kind())) {
UInt nb_element =
this->element_filter(element.type, element.ghost_type).size();
const ID name = this->getID() + ":" + id;
UInt nb_quads =
this->internal_vectors_real[name]->getFEEngine().getNbIntegrationPoints(
element.type, element.ghost_type);
const Array<Real> & internal =
this->getArray<Real>(id, element.type, element.ghost_type);
UInt nb_component = internal.getNbComponent();
Array<Real>::const_matrix_iterator internal_it =
internal.begin_reinterpret(nb_component, nb_quads, nb_element);
Element local_element = this->convertToLocalElement(element);
/// instead of really extrapolating, here the value of the first GP
/// is copied into the result vector. This works only for linear
/// elements
/// @todo extrapolate!!!!
AKANTU_DEBUG_WARNING("This is a fix, values are not truly extrapolated");
const Matrix<Real> & values = internal_it[local_element.element];
UInt index = 0;
Vector<Real> tmp(nb_component);
for (UInt j = 0; j < values.cols(); ++j) {
tmp = values(j);
if (tmp.norm() > 0) {
index = j;
break;
}
}
for (UInt i = 0; i < extrapolated.size(); ++i) {
extrapolated(i) = values(index);
}
} else {
Matrix<Real> default_values(extrapolated.rows(), extrapolated.cols(), 0.);
extrapolated = default_values;
}
}
/* -------------------------------------------------------------------------- */
void Material::applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const GhostType ghost_type) {
for (auto && type : element_filter.elementTypes(_all_dimensions, _not_ghost,
_ek_not_defined)) {
- if (!element_filter(type, ghost_type).size())
+ if (element_filter(type, ghost_type).empty()) {
continue;
- auto eigen_it = this->eigengradu(type, ghost_type)
- .begin(spatial_dimension, spatial_dimension);
- auto eigen_end = this->eigengradu(type, ghost_type)
- .end(spatial_dimension, spatial_dimension);
- for (; eigen_it != eigen_end; ++eigen_it) {
- auto & current_eigengradu = *eigen_it;
- current_eigengradu = prescribed_eigen_grad_u;
+ }
+
+ for (auto & eigengradu : make_view(this->eigengradu(type, ghost_type),
+ spatial_dimension, spatial_dimension)) {
+ eigengradu = prescribed_eigen_grad_u;
}
}
}
/* -------------------------------------------------------------------------- */
MaterialFactory & Material::getFactory() {
return MaterialFactory::getInstance();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/material.hh b/src/model/solid_mechanics/material.hh
index e028b6b95..cbb2c63da 100644
--- a/src/model/solid_mechanics/material.hh
+++ b/src/model/solid_mechanics/material.hh
@@ -1,696 +1,705 @@
/**
* @file material.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Mother class for all materials
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "aka_voigthelper.hh"
#include "data_accessor.hh"
#include "integration_point.hh"
#include "parsable.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#include "internal_field.hh"
#include "random_internal_field.hh"
/* -------------------------------------------------------------------------- */
#include "mesh_events.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_HH__
-#define __AKANTU_MATERIAL_HH__
+#ifndef AKANTU_MATERIAL_HH_
+#define AKANTU_MATERIAL_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
class SolidMechanicsModel;
class Material;
} // namespace akantu
namespace akantu {
using MaterialFactory =
Factory<Material, ID, UInt, const ID &, SolidMechanicsModel &, const ID &>;
/**
* Interface of all materials
* Prerequisites for a new material
* - inherit from this class
* - implement the following methods:
* \code
* virtual Real getStableTimeStep(Real h, const Element & element =
* ElementNull);
*
* virtual void computeStress(ElementType el_type,
* GhostType ghost_type = _not_ghost);
*
- * virtual void computeTangentStiffness(const ElementType & el_type,
+ * virtual void computeTangentStiffness(ElementType el_type,
* Array<Real> & tangent_matrix,
* GhostType ghost_type = _not_ghost);
* \endcode
*
*/
class Material : public Memory,
public DataAccessor<Element>,
public Parsable,
public MeshEventHandler,
protected SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Material(const Material & mat) = delete;
Material & operator=(const Material & mat) = delete;
/// Initialize material with defaults
Material(SolidMechanicsModel & model, const ID & id = "");
/// Initialize material with custom mesh & fe_engine
Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
/// Destructor
~Material() override;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Function that materials can/should reimplement */
/* ------------------------------------------------------------------------ */
protected:
/// constitutive law
virtual void computeStress(ElementType /* el_type */,
GhostType /* ghost_type */ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// compute the tangent stiffness matrix
- virtual void computeTangentModuli(const ElementType & /*el_type*/,
+ virtual void computeTangentModuli(ElementType /*el_type*/,
Array<Real> & /*tangent_matrix*/,
GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// compute the potential energy
virtual void computePotentialEnergy(ElementType el_type);
/// compute the potential energy for an element
virtual void
computePotentialEnergyByElement(ElementType /*type*/, UInt /*index*/,
Vector<Real> & /*epot_on_quad_points*/) {
AKANTU_TO_IMPLEMENT();
}
virtual void updateEnergies(ElementType /*el_type*/) {}
virtual void updateEnergiesAfterDamage(ElementType /*el_type*/) {}
/// set the material to steady state (to be implemented for materials that
/// need it)
virtual void setToSteadyState(ElementType /*el_type*/,
GhostType /*ghost_type*/ = _not_ghost) {}
/// function called to update the internal parameters when the modifiable
/// parameters are modified
virtual void updateInternalParameters() {}
public:
/// extrapolate internal values
virtual void extrapolateInternal(const ID & id, const Element & element,
const Matrix<Real> & points,
Matrix<Real> & extrapolated);
/// compute the p-wave speed in the material
virtual Real getPushWaveSpeed(const Element & /*element*/) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the s-wave speed in the material
virtual Real getShearWaveSpeed(const Element & /*element*/) const {
AKANTU_TO_IMPLEMENT();
}
/// get a material celerity to compute the stable time step (default: is the
/// push wave speed)
virtual Real getCelerity(const Element & element) const {
return getPushWaveSpeed(element);
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename T> void registerInternal(InternalField<T> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
}
template <typename T> void unregisterInternal(InternalField<T> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
}
/// initialize the material computed parameter
virtual void initMaterial();
/// compute the residual for this material
// virtual void updateResidual(GhostType ghost_type = _not_ghost);
/// assemble the residual for this material
virtual void assembleInternalForces(GhostType ghost_type);
/// save the stress in the previous_stress if needed
virtual void savePreviousState();
/// restore the stress from previous_stress if needed
virtual void restorePreviousState();
/// compute the stresses for this material
virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
// virtual void
// computeAllStressesFromTangentModuli(GhostType ghost_type = _not_ghost);
virtual void computeAllCauchyStresses(GhostType ghost_type = _not_ghost);
/// set material to steady state
void setToSteadyState(GhostType ghost_type = _not_ghost);
/// compute the stiffness matrix
virtual void assembleStiffnessMatrix(GhostType ghost_type);
/// add an element to the local mesh filter
- inline UInt addElement(const ElementType & type, UInt element,
- const GhostType & ghost_type);
+ inline UInt addElement(ElementType type, UInt element, GhostType ghost_type);
inline UInt addElement(const Element & element);
/// add many elements at once
void addElements(const Array<Element> & elements_to_add);
/// remove many element at once
void removeElements(const Array<Element> & elements_to_remove);
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
/**
* interpolate stress on given positions for each element by means
* of a geometrical interpolation on quadrature points
*/
void interpolateStress(ElementTypeMapArray<Real> & result,
- const GhostType ghost_type = _not_ghost);
+ GhostType ghost_type = _not_ghost);
/**
* interpolate stress on given positions for each element by means
* of a geometrical interpolation on quadrature points and store the
* results per facet
*/
void interpolateStressOnFacets(ElementTypeMapArray<Real> & result,
ElementTypeMapArray<Real> & by_elem_result,
- const GhostType ghost_type = _not_ghost);
+ GhostType ghost_type = _not_ghost);
/**
* function to initialize the elemental field interpolation
* function by inverting the quadrature points' coordinates
*/
void initElementalFieldInterpolation(
const ElementTypeMapArray<Real> & interpolation_points_coordinates);
/* ------------------------------------------------------------------------ */
/* Common part */
/* ------------------------------------------------------------------------ */
protected:
/* ------------------------------------------------------------------------ */
- inline UInt getTangentStiffnessVoigtSize(UInt spatial_dimension) const;
+ static inline UInt getTangentStiffnessVoigtSize(UInt dim);
/// compute the potential energy by element
void computePotentialEnergyByElements();
/// resize the intenals arrays
virtual void resizeInternals();
/* ------------------------------------------------------------------------ */
/* Finite deformation functions */
/* This functions area implementing what is described in the paper of Bathe */
/* et al, in IJNME, Finite Element Formulations For Large Deformation */
/* Dynamic Analysis, Vol 9, 353-386, 1975 */
/* ------------------------------------------------------------------------ */
protected:
/// assemble the residual
template <UInt dim> void assembleInternalForces(GhostType ghost_type);
template <UInt dim>
- void computeAllStressesFromTangentModuli(const ElementType & type,
+ void computeAllStressesFromTangentModuli(ElementType type,
GhostType ghost_type);
template <UInt dim>
- void assembleStiffnessMatrix(const ElementType & type, GhostType ghost_type);
+ void assembleStiffnessMatrix(ElementType type, GhostType ghost_type);
/// assembling in finite deformation
template <UInt dim>
- void assembleStiffnessMatrixNL(const ElementType & type,
- GhostType ghost_type);
+ void assembleStiffnessMatrixNL(ElementType type, GhostType ghost_type);
template <UInt dim>
- void assembleStiffnessMatrixL2(const ElementType & type,
- GhostType ghost_type);
+ void assembleStiffnessMatrixL2(ElementType type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Conversion functions */
/* ------------------------------------------------------------------------ */
public:
/// Size of the Stress matrix for the case of finite deformation see: Bathe et
/// al, IJNME, Vol 9, 353-386, 1975
- inline UInt getCauchyStressMatrixSize(UInt spatial_dimension) const;
+ static inline UInt getCauchyStressMatrixSize(UInt dim);
/// Sets the stress matrix according to Bathe et al, IJNME, Vol 9, 353-386,
/// 1975
template <UInt dim>
static inline void setCauchyStressMatrix(const Matrix<Real> & S_t,
Matrix<Real> & sigma);
/// write the stress tensor in the Voigt notation.
template <UInt dim>
static inline decltype(auto) stressToVoigt(const Matrix<Real> & stress) {
return VoigtHelper<dim>::matrixToVoigt(stress);
}
/// write the strain tensor in the Voigt notation.
template <UInt dim>
static inline decltype(auto) strainToVoigt(const Matrix<Real> & strain) {
return VoigtHelper<dim>::matrixToVoigtWithFactors(strain);
}
/// write a voigt vector to stress
template <UInt dim>
static inline void voigtToStress(const Vector<Real> & voigt,
Matrix<Real> & stress) {
VoigtHelper<dim>::voigtToMatrix(voigt, stress);
}
/// Computation of Cauchy stress tensor in the case of finite deformation from
/// the 2nd Piola-Kirchhoff for a given element type
template <UInt dim>
void StoCauchy(ElementType el_type, GhostType ghost_type = _not_ghost);
/// Computation the Cauchy stress the 2nd Piola-Kirchhoff and the deformation
/// gradient
template <UInt dim>
inline void StoCauchy(const Matrix<Real> & F, const Matrix<Real> & S,
Matrix<Real> & sigma, const Real & C33 = 1.0) const;
template <UInt dim>
static inline void gradUToF(const Matrix<Real> & grad_u, Matrix<Real> & F);
template <UInt dim>
static inline decltype(auto) gradUToF(const Matrix<Real> & grad_u);
static inline void rightCauchy(const Matrix<Real> & F, Matrix<Real> & C);
static inline void leftCauchy(const Matrix<Real> & F, Matrix<Real> & B);
template <UInt dim>
static inline void gradUToEpsilon(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon);
template <UInt dim>
static inline decltype(auto) gradUToEpsilon(const Matrix<Real> & grad_u);
template <UInt dim>
static inline void gradUToE(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon);
template <UInt dim>
static inline decltype(auto) gradUToE(const Matrix<Real> & grad_u);
static inline Real stressToVonMises(const Matrix<Real> & stress);
protected:
/// converts global element to local element
inline Element convertToLocalElement(const Element & global_element) const;
/// converts local element to global element
inline Element convertToGlobalElement(const Element & local_element) const;
/// converts global quadrature point to local quadrature point
inline IntegrationPoint
convertToLocalPoint(const IntegrationPoint & global_point) const;
/// converts local quadrature point to global quadrature point
inline IntegrationPoint
convertToGlobalPoint(const IntegrationPoint & local_point) const;
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
template <typename T>
inline void packElementDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID()) const;
template <typename T>
inline void unpackElementDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID());
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
- void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override{};
- void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
- const RemovedNodesEvent &) override{};
+ void onNodesAdded(const Array<UInt> & /*unused*/,
+ const NewNodesEvent & /*unused*/) override{};
+ void onNodesRemoved(const Array<UInt> & /*unused*/,
+ const Array<UInt> & /*unused*/,
+ const RemovedNodesEvent & /*unused*/) override{};
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
- void onElementsChanged(const Array<Element> &, const Array<Element> &,
- const ElementTypeMapArray<UInt> &,
- const ChangedElementsEvent &) override{};
+ void onElementsChanged(const Array<Element> & /*unused*/,
+ const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const ChangedElementsEvent & /*unused*/) override{};
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual void beforeSolveStep();
virtual void afterSolveStep(bool converged = true);
void onDamageIteration() override;
void onDamageUpdate() override;
void onDump() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Name, name, const std::string &);
AKANTU_GET_MACRO(Model, model, const SolidMechanicsModel &)
AKANTU_GET_MACRO(ID, Memory::getID(), const ID &);
AKANTU_GET_MACRO(Rho, rho, Real);
AKANTU_SET_MACRO(Rho, rho, Real);
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// return the potential energy for the subset of elements contained by the
/// material
Real getPotentialEnergy();
/// return the potential energy for the provided element
Real getPotentialEnergy(ElementType & type, UInt index);
/// return the energy (identified by id) for the subset of elements contained
/// by the material
- virtual Real getEnergy(const std::string & energy_id);
+ virtual Real getEnergy(const std::string & type);
/// return the energy (identified by id) for the provided element
virtual Real getEnergy(const std::string & energy_id, ElementType type,
UInt index);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ElementFilter, element_filter, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(GradU, gradu, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Stress, stress, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(PotentialEnergy, potential_energy,
Real);
AKANTU_GET_MACRO(GradU, gradu, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Stress, stress, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(ElementFilter, element_filter,
const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(FEEngine, fem, FEEngine &);
bool isNonLocal() const { return is_non_local; }
template <typename T>
- const Array<T> & getArray(const ID & id, const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const;
+ const Array<T> & getArray(const ID & id, ElementType type,
+ GhostType ghost_type = _not_ghost) const;
template <typename T>
- Array<T> & getArray(const ID & id, const ElementType & type,
- const GhostType & ghost_type = _not_ghost);
+ Array<T> & getArray(const ID & id, ElementType type,
+ GhostType ghost_type = _not_ghost);
template <typename T>
const InternalField<T> & getInternal(const ID & id) const;
template <typename T> InternalField<T> & getInternal(const ID & id);
template <typename T>
- inline bool isInternal(const ID & id, const ElementKind & element_kind) const;
+ inline bool isInternal(const ID & id, ElementKind element_kind) const;
template <typename T>
- ElementTypeMap<UInt>
- getInternalDataPerElem(const ID & id, const ElementKind & element_kind) const;
+ ElementTypeMap<UInt> getInternalDataPerElem(const ID & id,
+ ElementKind element_kind) const;
bool isFiniteDeformation() const { return finite_deformation; }
bool isInelasticDeformation() const { return inelastic_deformation; }
template <typename T> inline void setParam(const ID & param, T value);
inline const Parameter & getParam(const ID & param) const;
template <typename T>
void flattenInternal(const std::string & field_id,
ElementTypeMapArray<T> & internal_flat,
- const GhostType ghost_type = _not_ghost,
+ GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) const;
/// apply a constant eigengrad_u everywhere in the material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
- const GhostType = _not_ghost);
+ GhostType /*ghost_type*/ = _not_ghost);
bool hasMatrixChanged(const ID & id) {
if (id == "K") {
return hasStiffnessMatrixChanged() or finite_deformation;
}
return true;
}
MatrixType getMatrixType(const ID & id) {
if (id == "K") {
return getTangentType();
- } else if (id == "M") {
+ }
+
+ if (id == "M") {
return _symmetric;
}
return _mt_not_defined;
}
/// specify if the matrix need to be recomputed for this material
virtual bool hasStiffnessMatrixChanged() { return true; }
/// specify the type of matrix, if not overloaded the material is not valid
/// for static or implicit computations
virtual MatrixType getTangentType() { return _mt_not_defined; }
/// static method to reteive the material factory
static MaterialFactory & getFactory();
protected:
bool isInit() const { return is_init; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// boolean to know if the material has been initialized
bool is_init;
std::map<ID, InternalField<Real> *> internal_vectors_real;
std::map<ID, InternalField<UInt> *> internal_vectors_uint;
std::map<ID, InternalField<bool> *> internal_vectors_bool;
protected:
/// Link to the fem object in the model
FEEngine & fem;
/// Finite deformation
bool finite_deformation;
/// Finite deformation
bool inelastic_deformation;
/// material name
std::string name;
/// The model to witch the material belong
SolidMechanicsModel & model;
/// density : rho
Real rho;
/// spatial dimension
UInt spatial_dimension;
/// list of element handled by the material
ElementTypeMapArray<UInt> element_filter;
/// stresses arrays ordered by element types
InternalField<Real> stress;
/// eigengrad_u arrays ordered by element types
InternalField<Real> eigengradu;
/// grad_u arrays ordered by element types
InternalField<Real> gradu;
/// Green Lagrange strain (Finite deformation)
InternalField<Real> green_strain;
/// Second Piola-Kirchhoff stress tensor arrays ordered by element types
/// (Finite deformation)
InternalField<Real> piola_kirchhoff_2;
/// potential energy by element
InternalField<Real> potential_energy;
/// tell if using in non local mode or not
bool is_non_local;
/// tell if the material need the previous stress state
bool use_previous_stress;
/// tell if the material need the previous strain state
bool use_previous_gradu;
/// elemental field interpolation coordinates
InternalField<Real> interpolation_inverse_coordinates;
/// elemental field interpolation points
InternalField<Real> interpolation_points_matrices;
/// vector that contains the names of all the internals that need to
/// be transferred when material interfaces move
std::vector<ID> internals_to_transfer;
private:
/// eigen_grad_u for the parser
Matrix<Real> eigen_grad_u;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Material & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "material_inline_impl.hh"
#include "internal_field_tmpl.hh"
#include "random_internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* Auto loop */
/* -------------------------------------------------------------------------- */
/// This can be used to automatically write the loop on quadrature points in
/// functions such as computeStress. This macro in addition to write the loop
/// provides two tensors (matrices) sigma and grad_u
#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type) \
auto && grad_u_view = \
make_view(this->gradu(el_type, ghost_type), this->spatial_dimension, \
this->spatial_dimension); \
\
auto stress_view = \
make_view(this->stress(el_type, ghost_type), this->spatial_dimension, \
this->spatial_dimension); \
\
if (this->isFiniteDeformation()) { \
stress_view = make_view(this->piola_kirchhoff_2(el_type, ghost_type), \
this->spatial_dimension, this->spatial_dimension); \
} \
\
for (auto && data : zip(grad_u_view, stress_view)) { \
[[gnu::unused]] Matrix<Real> & grad_u = std::get<0>(data); \
[[gnu::unused]] Matrix<Real> & sigma = std::get<1>(data)
#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END }
/// This can be used to automatically write the loop on quadrature points in
/// functions such as computeTangentModuli. This macro in addition to write the
/// loop provides two tensors (matrices) sigma_tensor, grad_u, and a matrix
/// where the elemental tangent moduli should be stored in Voigt Notation
#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_mat) \
auto && grad_u_view = \
make_view(this->gradu(el_type, ghost_type), this->spatial_dimension, \
this->spatial_dimension); \
\
auto && stress_view = \
make_view(this->stress(el_type, ghost_type), this->spatial_dimension, \
this->spatial_dimension); \
\
auto tangent_size = \
this->getTangentStiffnessVoigtSize(this->spatial_dimension); \
\
auto && tangent_view = make_view(tangent_mat, tangent_size, tangent_size); \
\
for (auto && data : zip(grad_u_view, stress_view, tangent_view)) { \
[[gnu::unused]] Matrix<Real> & grad_u = std::get<0>(data); \
[[gnu::unused]] Matrix<Real> & sigma = std::get<1>(data); \
Matrix<Real> & tangent = std::get<2>(data);
#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END }
/* -------------------------------------------------------------------------- */
#define INSTANTIATE_MATERIAL_ONLY(mat_name) \
- template class mat_name<1>; \
- template class mat_name<2>; \
- template class mat_name<3>
+ template class mat_name<1>; /* NOLINT */ \
+ template class mat_name<2>; /* NOLINT */ \
+ template class mat_name<3> /* NOLINT */
#define MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name) \
[](UInt dim, const ID &, SolidMechanicsModel & model, \
- const ID & id) -> std::unique_ptr<Material> { \
- switch (dim) { \
- case 1: \
- return std::make_unique<mat_name<1>>(model, id); \
- case 2: \
- return std::make_unique<mat_name<2>>(model, id); \
- case 3: \
- return std::make_unique<mat_name<3>>(model, id); \
- default: \
- AKANTU_EXCEPTION("The dimension " \
- << dim << "is not a valid dimension for the material " \
- << #id); \
- } \
+ const ID & id) /* NOLINT */ \
+ -> std::unique_ptr< \
+ Material> { /* NOLINT */ \
+ switch (dim) { \
+ case 1: \
+ return std::make_unique<mat_name<1>>(/* NOLINT */ \
+ model, id); \
+ case 2: \
+ return std::make_unique<mat_name<2>>(/* NOLINT */ \
+ model, id); \
+ case 3: \
+ return std::make_unique<mat_name<3>>(/* NOLINT */ \
+ model, id); \
+ default: \
+ AKANTU_EXCEPTION( \
+ "The dimension " \
+ << dim \
+ << "is not a valid dimension for the material " \
+ << #id); \
+ } \
}
#define INSTANTIATE_MATERIAL(id, mat_name) \
INSTANTIATE_MATERIAL_ONLY(mat_name); \
static bool material_is_alocated_##id [[gnu::unused]] = \
MaterialFactory::getInstance().registerAllocator( \
#id, MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name))
-#endif /* __AKANTU_MATERIAL_HH__ */
+#endif /* AKANTU_MATERIAL_HH_ */
diff --git a/src/model/solid_mechanics/material_inline_impl.hh b/src/model/solid_mechanics/material_inline_impl.hh
index 026de291a..6ff2cdf0c 100644
--- a/src/model/solid_mechanics/material_inline_impl.hh
+++ b/src/model/solid_mechanics/material_inline_impl.hh
@@ -1,441 +1,449 @@
/**
* @file material_inline_impl.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the inline functions of the class material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_INLINE_IMPL_HH__
-#define __AKANTU_MATERIAL_INLINE_IMPL_HH__
+#ifndef AKANTU_MATERIAL_INLINE_IMPL_HH_
+#define AKANTU_MATERIAL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
-inline UInt Material::addElement(const ElementType & type, UInt element,
- const GhostType & ghost_type) {
+inline UInt Material::addElement(ElementType type, UInt element,
+ GhostType ghost_type) {
Array<UInt> & el_filter = this->element_filter(type, ghost_type);
el_filter.push_back(element);
return el_filter.size() - 1;
}
/* -------------------------------------------------------------------------- */
inline UInt Material::addElement(const Element & element) {
return this->addElement(element.type, element.element, element.ghost_type);
}
/* -------------------------------------------------------------------------- */
-inline UInt Material::getTangentStiffnessVoigtSize(UInt dim) const {
+inline UInt Material::getTangentStiffnessVoigtSize(UInt dim) {
return (dim * (dim - 1) / 2 + dim);
}
/* -------------------------------------------------------------------------- */
-inline UInt Material::getCauchyStressMatrixSize(UInt dim) const {
+inline UInt Material::getCauchyStressMatrixSize(UInt dim) {
return (dim * dim);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToF(const Matrix<Real> & grad_u, Matrix<Real> & F) {
AKANTU_DEBUG_ASSERT(F.size() >= grad_u.size() && grad_u.size() == dim * dim,
"The dimension of the tensor F should be greater or "
"equal to the dimension of the tensor grad_u.");
F.eye();
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
F(i, j) += grad_u(i, j);
+ }
+ }
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline decltype(auto) Material::gradUToF(const Matrix<Real> & grad_u) {
Matrix<Real> F(dim, dim);
gradUToF<dim>(grad_u, F);
return F;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::StoCauchy(const Matrix<Real> & F, const Matrix<Real> & S,
Matrix<Real> & sigma, const Real & C33) const {
Real J = F.det() * sqrt(C33);
Matrix<Real> F_S(dim, dim);
F_S = F * S;
Real constant = J ? 1. / J : 0;
sigma.mul<false, true>(F_S, F, constant);
}
/* -------------------------------------------------------------------------- */
inline void Material::rightCauchy(const Matrix<Real> & F, Matrix<Real> & C) {
C.mul<true, false>(F, F);
}
/* -------------------------------------------------------------------------- */
inline void Material::leftCauchy(const Matrix<Real> & F, Matrix<Real> & B) {
B.mul<false, true>(F, F);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToEpsilon(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon) {
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
epsilon(i, j) = 0.5 * (grad_u(i, j) + grad_u(j, i));
+ }
+ }
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline decltype(auto) Material::gradUToEpsilon(const Matrix<Real> & grad_u) {
Matrix<Real> epsilon(dim, dim);
Material::template gradUToEpsilon<dim>(grad_u, epsilon);
return epsilon;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToE(const Matrix<Real> & grad_u, Matrix<Real> & E) {
E.mul<true, false>(grad_u, grad_u, .5);
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
E(i, j) += 0.5 * (grad_u(i, j) + grad_u(j, i));
+ }
+ }
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline decltype(auto) Material::gradUToE(const Matrix<Real> & grad_u) {
Matrix<Real> E(dim, dim);
gradUToE<dim>(grad_u, E);
return E;
}
/* -------------------------------------------------------------------------- */
inline Real Material::stressToVonMises(const Matrix<Real> & stress) {
// compute deviatoric stress
UInt dim = stress.cols();
Matrix<Real> deviatoric_stress =
Matrix<Real>::eye(dim, -1. * stress.trace() / 3.);
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
deviatoric_stress(i, j) += stress(i, j);
+ }
+ }
// return Von Mises stress
return std::sqrt(3. * deviatoric_stress.doubleDot(deviatoric_stress) / 2.);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::setCauchyStressMatrix(const Matrix<Real> & S_t,
Matrix<Real> & sigma) {
AKANTU_DEBUG_IN();
- sigma.clear();
+ sigma.zero();
/// see Finite ekement formulations for large deformation dynamic analysis,
/// Bathe et al. IJNME vol 9, 1975, page 364 ^t \f$\tau\f$
for (UInt i = 0; i < dim; ++i) {
for (UInt m = 0; m < dim; ++m) {
for (UInt n = 0; n < dim; ++n) {
sigma(i * dim + m, i * dim + n) = S_t(m, n);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline Element
Material::convertToLocalElement(const Element & global_element) const {
UInt ge = global_element.element;
#ifndef AKANTU_NDEBUG
UInt model_mat_index = this->model.getMaterialByElement(
global_element.type, global_element.ghost_type)(ge);
UInt mat_index = this->model.getMaterialIndex(this->name);
AKANTU_DEBUG_ASSERT(model_mat_index == mat_index,
"Conversion of a global element in a local element for "
"the wrong material "
<< this->name << std::endl);
#endif
UInt le = this->model.getMaterialLocalNumbering(
global_element.type, global_element.ghost_type)(ge);
Element tmp_quad{global_element.type, le, global_element.ghost_type};
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline Element
Material::convertToGlobalElement(const Element & local_element) const {
UInt le = local_element.element;
UInt ge =
this->element_filter(local_element.type, local_element.ghost_type)(le);
Element tmp_quad{local_element.type, ge, local_element.ghost_type};
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline IntegrationPoint
Material::convertToLocalPoint(const IntegrationPoint & global_point) const {
const FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = fem.getNbIntegrationPoints(global_point.type);
Element el =
this->convertToLocalElement(static_cast<const Element &>(global_point));
IntegrationPoint tmp_quad(el, global_point.num_point, nb_quad);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline IntegrationPoint
Material::convertToGlobalPoint(const IntegrationPoint & local_point) const {
const FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = fem.getNbIntegrationPoints(local_point.type);
Element el =
this->convertToGlobalElement(static_cast<const Element &>(local_point));
IntegrationPoint tmp_quad(el, local_point.num_point, nb_quad);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_smm_stress) {
return (this->isFiniteDeformation() ? 3 : 1) * spatial_dimension *
spatial_dimension * sizeof(Real) *
this->getModel().getNbIntegrationPoints(elements);
}
return 0;
}
/* -------------------------------------------------------------------------- */
inline void Material::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_smm_stress) {
if (this->isFiniteDeformation()) {
packElementDataHelper(piola_kirchhoff_2, buffer, elements);
packElementDataHelper(gradu, buffer, elements);
}
packElementDataHelper(stress, buffer, elements);
}
}
/* -------------------------------------------------------------------------- */
inline void Material::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == SynchronizationTag::_smm_stress) {
if (this->isFiniteDeformation()) {
unpackElementDataHelper(piola_kirchhoff_2, buffer, elements);
unpackElementDataHelper(gradu, buffer, elements);
}
unpackElementDataHelper(stress, buffer, elements);
}
}
/* -------------------------------------------------------------------------- */
inline const Parameter & Material::getParam(const ID & param) const {
try {
return get(param);
} catch (...) {
AKANTU_EXCEPTION("No parameter " << param << " in the material "
<< getID());
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::setParam(const ID & param, T value) {
try {
set<T>(param, value);
} catch (...) {
AKANTU_EXCEPTION("No parameter " << param << " in the material "
<< getID());
}
updateInternalParameters();
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::packElementDataHelper(
const ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) const {
DataAccessor::packElementalDataHelper<T>(data_to_pack, buffer, elements, true,
model.getFEEngine(fem_id));
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::unpackElementDataHelper(
ElementTypeMapArray<T> & data_to_unpack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) {
DataAccessor::unpackElementalDataHelper<T>(data_to_unpack, buffer, elements,
true, model.getFEEngine(fem_id));
}
/* -------------------------------------------------------------------------- */
template <>
inline void Material::registerInternal<Real>(InternalField<Real> & vect) {
internal_vectors_real[vect.getID()] = &vect;
}
template <>
inline void Material::registerInternal<UInt>(InternalField<UInt> & vect) {
internal_vectors_uint[vect.getID()] = &vect;
}
template <>
inline void Material::registerInternal<bool>(InternalField<bool> & vect) {
internal_vectors_bool[vect.getID()] = &vect;
}
/* -------------------------------------------------------------------------- */
template <>
inline void Material::unregisterInternal<Real>(InternalField<Real> & vect) {
internal_vectors_real.erase(vect.getID());
}
template <>
inline void Material::unregisterInternal<UInt>(InternalField<UInt> & vect) {
internal_vectors_uint.erase(vect.getID());
}
template <>
inline void Material::unregisterInternal<bool>(InternalField<bool> & vect) {
internal_vectors_bool.erase(vect.getID());
}
/* -------------------------------------------------------------------------- */
template <typename T>
-inline bool Material::isInternal(__attribute__((unused)) const ID & id,
- __attribute__((unused))
- const ElementKind & element_kind) const {
+inline bool Material::isInternal(const ID & /*id*/,
+ ElementKind /*element_kind*/) const {
AKANTU_TO_IMPLEMENT();
}
template <>
inline bool Material::isInternal<Real>(const ID & id,
- const ElementKind & element_kind) const {
+ ElementKind element_kind) const {
auto internal_array = internal_vectors_real.find(this->getID() + ":" + id);
- if (internal_array == internal_vectors_real.end() ||
- internal_array->second->getElementKind() != element_kind)
- return false;
- return true;
+ return not (internal_array == internal_vectors_real.end() ||
+ internal_array->second->getElementKind() != element_kind);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMap<UInt>
Material::getInternalDataPerElem(const ID & field_id,
- const ElementKind & element_kind) const {
+ ElementKind element_kind) const {
- if (!this->template isInternal<T>(field_id, element_kind))
+ if (!this->template isInternal<T>(field_id, element_kind)) {
AKANTU_EXCEPTION("Cannot find internal field " << id << " in material "
<< this->name);
+ }
const InternalField<T> & internal_field =
this->template getInternal<T>(field_id);
const FEEngine & fe_engine = internal_field.getFEEngine();
UInt nb_data_per_quad = internal_field.getNbComponent();
ElementTypeMap<UInt> res;
for (auto ghost_type : ghost_types) {
for (auto & type : internal_field.elementTypes(ghost_type)) {
UInt nb_quadrature_points =
fe_engine.getNbIntegrationPoints(type, ghost_type);
res(type, ghost_type) = nb_data_per_quad * nb_quadrature_points;
}
}
return res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Material::flattenInternal(const std::string & field_id,
ElementTypeMapArray<T> & internal_flat,
const GhostType ghost_type,
ElementKind element_kind) const {
- if (!this->template isInternal<T>(field_id, element_kind))
+ if (!this->template isInternal<T>(field_id, element_kind)) {
AKANTU_EXCEPTION("Cannot find internal field " << id << " in material "
<< this->name);
+ }
const InternalField<T> & internal_field =
this->template getInternal<T>(field_id);
const FEEngine & fe_engine = internal_field.getFEEngine();
const Mesh & mesh = fe_engine.getMesh();
for (auto && type : internal_field.filterTypes(ghost_type)) {
const Array<Real> & src_vect = internal_field(type, ghost_type);
const Array<UInt> & filter = internal_field.getFilter(type, ghost_type);
// total number of elements in the corresponding mesh
UInt nb_element_dst = mesh.getNbElement(type, ghost_type);
// number of element in the internal field
UInt nb_element_src = filter.size();
// number of quadrature points per elem
UInt nb_quad_per_elem = fe_engine.getNbIntegrationPoints(type);
// number of data per quadrature point
UInt nb_data_per_quad = internal_field.getNbComponent();
if (!internal_flat.exists(type, ghost_type)) {
internal_flat.alloc(nb_element_dst * nb_quad_per_elem, nb_data_per_quad,
type, ghost_type);
}
- if (nb_element_src == 0)
+ if (nb_element_src == 0) {
continue;
+ }
// number of data per element
UInt nb_data = nb_quad_per_elem * nb_data_per_quad;
Array<Real> & dst_vect = internal_flat(type, ghost_type);
dst_vect.resize(nb_element_dst * nb_quad_per_elem);
auto it_dst = make_view(dst_vect, nb_data).begin();
for (auto && data : zip(filter, make_view(src_vect, nb_data))) {
it_dst[std::get<0>(data)] = std::get<1>(data);
}
}
}
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_INLINE_IMPL_HH__ */
+#endif /* AKANTU_MATERIAL_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/material_selector.hh b/src/model/solid_mechanics/material_selector.hh
index 9ebc4839e..311c72adb 100644
--- a/src/model/solid_mechanics/material_selector.hh
+++ b/src/model/solid_mechanics/material_selector.hh
@@ -1,160 +1,163 @@
/**
* @file material_selector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Mon Dec 18 2017
*
* @brief class describing how to choose a material for a given element
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_SELECTOR_HH__
-#define __AKANTU_MATERIAL_SELECTOR_HH__
+#ifndef AKANTU_MATERIAL_SELECTOR_HH_
+#define AKANTU_MATERIAL_SELECTOR_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModel;
/**
* main class to assign same or different materials for different
* elements
*/
class MaterialSelector : public std::enable_shared_from_this<MaterialSelector> {
public:
MaterialSelector() = default;
virtual ~MaterialSelector() = default;
virtual inline UInt operator()(const Element & element) {
- if (fallback_selector)
+ if (fallback_selector) {
return (*fallback_selector)(element);
+ }
return fallback_value;
}
inline void setFallback(UInt f) { fallback_value = f; }
inline void
setFallback(const std::shared_ptr<MaterialSelector> & fallback_selector) {
this->fallback_selector = fallback_selector;
}
inline void setFallback(MaterialSelector & fallback_selector) {
this->fallback_selector = fallback_selector.shared_from_this();
}
inline std::shared_ptr<MaterialSelector> & getFallbackSelector() {
return this->fallback_selector;
}
- inline UInt getFallbackValue() { return this->fallback_value; }
+ inline UInt getFallbackValue() const { return this->fallback_value; }
protected:
UInt fallback_value{0};
std::shared_ptr<MaterialSelector> fallback_selector;
};
/* -------------------------------------------------------------------------- */
/**
* class that assigns the first material to regular elements by default
*/
class DefaultMaterialSelector : public MaterialSelector {
public:
explicit DefaultMaterialSelector(
const ElementTypeMapArray<UInt> & material_index)
: material_index(material_index) {}
UInt operator()(const Element & element) override {
- if (not material_index.exists(element.type, element.ghost_type))
+ if (not material_index.exists(element.type, element.ghost_type)) {
return MaterialSelector::operator()(element);
+ }
const auto & mat_indexes = material_index(element.type, element.ghost_type);
if (element.element < mat_indexes.size()) {
auto && tmp_mat = mat_indexes(element.element);
- if (tmp_mat != UInt(-1))
+ if (tmp_mat != UInt(-1)) {
return tmp_mat;
+ }
}
return MaterialSelector::operator()(element);
}
private:
const ElementTypeMapArray<UInt> & material_index;
};
/* -------------------------------------------------------------------------- */
/**
* Use elemental data to assign materials
*/
template <typename T>
class ElementDataMaterialSelector : public MaterialSelector {
public:
ElementDataMaterialSelector(const ElementTypeMapArray<T> & element_data,
const SolidMechanicsModel & model,
UInt first_index = 1)
: element_data(element_data), model(model), first_index(first_index) {}
inline T elementData(const Element & element) {
DebugLevel dbl = debug::getDebugLevel();
debug::setDebugLevel(dblError);
T data = element_data(element.type, element.ghost_type)(element.element);
debug::setDebugLevel(dbl);
return data;
}
inline UInt operator()(const Element & element) override {
return MaterialSelector::operator()(element);
}
protected:
/// list of element with the specified data (i.e. tag value)
const ElementTypeMapArray<T> & element_data;
/// the model that the materials belong
const SolidMechanicsModel & model;
/// first material index: equal to 1 if none specified
UInt first_index;
};
/* -------------------------------------------------------------------------- */
/**
* class to use mesh data information to assign different materials
* where name is the tag value: tag_0, tag_1
*/
template <typename T>
class MeshDataMaterialSelector : public ElementDataMaterialSelector<T> {
public:
MeshDataMaterialSelector(const std::string & name,
const SolidMechanicsModel & model,
UInt first_index = 1);
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_SELECTOR_HH__ */
+#endif /* AKANTU_MATERIAL_SELECTOR_HH_ */
diff --git a/src/model/solid_mechanics/material_selector_tmpl.hh b/src/model/solid_mechanics/material_selector_tmpl.hh
index fcc687b1d..6ff23cb5b 100644
--- a/src/model/solid_mechanics/material_selector_tmpl.hh
+++ b/src/model/solid_mechanics/material_selector_tmpl.hh
@@ -1,73 +1,73 @@
/**
* @file material_selector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Tue Nov 07 2017
*
* @brief Implementation of the template MaterialSelector
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_selector.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_SELECTOR_TMPL_HH__
-#define __AKANTU_MATERIAL_SELECTOR_TMPL_HH__
+#ifndef AKANTU_MATERIAL_SELECTOR_TMPL_HH_
+#define AKANTU_MATERIAL_SELECTOR_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline UInt ElementDataMaterialSelector<std::string>::
operator()(const Element & element) {
try {
std::string material_name = this->elementData(element);
return model.getMaterialIndex(material_name);
} catch (...) {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
template <>
inline UInt ElementDataMaterialSelector<UInt>::
operator()(const Element & element) {
try {
return this->elementData(element) - first_index;
} catch (...) {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
MeshDataMaterialSelector<T>::MeshDataMaterialSelector(
const std::string & name, const SolidMechanicsModel & model,
UInt first_index)
: ElementDataMaterialSelector<T>(model.getMesh().getData<T>(name), model,
first_index) {}
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_SELECTOR_TMPL_HH__ */
+#endif /* AKANTU_MATERIAL_SELECTOR_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/internal_field.hh b/src/model/solid_mechanics/materials/internal_field.hh
index e9c86c06c..4dbb2895e 100644
--- a/src/model/solid_mechanics/materials/internal_field.hh
+++ b/src/model/solid_mechanics/materials/internal_field.hh
@@ -1,277 +1,277 @@
/**
* @file internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Feb 08 2018
*
* @brief Material internal properties
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_INTERNAL_FIELD_HH__
-#define __AKANTU_INTERNAL_FIELD_HH__
+#ifndef AKANTU_INTERNAL_FIELD_HH_
+#define AKANTU_INTERNAL_FIELD_HH_
namespace akantu {
class Material;
class FEEngine;
/**
* class for the internal fields of materials
* to store values for each quadrature
*/
template <typename T> class InternalField : public ElementTypeMapArray<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
InternalField(const ID & id, Material & material);
~InternalField() override;
/// This constructor is only here to let cohesive elements compile
InternalField(const ID & id, Material & material, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter);
/// More general constructor
InternalField(const ID & id, Material & material, UInt dim, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter);
InternalField(const ID & id, const InternalField<T> & other);
-private:
+
InternalField operator=(const InternalField &) = delete;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to reset the FEEngine for the internal field
virtual void setFEEngine(FEEngine & fe_engine);
/// function to reset the element kind for the internal
virtual void setElementKind(ElementKind element_kind);
/// initialize the field to a given number of component
virtual void initialize(UInt nb_component);
/// activate the history of this field
virtual void initializeHistory();
/// resize the arrays and set the new element to 0
virtual void resize();
/// set the field to a given value v
virtual void setDefaultValue(const T & v);
/// reset all the fields to the default value
virtual void reset();
/// save the current values in the history
virtual void saveCurrentValues();
/// restore the previous values from the history
virtual void restorePreviousValues();
/// remove the quadrature points corresponding to suppressed elements
virtual void
removeIntegrationPoints(const ElementTypeMapArray<UInt> & new_numbering);
/// print the content
void printself(std::ostream & stream, int /*indent*/ = 0) const override;
/// get the default value
inline operator T() const;
virtual FEEngine & getFEEngine() { return *fem; }
virtual const FEEngine & getFEEngine() const { return *fem; }
/// AKANTU_GET_MACRO(FEEngine, *fem, FEEngine &);
protected:
/// initialize the arrays in the ElementTypeMapArray<T>
void internalInitialize(UInt nb_component);
/// set the values for new internals
virtual void setArrayValues(T * begin, T * end);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
// using type_iterator = typename ElementTypeMapArray<T>::type_iterator;
// using filter_type_iterator =
// typename ElementTypeMapArray<UInt>::type_iterator;
// /// get the type iterator on all types contained in the internal field
- // type_iterator firstType(const GhostType & ghost_type = _not_ghost) const {
+ // type_iterator firstType(GhostType ghost_type = _not_ghost) const {
// return ElementTypeMapArray<T>::firstType(this->spatial_dimension,
// ghost_type, this->element_kind);
// }
// /// get the type iterator on the last type contained in the internal field
- // type_iterator lastType(const GhostType & ghost_type = _not_ghost) const {
+ // type_iterator lastType(GhostType ghost_type = _not_ghost) const {
// return ElementTypeMapArray<T>::lastType(this->spatial_dimension,
// ghost_type,
// this->element_kind);
// }
// /// get the type iterator on all types contained in the internal field
// filter_type_iterator
- // filterFirstType(const GhostType & ghost_type = _not_ghost) const {
+ // filterFirstType(GhostType ghost_type = _not_ghost) const {
// return this->element_filter.firstType(this->spatial_dimension,
// ghost_type,
// this->element_kind);
// }
// /// get the type iterator on the last type contained in the internal field
// filter_type_iterator
- // filterLastType(const GhostType & ghost_type = _not_ghost) const {
+ // filterLastType(GhostType ghost_type = _not_ghost) const {
// return this->element_filter.lastType(this->spatial_dimension, ghost_type,
// this->element_kind);
// }
/// get filter types for range loop
- decltype(auto) elementTypes(const GhostType & ghost_type = _not_ghost) const {
+ decltype(auto) elementTypes(GhostType ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::elementTypes(
_spatial_dimension = this->spatial_dimension,
_element_kind = this->element_kind, _ghost_type = ghost_type);
}
/// get filter types for range loop
- decltype(auto) filterTypes(const GhostType & ghost_type = _not_ghost) const {
+ decltype(auto) filterTypes(GhostType ghost_type = _not_ghost) const {
return this->element_filter.elementTypes(
_spatial_dimension = this->spatial_dimension,
_element_kind = this->element_kind, _ghost_type = ghost_type);
}
/// get the array for a given type of the element_filter
const Array<UInt> &
- getFilter(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const {
+ getFilter(ElementType type,
+ GhostType ghost_type = _not_ghost) const {
return this->element_filter(type, ghost_type);
}
/// get the Array corresponding to the type en ghost_type specified
- virtual Array<T> & operator()(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) {
+ virtual Array<T> & operator()(ElementType type,
+ GhostType ghost_type = _not_ghost) {
return ElementTypeMapArray<T>::operator()(type, ghost_type);
}
virtual const Array<T> &
- operator()(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const {
+ operator()(ElementType type,
+ GhostType ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::operator()(type, ghost_type);
}
- virtual Array<T> & previous(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) {
+ virtual Array<T> & previous(ElementType type,
+ GhostType ghost_type = _not_ghost) {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return this->previous_values->operator()(type, ghost_type);
}
virtual const Array<T> &
- previous(const ElementType & type,
- const GhostType & ghost_type = _not_ghost) const {
+ previous(ElementType type,
+ GhostType ghost_type = _not_ghost) const {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return this->previous_values->operator()(type, ghost_type);
}
virtual InternalField<T> & previous() {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return *(this->previous_values);
}
virtual const InternalField<T> & previous() const {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return *(this->previous_values);
}
/// check if the history is used or not
bool hasHistory() const { return (previous_values != nullptr); }
/// get the kind treated by the internal
- const ElementKind & getElementKind() const { return element_kind; }
+ ElementKind getElementKind() const { return element_kind; }
/// return the number of components
UInt getNbComponent() const { return nb_component; }
/// return the spatial dimension corresponding to the internal element type
/// loop filter
UInt getSpatialDimension() const { return this->spatial_dimension; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the material for which this is an internal parameter
Material & material;
/// the fem containing the mesh and the element informations
FEEngine * fem{nullptr};
/// Element filter if needed
const ElementTypeMapArray<UInt> & element_filter;
/// default value
T default_value{};
/// spatial dimension of the element to consider
UInt spatial_dimension{0};
/// ElementKind of the element to consider
ElementKind element_kind{_ek_regular};
/// Number of component of the internal field
UInt nb_component{0};
/// Is the field initialized
bool is_init{false};
/// previous values
std::unique_ptr<InternalField<T>> previous_values;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const InternalField<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AKANTU_INTERNAL_FIELD_HH__ */
+#endif /* AKANTU_INTERNAL_FIELD_HH_ */
diff --git a/src/model/solid_mechanics/materials/internal_field_tmpl.hh b/src/model/solid_mechanics/materials/internal_field_tmpl.hh
index 2a0422dd8..623e78b15 100644
--- a/src/model/solid_mechanics/materials/internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/materials/internal_field_tmpl.hh
@@ -1,307 +1,322 @@
/**
* @file internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Wed Feb 21 2018
*
* @brief Material internal properties
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_INTERNAL_FIELD_TMPL_HH__
-#define __AKANTU_INTERNAL_FIELD_TMPL_HH__
+#ifndef AKANTU_INTERNAL_FIELD_TMPL_HH_
+#define AKANTU_INTERNAL_FIELD_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(const ID & id, Material & material)
: ElementTypeMapArray<T>(id, material.getID(), material.getMemoryID()),
material(material), fem(&(material.getModel().getFEEngine())),
element_filter(material.getElementFilter()),
spatial_dimension(material.getModel().getSpatialDimension()) {}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(
const ID & id, Material & material, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter)
: ElementTypeMapArray<T>(id, material.getID(), material.getMemoryID()),
material(material), fem(&fem), element_filter(element_filter),
spatial_dimension(material.getSpatialDimension()) {}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(
const ID & id, Material & material, UInt dim, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter)
: ElementTypeMapArray<T>(id, material.getID(), material.getMemoryID()),
material(material), fem(&fem), element_filter(element_filter),
spatial_dimension(dim) {}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(const ID & id, const InternalField<T> & other)
: ElementTypeMapArray<T>(id, other.material.getID(),
other.material.getMemoryID()),
material(other.material), fem(other.fem),
element_filter(other.element_filter), default_value(other.default_value),
spatial_dimension(other.spatial_dimension),
element_kind(other.element_kind), nb_component(other.nb_component) {
AKANTU_DEBUG_ASSERT(other.is_init,
"Cannot create a copy of a non initialized field");
this->internalInitialize(this->nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T> InternalField<T>::~InternalField() {
if (this->is_init) {
this->material.unregisterInternal(*this);
}
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::setFEEngine(FEEngine & fe_engine) {
this->fem = &fe_engine;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::setElementKind(ElementKind element_kind) {
this->element_kind = element_kind;
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::initialize(UInt nb_component) {
internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::initializeHistory() {
- if (!previous_values)
+ if (!previous_values) {
previous_values =
std::make_unique<InternalField<T>>("previous_" + this->getID(), *this);
+ }
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::resize() {
- if (!this->is_init)
+ if (!this->is_init) {
return;
+ }
- for (auto ghost : ghost_types)
+ for (auto ghost : ghost_types) {
for (const auto & type : this->filterTypes(ghost)) {
UInt nb_element = this->element_filter(type, ghost).size();
UInt nb_quadrature_points =
this->fem->getNbIntegrationPoints(type, ghost);
UInt new_size = nb_element * nb_quadrature_points;
UInt old_size = 0;
Array<T> * vect = nullptr;
if (this->exists(type, ghost)) {
vect = &(this->operator()(type, ghost));
old_size = vect->size();
vect->resize(new_size);
} else {
vect = &(this->alloc(nb_element * nb_quadrature_points, nb_component,
type, ghost));
}
this->setArrayValues(vect->storage() + old_size * vect->getNbComponent(),
vect->storage() + new_size * vect->getNbComponent());
}
+ }
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::setDefaultValue(const T & value) {
this->default_value = value;
this->reset();
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::reset() {
- for (auto ghost_type : ghost_types)
+ for (auto ghost_type : ghost_types) {
for (const auto & type : this->elementTypes(ghost_type)) {
Array<T> & vect = (*this)(type, ghost_type);
- vect.clear();
+ //vect.zero();
this->setArrayValues(
vect.storage(), vect.storage() + vect.size() * vect.getNbComponent());
}
+ }
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::internalInitialize(UInt nb_component) {
if (!this->is_init) {
this->nb_component = nb_component;
for (auto ghost : ghost_types) {
for (const auto & type : this->filterTypes(ghost)) {
UInt nb_element = this->element_filter(type, ghost).size();
UInt nb_quadrature_points =
this->fem->getNbIntegrationPoints(type, ghost);
- if (this->exists(type, ghost))
+ if (this->exists(type, ghost)) {
this->operator()(type, ghost)
.resize(nb_element * nb_quadrature_points);
- else
+ } else {
this->alloc(nb_element * nb_quadrature_points, nb_component, type,
ghost);
+ }
}
}
this->material.registerInternal(*this);
this->is_init = true;
}
this->reset();
- if (this->previous_values)
+ if (this->previous_values) {
this->previous_values->internalInitialize(nb_component);
+ }
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::setArrayValues(T * begin, T * end) {
- for (; begin < end; ++begin)
+ for (; begin < end; ++begin) {
*begin = this->default_value;
+ }
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::saveCurrentValues() {
AKANTU_DEBUG_ASSERT(this->previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
- if (not this->is_init)
+ if (not this->is_init) {
return;
+ }
- for (auto ghost_type : ghost_types)
- for (const auto & type : this->elementTypes(ghost_type))
+ for (auto ghost_type : ghost_types) {
+ for (const auto & type : this->elementTypes(ghost_type)) {
(*this->previous_values)(type, ghost_type)
.copy((*this)(type, ghost_type));
+ }
+ }
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::restorePreviousValues() {
AKANTU_DEBUG_ASSERT(this->previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
- if (not this->is_init)
+ if (not this->is_init) {
return;
+ }
- for (auto ghost_type : ghost_types)
- for (const auto & type : this->elementTypes(ghost_type))
+ for (auto ghost_type : ghost_types) {
+ for (const auto & type : this->elementTypes(ghost_type)) {
(*this)(type, ghost_type)
.copy((*this->previous_values)(type, ghost_type));
+ }
+ }
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::removeIntegrationPoints(
const ElementTypeMapArray<UInt> & new_numbering) {
for (auto ghost_type : ghost_types) {
for (auto type : new_numbering.elementTypes(_all_dimensions, ghost_type,
_ek_not_defined)) {
- if (not this->exists(type, ghost_type))
+ if (not this->exists(type, ghost_type)) {
continue;
+ }
Array<T> & vect = (*this)(type, ghost_type);
- if (vect.size() == 0)
+ if (vect.empty()) {
continue;
+ }
const Array<UInt> & renumbering = new_numbering(type, ghost_type);
UInt nb_quad_per_elem = fem->getNbIntegrationPoints(type, ghost_type);
UInt nb_component = vect.getNbComponent();
Array<T> tmp(renumbering.size() * nb_quad_per_elem, nb_component);
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created from nowhere!!");
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created or disappeared in "
<< vect.getID() << "(" << vect.size() << "!=" << tmp.size()
<< ") "
"!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
memcpy(tmp.storage() + new_i * nb_component * nb_quad_per_elem,
vect.storage() + i * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem * sizeof(T));
++new_size;
}
}
tmp.resize(new_size * nb_quad_per_elem);
vect.copy(tmp);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::printself(std::ostream & stream,
int indent [[gnu::unused]]) const {
stream << "InternalField [ " << this->getID();
#if !defined(AKANTU_NDEBUG)
if (AKANTU_DEBUG_TEST(dblDump)) {
stream << std::endl;
ElementTypeMapArray<T>::printself(stream, indent + 3);
} else {
#endif
stream << " {" << this->getData(_not_ghost).size() << " types - "
<< this->getData(_ghost).size() << " ghost types"
<< "}";
#if !defined(AKANTU_NDEBUG)
}
#endif
stream << " ]";
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<InternalField<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Real r = in_param;
param.setDefaultValue(r);
}
/* -------------------------------------------------------------------------- */
template <typename T> inline InternalField<T>::operator T() const {
return default_value;
}
} // namespace akantu
-#endif /* __AKANTU_INTERNAL_FIELD_TMPL_HH__ */
+#endif /* AKANTU_INTERNAL_FIELD_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_core_includes.hh b/src/model/solid_mechanics/materials/material_core_includes.hh
index 490c60aab..ff2a64561 100644
--- a/src/model/solid_mechanics/materials/material_core_includes.hh
+++ b/src/model/solid_mechanics/materials/material_core_includes.hh
@@ -1,67 +1,67 @@
/**
* @file material_core_includes.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Feb 03 2016
*
* @brief List of materials for core package
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_CORE_INCLUDES_HH__
-#define __AKANTU_MATERIAL_CORE_INCLUDES_HH__
+#ifndef AKANTU_MATERIAL_CORE_INCLUDES_HH_
+#define AKANTU_MATERIAL_CORE_INCLUDES_HH_
/* -------------------------------------------------------------------------- */
/* Material list */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_CMAKE_LIST_MATERIALS
// elastic materials
#include "material_elastic.hh"
#include "material_elastic_linear_anisotropic.hh"
#include "material_elastic_orthotropic.hh"
#include "material_neohookean.hh"
// visco-elastic materials
#include "material_standard_linear_solid_deviatoric.hh"
// damage laws
#include "material_marigo.hh"
#include "material_mazars.hh"
// small-deformation plasticity
#include "material_linear_isotropic_hardening.hh"
#endif
#define AKANTU_CORE_MATERIAL_LIST \
((2, (elastic, MaterialElastic)))((2, (neohookean, MaterialNeohookean)))( \
(2, (elastic_orthotropic, MaterialElasticOrthotropic)))( \
(2, (elastic_anisotropic, MaterialElasticLinearAnisotropic)))( \
(2, (sls_deviatoric, MaterialStandardLinearSolidDeviatoric)))( \
(2, (marigo, MaterialMarigo)))((2, (mazars, MaterialMazars)))( \
(2, (plastic_linear_isotropic_hardening, \
MaterialLinearIsotropicHardening)))
-#endif /* __AKANTU_MATERIAL_CORE_INCLUDES_HH__ */
+#endif /* AKANTU_MATERIAL_CORE_INCLUDES_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc
index acbaaa666..b5c897168 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc
@@ -1,78 +1,80 @@
/**
* @file material_anisotropic_damage.cc
*
* @author Nicolas Richart
*
* @date creation mer jun 26 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_anisotropic_damage.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
namespace {
template <UInt dim>
std::unique_ptr<Material>
- materialAnisotropicDamage(std::integral_constant<UInt, dim>,
+ materialAnisotropicDamage(std::integral_constant<UInt, dim> /*unused*/,
const ID & option, SolidMechanicsModel & model,
const ID & id) {
- if (option == "" or option == "mazars") {
+ if (option.empty() or option == "mazars") {
return std::make_unique<MaterialAnisotropicDamage<
dim, EquivalentStrainMazars, DamageThresholdTan>>(model, id);
- } else if (option == "mazars-drucker-prager") {
+ }
+ if (option == "mazars-drucker-prager") {
return std::make_unique<MaterialAnisotropicDamage<
dim, EquivalentStrainMazarsDruckerPrager, DamageThresholdTan>>(model,
id);
- } else {
- AKANTU_EXCEPTION("The option "
- << option << " is not valid for the material " << id);
}
+ AKANTU_EXCEPTION("The option " << option
+ << " is not valid for the material " << id);
}
template <class... Args>
decltype(auto) dimensionDispatch(UInt dim, Args &&... args) {
switch (dim) {
case 1:
return materialAnisotropicDamage(std::integral_constant<UInt, 1>{},
std::forward<Args>(args)...);
case 2:
return materialAnisotropicDamage(std::integral_constant<UInt, 2>{},
std::forward<Args>(args)...);
case 3:
return materialAnisotropicDamage(std::integral_constant<UInt, 3>{},
std::forward<Args>(args)...);
- default: { AKANTU_EXCEPTION("In what dimension are you leaving ?"); }
+ default: {
+ AKANTU_EXCEPTION("In what dimension are you leaving ?");
+ }
}
}
} // namespace
static bool material_is_alocated_anisotropic_damage [[gnu::unused]] =
MaterialFactory::getInstance().registerAllocator(
"anisotropic_damage",
[](UInt dim, const ID & option, SolidMechanicsModel & model,
const ID & id) -> std::unique_ptr<Material> {
return dimensionDispatch(dim, option, model, id);
});
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh
index e509d96cd..7583b31f0 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh
@@ -1,87 +1,87 @@
/**
* @file material_anisotropic_damage.hh
*
* @author Nicolas Richart
*
* @date creation mar jun 25 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_HH__
-#define __AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_HH__
+#ifndef AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_HH_
+#define AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_HH_
namespace akantu {
template <UInt dim, template <UInt> class EquivalentStrain,
template <UInt> class DamageThreshold,
template <UInt> class Parent = MaterialElastic>
class MaterialAnisotropicDamage : public Parent<dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialAnisotropicDamage(SolidMechanicsModel & model, const ID & id = "");
~MaterialAnisotropicDamage() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void computeStress(ElementType el_type, GhostType ghost_type) override;
private:
void damageStress(Matrix<double> & sigma, const Matrix<double> & sigma_el,
const Matrix<double> & D, Real TrD);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
Real Dc{0.99};
/// damage internal variable
InternalField<Real> damage;
/// elastic stress
InternalField<Real> elastic_stress;
/// equivalent strain
InternalField<Real> equivalent_strain;
/// trace of the damageThreshold
InternalField<Real> trace_damage;
/// damage criteria
EquivalentStrain<dim> equivalent_strain_function;
/// damage evolution
DamageThreshold<dim> damage_threshold_function;
};
} // namespace akantu
#include "material_anisotropic_damage_tmpl.hh"
-#endif /* __AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_HH__ */
+#endif /* AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh
index 408a2cdfd..b48dbac7d 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh
@@ -1,365 +1,375 @@
/**
* @file material_anisotropic_damage_tmpl.hh
*
* @author Nicolas Richart
*
* @date creation mar jun 25 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "material_anisotropic_damage.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_TMPL_HH__
-#define __AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_TMPL_HH__
+#ifndef AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_TMPL_HH_
+#define AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_TMPL_HH_
namespace akantu {
struct EmptyIteratorContainer {
struct iterator {
auto & operator++() { return *this; }
Real operator*() { return 0; }
- bool operator!=(const iterator &) const { return true; }
- bool operator==(const iterator &) const { return false; }
+ bool operator!=(const iterator & /*unused*/) const { return true; }
+ bool operator==(const iterator & /*unused*/) const { return false; }
};
- auto begin() { return iterator(); }
- auto end() { return iterator(); }
+ auto begin() const // NOLINT(readability-convert-member-functions-to-static)
+ {
+ return iterator();
+ }
+
+ auto end() const // NOLINT(readability-convert-member-functions-to-static)
+ {
+ return iterator();
+ }
};
} // namespace akantu
namespace std {
template <> struct iterator_traits<::akantu::EmptyIteratorContainer::iterator> {
using iterator_category = forward_iterator_tag;
using value_type = akantu::Real;
using difference_type = std::ptrdiff_t;
using pointer = akantu::Real *;
using reference = akantu::Real &;
};
} // namespace std
namespace akantu {
namespace {
template <UInt dim, class Op>
void tensorPlus_(const Matrix<Real> & A, Op && oper) {
Vector<Real> A_eigs(dim);
A.eig(A_eigs);
for (auto & ap : A_eigs) {
oper(ap);
}
}
template <UInt dim> auto tensorPlus2(const Matrix<Real> & A) {
Real square = 0;
tensorPlus_<dim>(A, [&](Real eig) {
eig = std::max(eig, 0.);
square += eig * eig;
});
return square;
}
template <UInt dim> auto tensorPlusTrace(const Matrix<Real> & A) {
Real trace_plus = 0;
Real trace_minus = 0;
tensorPlus_<dim>(A, [&](Real eig) {
trace_plus += std::max(eig, 0.);
trace_minus += std::min(eig, 0.);
});
return std::make_pair(trace_plus, trace_minus);
}
template <UInt dim, class Op>
auto tensorPlusOp(const Matrix<Real> & A, Matrix<Real> & A_directions,
Op && oper, bool sorted = false) {
Vector<Real> A_eigs(dim);
Matrix<Real> A_diag(dim, dim);
A.eig(A_eigs, A_directions, sorted);
for (auto && data : enumerate(A_eigs)) {
auto i = std::get<0>(data);
A_diag(i, i) = oper(std::max(std::get<1>(data), 0.), i);
}
return A_directions * A_diag * A_directions.transpose();
}
template <UInt dim, class Op>
auto tensorPlus(const Matrix<Real> & A, Matrix<Real> & A_directions,
bool sorted = false) {
- return tensorPlusOp<dim>(A, A_directions, [](Real x, Real) { return x; },
- sorted);
+ return tensorPlusOp<dim>(
+ A, A_directions, [](Real x, Real /*unused*/) { return x; }, sorted);
}
template <UInt dim, class Op>
auto tensorPlusOp(const Matrix<Real> & A, Op && oper) {
Matrix<Real> A_directions(dim, dim);
return tensorPlusOp<dim>(A, A_directions, std::forward<Op>(oper));
}
template <UInt dim> auto tensorPlus(const Matrix<Real> & A) {
- return tensorPlusOp<dim>(A, [](Real x, Real) { return x; });
+ return tensorPlusOp<dim>(A, [](Real x, Real /*unused*/) { return x; });
}
template <UInt dim> auto tensorSqrt(const Matrix<Real> & A) {
- return tensorPlusOp<dim>(A, [](Real x, UInt) { return std::sqrt(x); });
+ return tensorPlusOp<dim>(
+ A, [](Real x, UInt /*unused*/) { return std::sqrt(x); });
}
} // namespace
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <UInt dim, template <UInt> class EquivalentStrain,
template <UInt> class DamageThreshold, template <UInt> class Parent>
MaterialAnisotropicDamage<dim, EquivalentStrain, DamageThreshold, Parent>::
MaterialAnisotropicDamage(SolidMechanicsModel & model, const ID & id)
: Parent<dim>(model, id), damage("damage_tensor", *this),
elastic_stress("elastic_stress", *this),
equivalent_strain("equivalent_strain", *this),
trace_damage("trace_damage", *this), equivalent_strain_function(*this),
damage_threshold_function(*this) {
this->registerParam("Dc", Dc, _pat_parsable, "Critical damage");
this->damage.initialize(dim * dim);
this->elastic_stress.initialize(dim * dim);
this->equivalent_strain.initialize(1);
this->trace_damage.initialize(1);
this->trace_damage.initializeHistory();
}
/* -------------------------------------------------------------------------- */
template <UInt dim, template <UInt> class EquivalentStrain,
template <UInt> class DamageThreshold, template <UInt> class Parent>
void MaterialAnisotropicDamage<dim, EquivalentStrain, DamageThreshold, Parent>::
damageStress(Matrix<Real> & sigma, const Matrix<Real> & sigma_el,
const Matrix<Real> & D, Real TrD) {
// σ_(n + 1) = (1 − D_(n + 1))^(1/2) σ~_(n + 1) (1 − D_(n + 1))^(1 / 2)
// - ((1 − D_(n + 1)) : σ~_(n + 1))/ (3 - Tr(D_(n+1))) (1 − D_(n + 1))
// + 1/3 (1 - Tr(D_(n+1)) <Tr(σ~_(n + 1))>_+ + <Tr(σ~_(n + 1))>_-) I
auto one_D = Matrix<Real>::eye(dim) - D;
auto sqrt_one_D = tensorSqrt<dim>(one_D);
- Real Tr_sigma_plus, Tr_sigma_minus;
+ Real Tr_sigma_plus;
+ Real Tr_sigma_minus;
std::tie(Tr_sigma_plus, Tr_sigma_minus) = tensorPlusTrace<dim>(sigma_el);
auto I = Matrix<Real>::eye(dim);
sigma = sqrt_one_D * sigma_el * sqrt_one_D -
(one_D.doubleDot(sigma_el) / (dim - TrD) * one_D) +
1. / dim * ((1 - TrD) * Tr_sigma_plus - Tr_sigma_minus) * I;
}
/* -------------------------------------------------------------------------- */
template <UInt dim, template <UInt> class EquivalentStrain,
template <UInt> class DamageThreshold, template <UInt> class Parent>
void MaterialAnisotropicDamage<dim, EquivalentStrain, DamageThreshold,
Parent>::computeStress(ElementType type,
GhostType ghost_type) {
for (auto && data :
zip(make_view(this->stress(type, ghost_type), dim, dim),
make_view(this->gradu(type, ghost_type), dim, dim),
make_view(this->sigma_th(type, ghost_type)),
make_view(this->elastic_stress(type, ghost_type), dim, dim),
make_view(this->equivalent_strain(type, ghost_type)),
make_view(this->damage(type, ghost_type), dim, dim),
make_view(this->trace_damage(type, ghost_type)),
make_view(this->trace_damage.previous(type, ghost_type)),
equivalent_strain_function, damage_threshold_function)) {
auto & sigma = std::get<0>(data);
auto & grad_u = std::get<1>(data);
auto & sigma_th = std::get<2>(data);
auto & sigma_el = std::get<3>(data);
auto & epsilon_hat = std::get<4>(data);
auto & D = std::get<5>(data);
auto & TrD_n_1 = std::get<6>(data);
auto & TrD = std::get<7>(data);
auto & equivalent_strain_data = std::get<8>(data);
auto & damage_threshold_data = std::get<9>(data);
Matrix<Real> Dtmp(dim, dim);
Real TrD_n_1_tmp;
Matrix<Real> epsilon(dim, dim);
// yes you read properly this is a label for a goto
auto computeDamage = [&]() {
MaterialElastic<dim>::computeStressOnQuad(grad_u, sigma_el, sigma_th);
this->template gradUToEpsilon<dim>(grad_u, epsilon);
// evaluate the damage criteria
epsilon_hat = equivalent_strain_function(epsilon, equivalent_strain_data);
// evolve the damage if needed
auto K_TrD = damage_threshold_function.K(TrD, damage_threshold_data);
auto f = epsilon_hat - K_TrD;
// if test function > 0 evolve the damage
if (f > 0) {
TrD_n_1_tmp =
damage_threshold_function.K_inv(epsilon_hat, damage_threshold_data);
auto epsilon_plus = tensorPlus<dim>(epsilon);
auto delta_lambda = (TrD_n_1_tmp - TrD) / (epsilon_hat * epsilon_hat);
Dtmp = D + delta_lambda * epsilon_plus;
return true;
}
return false;
};
// compute a temporary version of the new damage
auto is_damage_updated = computeDamage();
if (is_damage_updated) {
/// Check and correct for broken case
if (Dtmp.trace() > Dc) {
if (epsilon.trace() > 0) { // tensile loading
auto kpa = this->kpa;
auto lambda = this->lambda;
// change kappa to Kappa_broken = (1-Dc) Kappa
kpa = (1 - Dc) * kpa;
this->E = 9 * kpa * (kpa - lambda) / (3 * kpa - lambda);
this->nu = lambda / (3 * kpa - lambda);
this->updateInternalParameters();
computeDamage();
} else if (std::abs(epsilon.trace()) < 1e-10) { // deviatoric case
Matrix<Real> n(dim, dim);
std::vector<UInt> ns;
- tensorPlusOp<dim>(Dtmp, n,
- [&](Real x, UInt i) {
- if (x > this->Dc) {
- ns.push_back(i);
- return this->Dc;
- }
-
- return x;
- },
- true);
+ tensorPlusOp<dim>(
+ Dtmp, n,
+ [&](Real x, UInt i) {
+ if (x > this->Dc) {
+ ns.push_back(i);
+ return this->Dc;
+ }
+
+ return x;
+ },
+ true);
}
}
TrD_n_1 = TrD_n_1_tmp;
D = Dtmp;
} else {
TrD_n_1 = TrD;
}
// apply the damage to the stress
damageStress(sigma, sigma_el, D, TrD_n_1);
}
}
/* -------------------------------------------------------------------------- */
/* EquivalentStrain functions */
/* -------------------------------------------------------------------------- */
template <UInt dim>
class EquivalentStrainMazars : public EmptyIteratorContainer {
public:
EquivalentStrainMazars(Material & /*mat*/) {}
template <class... Other>
Real operator()(const Matrix<Real> & epsilon, Other &&... /*other*/) {
Real epsilon_hat = 0.;
std::tie(epsilon_hat, std::ignore) = tensorPlusTrace<dim>(epsilon);
return std::sqrt(epsilon_hat);
}
};
template <UInt dim>
class EquivalentStrainMazarsDruckerPrager : public EquivalentStrainMazars<dim> {
public:
EquivalentStrainMazarsDruckerPrager(Material & mat)
: EquivalentStrainMazars<dim>(mat) {
mat.registerParam("k", k, _pat_parsable, "k");
}
template <class... Other>
- Real operator()(const Matrix<Real> & epsilon, Real) {
+ Real operator()(const Matrix<Real> & epsilon, Real /*unused*/) {
Real epsilon_hat = EquivalentStrainMazars<dim>::operator()(epsilon);
epsilon_hat += k * epsilon.trace();
return epsilon_hat;
}
protected:
Real k;
};
/* -------------------------------------------------------------------------- */
/* DamageThreshold functions */
/* -------------------------------------------------------------------------- */
template <UInt dim>
class DamageThresholdLinear : public EmptyIteratorContainer {
public:
DamageThresholdLinear(Material & mat) : mat(mat) {
mat.registerParam("A", A, _pat_parsable, "A");
mat.registerParam("K0", K0, _pat_parsable, "K0");
}
template <class... Other> Real K(Real x, Other &&... /*other*/) {
return 1. / A * x + K0;
}
template <class... Other> Real K_inv(Real x, Other &&... /*other*/) {
return A * (x - K0);
}
private:
Material & mat;
Real A;
Real K0;
};
template <UInt dim> class DamageThresholdTan : public EmptyIteratorContainer {
public:
DamageThresholdTan(Material & mat) : mat(mat) {
mat.registerParam("a", a, _pat_parsable, "a");
mat.registerParam("A", A, _pat_parsable, "A");
mat.registerParam("K0", K0, _pat_parsable, "K0");
}
template <class... Other> Real K(Real x, Other &&... /*other*/) {
return a * std::tan(std::atan2(x, a) - std::atan2(K0, a));
}
template <class... Other> Real K_inv(Real x, Other &&... /*other*/) {
return a * A * (std::atan2(x, a) - std::atan2(K0, a));
}
private:
Material & mat;
Real a{2.93e-4};
Real A{5e3};
Real K0{5e-5};
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_TMPL_HH__ */
+#endif /* AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage.hh b/src/model/solid_mechanics/materials/material_damage/material_damage.hh
index 3704eb492..85653ab75 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage.hh
@@ -1,112 +1,112 @@
/**
* @file material_damage.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Material isotropic elastic
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_DAMAGE_HH__
-#define __AKANTU_MATERIAL_DAMAGE_HH__
+#ifndef AKANTU_MATERIAL_DAMAGE_HH_
+#define AKANTU_MATERIAL_DAMAGE_HH_
namespace akantu {
template <UInt spatial_dimension,
template <UInt> class Parent = MaterialElastic>
class MaterialDamage : public Parent<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialDamage(SolidMechanicsModel & model, const ID & id = "");
~MaterialDamage() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// compute the tangent stiffness matrix for an element type
- void computeTangentModuli(const ElementType & el_type,
+ void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
bool hasStiffnessMatrixChanged() override { return true; }
protected:
/// update the dissipated energy, must be called after the stress have been
/// computed
void updateEnergies(ElementType el_type) override;
/// compute the tangent stiffness matrix for a given quadrature point
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent, Real & dam);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy for the time step
Real getDissipatedEnergy() const;
Real getEnergy(const std::string & type) override;
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override {
return Parent<spatial_dimension>::getEnergy(energy_id, type, index);
};
AKANTU_GET_MACRO_NOT_CONST(Damage, damage, ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Damage, damage, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real)
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage internal variable
InternalField<Real> damage;
/// dissipated energy
InternalField<Real> dissipated_energy;
/// contain the current value of @f$ \int_0^{\epsilon}\sigma(\omega)d\omega
/// @f$ the dissipated energy
InternalField<Real> int_sigma;
};
} // namespace akantu
#include "material_damage_tmpl.hh"
-#endif /* __AKANTU_MATERIAL_DAMAGE_HH__ */
+#endif /* AKANTU_MATERIAL_DAMAGE_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
index f52607f10..ce9d1dba1 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
@@ -1,72 +1,73 @@
/**
* @file material_damage_non_local.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 23 2012
* @date last modification: Mon Sep 11 2017
*
* @brief interface for non local damage material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH__
-#define __AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH__
+#ifndef AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH_
+#define AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH_
namespace akantu {
template <UInt dim, class MaterialDamageLocal>
class MaterialDamageNonLocal
: public MaterialNonLocal<dim, MaterialDamageLocal> {
public:
using MaterialParent = MaterialNonLocal<dim, MaterialDamageLocal>;
MaterialDamageNonLocal(SolidMechanicsModel & model, const ID & id)
: MaterialParent(model, id){};
protected:
/* ------------------------------------------------------------------------ */
virtual void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost) = 0;
/* ------------------------------------------------------------------------ */
void computeNonLocalStresses(GhostType ghost_type) override {
AKANTU_DEBUG_IN();
for (auto type : this->element_filter.elementTypes(dim, ghost_type)) {
auto & elem_filter = this->element_filter(type, ghost_type);
- if (elem_filter.size() == 0)
+ if (elem_filter.empty()) {
continue;
+ }
computeNonLocalStress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH__ */
+#endif /* AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh b/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
index d46427ce8..78b73ec23 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
@@ -1,174 +1,173 @@
/**
* @file material_damage_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Specialization of the material class for the damage material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
MaterialDamage<spatial_dimension, Parent>::MaterialDamage(
SolidMechanicsModel & model, const ID & id)
: Parent<spatial_dimension>(model, id), damage("damage", *this),
dissipated_energy("damage dissipated energy", *this),
int_sigma("integral of sigma", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = false;
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->damage.initialize(1);
this->dissipated_energy.initialize(1);
this->int_sigma.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::initMaterial() {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the dissipated energy in each element by a trapezoidal approximation
* of
* @f$ Ed = \int_0^{\epsilon}\sigma(\omega)d\omega -
* \frac{1}{2}\sigma:\epsilon@f$
*/
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::updateEnergies(
ElementType el_type) {
Parent<spatial_dimension>::updateEnergies(el_type);
this->computePotentialEnergy(el_type);
auto epsilon_p =
this->gradu.previous(el_type).begin(spatial_dimension, spatial_dimension);
auto sigma_p = this->stress.previous(el_type).begin(spatial_dimension,
spatial_dimension);
auto epot = this->potential_energy(el_type).begin();
auto ints = this->int_sigma(el_type).begin();
auto ed = this->dissipated_energy(el_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
Matrix<Real> delta_gradu(grad_u);
delta_gradu -= *epsilon_p;
Matrix<Real> sigma_h(sigma);
sigma_h += *sigma_p;
Real dint = .5 * sigma_h.doubleDot(delta_gradu);
*ints += dint;
*ed = *ints - *epot;
++epsilon_p;
++sigma_p;
++epot;
++ints;
++ed;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::computeTangentModuli(
- const ElementType & el_type, Array<Real> & tangent_matrix,
- GhostType ghost_type) {
+ ElementType el_type, Array<Real> & tangent_matrix, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::computeTangentModuli(el_type, tangent_matrix,
ghost_type);
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, *dam);
++dam;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, Real & dam) {
tangent *= (1 - dam);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
Real MaterialDamage<spatial_dimension, Parent>::getDissipatedEnergy() const {
AKANTU_DEBUG_IN();
Real de = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
de +=
this->fem.integrate(dissipated_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
Real MaterialDamage<spatial_dimension, Parent>::getEnergy(
const std::string & type) {
- if (type == "dissipated")
+ if (type == "dissipated") {
return getDissipatedEnergy();
- else
- return Parent<spatial_dimension>::getEnergy(type);
+ }
+ return Parent<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo.cc b/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
index b6ba0c70c..c95d35cf4 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
@@ -1,105 +1,102 @@
/**
* @file material_marigo.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Jul 09 2017
*
* @brief Specialization of the material class for the marigo material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_marigo.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMarigo<spatial_dimension>::MaterialMarigo(SolidMechanicsModel & model,
const ID & id)
: MaterialDamage<spatial_dimension>(model, id), Yd("Yd", *this),
damage_in_y(false), yc_limit(false) {
AKANTU_DEBUG_IN();
this->registerParam("Sd", Sd, Real(5000.), _pat_parsable | _pat_modifiable);
this->registerParam("epsilon_c", epsilon_c, Real(0.), _pat_parsable,
"Critical strain");
this->registerParam("Yc limit", yc_limit, false, _pat_internal,
"As the material a critical Y");
this->registerParam("damage_in_y", damage_in_y, false, _pat_parsable,
"Use threshold (1-D)Y");
this->registerParam("Yd", Yd, _pat_parsable, "Damaging energy threshold");
this->Yd.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialDamage<spatial_dimension>::initMaterial();
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::updateInternalParameters() {
MaterialDamage<spatial_dimension>::updateInternalParameters();
Yc = .5 * epsilon_c * this->E * epsilon_c;
- if (std::abs(epsilon_c) > std::numeric_limits<Real>::epsilon())
- yc_limit = true;
- else
- yc_limit = false;
+ yc_limit = (std::abs(epsilon_c) > std::numeric_limits<Real>::epsilon());
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
- Array<Real>::scalar_iterator dam = this->damage(el_type, ghost_type).begin();
- Array<Real>::scalar_iterator Yd_q = this->Yd(el_type, ghost_type).begin();
+ auto dam = this->damage(el_type, ghost_type).begin();
+ auto Yd_q = this->Yd(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Real Y = 0.;
computeStressOnQuad(grad_u, sigma, *dam, Y, *Yd_q);
++dam;
++Yd_q;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(marigo, MaterialMarigo);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
index a290d7e61..6663304d2 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
@@ -1,122 +1,122 @@
/**
* @file material_marigo.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Marigo damage law
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_MARIGO_HH__
-#define __AKANTU_MATERIAL_MARIGO_HH__
+#ifndef AKANTU_MATERIAL_MARIGO_HH_
+#define AKANTU_MATERIAL_MARIGO_HH_
namespace akantu {
/**
* Material marigo
*
* parameters in the material files :
* - Yd : (default: 50)
* - Sd : (default: 5000)
* - Ydrandomness : (default:0)
*/
template <UInt spatial_dimension>
class MaterialMarigo : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialMarigo(SolidMechanicsModel & model, const ID & id = "");
~MaterialMarigo() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
void updateInternalParameters() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real & dam, Real & Y, Real & Ydq);
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma, Real & dam,
Real & Y, Real & Ydq);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// resistance to damage
RandomInternalField<Real> Yd;
/// damage threshold
Real Sd;
/// critical epsilon when the material is considered as broken
Real epsilon_c;
Real Yc;
bool damage_in_y;
bool yc_limit;
};
} // namespace akantu
#include "material_marigo_inline_impl.hh"
-#endif /* __AKANTU_MATERIAL_MARIGO_HH__ */
+#endif /* AKANTU_MATERIAL_MARIGO_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.hh
index 47329d45b..b67f5af9e 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.hh
@@ -1,130 +1,133 @@
/**
* @file material_marigo_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Fri Dec 02 2016
*
* @brief Implementation of the inline functions of the material marigo
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_marigo.hh"
-#ifndef __AKANTU_MATERIAL_MARIGO_INLINE_IMPL_HH__
-#define __AKANTU_MATERIAL_MARIGO_INLINE_IMPL_HH__
+#ifndef AKANTU_MATERIAL_MARIGO_INLINE_IMPL_HH_
+#define AKANTU_MATERIAL_MARIGO_INLINE_IMPL_HH_
namespace akantu {
template <UInt spatial_dimension>
inline void MaterialMarigo<spatial_dimension>::computeStressOnQuad(
Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam, Real & Y,
Real & Ydq) {
MaterialElastic<spatial_dimension>::computeStressOnQuad(grad_u, sigma);
Y = 0;
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
Y += sigma(i, j) * (grad_u(i, j) + grad_u(j, i)) / 2.;
}
}
Y *= 0.5;
- if (damage_in_y)
+ if (damage_in_y) {
Y *= (1 - dam);
+ }
- if (yc_limit)
+ if (yc_limit) {
Y = std::min(Y, Yc);
+ }
if (!this->is_non_local) {
computeDamageAndStressOnQuad(sigma, dam, Y, Ydq);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMarigo<spatial_dimension>::computeDamageAndStressOnQuad(
Matrix<Real> & sigma, Real & dam, Real & Y, Real & Ydq) {
Real Fd = Y - Ydq - Sd * dam;
- if (Fd > 0)
+ if (Fd > 0) {
dam = (Y - Ydq) / Sd;
+ }
dam = std::min(dam, Real(1.));
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline UInt MaterialMarigo<spatial_dimension>::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (tag == SynchronizationTag::_smm_init_mat) {
size += sizeof(Real) * this->getModel().getNbIntegrationPoints(elements);
}
size += MaterialDamage<spatial_dimension>::getNbData(elements, tag);
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMarigo<spatial_dimension>::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (tag == SynchronizationTag::_smm_init_mat) {
this->packElementDataHelper(Yd, buffer, elements);
}
MaterialDamage<spatial_dimension>::packData(buffer, elements, tag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void
MaterialMarigo<spatial_dimension>::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (tag == SynchronizationTag::_smm_init_mat) {
this->unpackElementDataHelper(Yd, buffer, elements);
}
MaterialDamage<spatial_dimension>::unpackData(buffer, elements, tag);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_MARIGO_INLINE_IMPL_HH__ */
+#endif /* AKANTU_MATERIAL_MARIGO_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
index b23a08e5d..0e91c567b 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
@@ -1,92 +1,91 @@
/**
* @file material_marigo_non_local.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Marigo non-local description
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_non_local.hh"
#include "material_marigo.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH__
-#define __AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH__
+#ifndef AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH_
+#define AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* Material Marigo
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialMarigoNonLocal
: public MaterialDamageNonLocal<spatial_dimension,
MaterialMarigo<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- typedef MaterialDamageNonLocal<spatial_dimension,
- MaterialMarigo<spatial_dimension>>
- MaterialMarigoNonLocalParent;
+ using MaterialMarigoNonLocalParent = MaterialDamageNonLocal<spatial_dimension,
+ MaterialMarigo<spatial_dimension>>;
MaterialMarigoNonLocal(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
void registerNonLocalVariables() override;
/// constitutive law
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost) override;
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Y, Y, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> Y;
InternalField<Real> Ynl;
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH__ */
+#endif /* AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
index e2f02e872..8f332e749 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
@@ -1,124 +1,124 @@
/**
* @file material_mazars.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Material Following the Mazars law for damage evolution
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_MAZARS_HH__
-#define __AKANTU_MATERIAL_MAZARS_HH__
+#ifndef AKANTU_MATERIAL_MAZARS_HH_
+#define AKANTU_MATERIAL_MAZARS_HH_
namespace akantu {
/**
* Material Mazars
*
* parameters in the material files :
* - rho : density (default: 0)
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - K0 : Damage threshold
* - At : Parameter damage traction 1
* - Bt : Parameter damage traction 2
* - Ac : Parameter damage compression 1
* - Bc : Parameter damage compression 2
* - beta : Parameter for shear
*/
template <UInt spatial_dimension>
class MaterialMazars : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialMazars(SolidMechanicsModel & model, const ID & id = "");
~MaterialMazars() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & damage,
Real & Ehat);
inline void computeDamageAndStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & damage,
Real & Ehat);
inline void computeDamageOnQuad(const Real & epsilon_equ,
const Matrix<Real> & sigma,
const Vector<Real> & epsilon_princ,
Real & dam);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage threshold
RandomInternalField<Real> K0;
/// parameter damage traction 1
Real At;
/// parameter damage traction 2
Real Bt;
/// parameter damage compression 1
Real Ac;
/// parameter damage compression 2
Real Bc;
/// parameter for shear
Real beta;
/// specify the variable to average false = ehat, true = damage (only valid
/// for non local version)
bool damage_in_compute_stress;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "material_mazars_inline_impl.hh"
-#endif /* __AKANTU_MATERIAL_MAZARS_HH__ */
+#endif /* AKANTU_MATERIAL_MAZARS_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.hh
index 7df15bde3..296593f8d 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.hh
@@ -1,157 +1,162 @@
/**
* @file material_mazars_inline_impl.hh
*
* @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 06 2011
* @date last modification: Wed Feb 03 2016
*
* @brief Implementation of the inline functions of the material damage
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_mazars.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMazars<spatial_dimension>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam,
Real & Ehat) {
Matrix<Real> epsilon(3, 3);
- epsilon.clear();
+ epsilon.zero();
- for (UInt i = 0; i < spatial_dimension; ++i)
- for (UInt j = 0; j < spatial_dimension; ++j)
+ for (UInt i = 0; i < spatial_dimension; ++i) {
+ for (UInt j = 0; j < spatial_dimension; ++j) {
epsilon(i, j) = .5 * (grad_u(i, j) + grad_u(j, i));
+ }
+ }
Vector<Real> Fdiag(3);
Math::matrixEig(3, epsilon.storage(), Fdiag.storage());
Ehat = 0.;
for (UInt i = 0; i < 3; ++i) {
Real epsilon_p = std::max(Real(0.), Fdiag(i));
Ehat += epsilon_p * epsilon_p;
}
Ehat = sqrt(Ehat);
MaterialElastic<spatial_dimension>::computeStressOnQuad(grad_u, sigma);
if (damage_in_compute_stress) {
computeDamageOnQuad(Ehat, sigma, Fdiag, dam);
}
if (not this->is_non_local) {
computeDamageAndStressOnQuad(grad_u, sigma, dam, Ehat);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMazars<spatial_dimension>::computeDamageAndStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam,
Real & Ehat) {
if (!damage_in_compute_stress) {
Vector<Real> Fdiag(3);
- Fdiag.clear();
+ Fdiag.zero();
Matrix<Real> epsilon(3, 3);
- epsilon.clear();
- for (UInt i = 0; i < spatial_dimension; ++i)
- for (UInt j = 0; j < spatial_dimension; ++j)
+ epsilon.zero();
+ for (UInt i = 0; i < spatial_dimension; ++i) {
+ for (UInt j = 0; j < spatial_dimension; ++j) {
epsilon(i, j) = .5 * (grad_u(i, j) + grad_u(j, i));
+ }
+ }
Math::matrixEig(3, epsilon.storage(), Fdiag.storage());
computeDamageOnQuad(Ehat, sigma, Fdiag, dam);
}
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMazars<spatial_dimension>::computeDamageOnQuad(
const Real & epsilon_equ,
__attribute__((unused)) const Matrix<Real> & sigma,
const Vector<Real> & epsilon_princ, Real & dam) {
Real Fs = epsilon_equ - K0;
if (Fs > 0.) {
Real dam_t;
Real dam_c;
dam_t =
1 - K0 * (1 - At) / epsilon_equ - At * (exp(-Bt * (epsilon_equ - K0)));
dam_c =
1 - K0 * (1 - Ac) / epsilon_equ - Ac * (exp(-Bc * (epsilon_equ - K0)));
Real Cdiag;
Cdiag = this->E * (1 - this->nu) / ((1 + this->nu) * (1 - 2 * this->nu));
Vector<Real> sigma_princ(3);
sigma_princ(0) = Cdiag * epsilon_princ(0) +
this->lambda * (epsilon_princ(1) + epsilon_princ(2));
sigma_princ(1) = Cdiag * epsilon_princ(1) +
this->lambda * (epsilon_princ(0) + epsilon_princ(2));
sigma_princ(2) = Cdiag * epsilon_princ(2) +
this->lambda * (epsilon_princ(1) + epsilon_princ(0));
Vector<Real> sigma_p(3);
- for (UInt i = 0; i < 3; i++)
+ for (UInt i = 0; i < 3; i++) {
sigma_p(i) = std::max(Real(0.), sigma_princ(i));
+ }
// sigma_p *= 1. - dam;
Real trace_p = this->nu / this->E * (sigma_p(0) + sigma_p(1) + sigma_p(2));
Real alpha_t = 0;
for (UInt i = 0; i < 3; ++i) {
Real epsilon_t = (1 + this->nu) / this->E * sigma_p(i) - trace_p;
Real epsilon_p = std::max(Real(0.), epsilon_princ(i));
alpha_t += epsilon_t * epsilon_p;
}
alpha_t /= epsilon_equ * epsilon_equ;
alpha_t = std::min(alpha_t, Real(1.));
Real alpha_c = 1. - alpha_t;
alpha_t = std::pow(alpha_t, beta);
alpha_c = std::pow(alpha_c, beta);
Real damtemp;
damtemp = alpha_t * dam_t + alpha_c * dam_c;
dam = std::max(damtemp, dam);
dam = std::min(dam, Real(1.));
}
}
/* -------------------------------------------------------------------------- */
// template<UInt spatial_dimension>
// inline void
// MaterialMazars<spatial_dimension>::computeTangentModuliOnQuad(Matrix<Real> &
// tangent) {
// MaterialElastic<spatial_dimension>::computeTangentModuliOnQuad(tangent);
// tangent *= (1-dam);
// }
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
index 1460cec6f..f046b3079 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
@@ -1,122 +1,123 @@
/**
* @file material_mazars_non_local.cc
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Sep 11 2017
*
* @brief Specialization of the material class for the non-local mazars
* material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_mazars_non_local.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMazarsNonLocal<spatial_dimension>::MaterialMazarsNonLocal(
SolidMechanicsModel & model, const ID & id)
: MaterialNonLocalParent(model, id), Ehat("epsilon_equ", *this),
non_local_variable("mazars_non_local", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = true;
this->Ehat.initialize(1);
this->non_local_variable.initialize(1);
this->registerParam("average_on_damage", this->damage_in_compute_stress,
false, _pat_parsable | _pat_modifiable,
"Is D the non local variable");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::registerNonLocalVariables() {
ID local;
- if (this->damage_in_compute_stress)
+ if (this->damage_in_compute_stress) {
local = this->damage.getName();
- else
+ } else {
local = this->Ehat.getName();
+ }
this->model.getNonLocalManager().registerNonLocalVariable(
local, non_local_variable.getName(), 1);
this->model.getNonLocalManager()
.getNeighborhood(this->name)
.registerNonLocalVariable(non_local_variable.getName());
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * damage = this->damage(el_type, ghost_type).storage();
Real * epsilon_equ = this->Ehat(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
MaterialMazars<spatial_dimension>::computeStressOnQuad(grad_u, sigma, *damage,
*epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::computeNonLocalStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & non_loc_var = non_local_variable(el_type, ghost_type);
Real * damage;
Real * epsilon_equ;
if (this->damage_in_compute_stress) {
damage = non_loc_var.storage();
epsilon_equ = this->Ehat(el_type, ghost_type).storage();
} else {
damage = this->damage(el_type, ghost_type).storage();
epsilon_equ = non_loc_var.storage();
}
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeDamageAndStressOnQuad(grad_u, sigma, *damage, *epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(mazars_non_local, MaterialMazarsNonLocal);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
index 4b919d0b8..5168b3730 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
@@ -1,90 +1,90 @@
/**
* @file material_mazars_non_local.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Sep 11 2017
*
* @brief Mazars non-local description
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_non_local.hh"
#include "material_mazars.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH__
-#define __AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH__
+#ifndef AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH_
+#define AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH_
namespace akantu {
/**
* Material Mazars Non local
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialMazarsNonLocal
: public MaterialDamageNonLocal<spatial_dimension,
MaterialMazars<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MaterialNonLocalParent =
MaterialDamageNonLocal<spatial_dimension,
MaterialMazars<spatial_dimension>>;
MaterialMazarsNonLocal(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void computeNonLocalStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void registerNonLocalVariables() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the ehat per quadrature points to perform the averaging
InternalField<Real> Ehat;
InternalField<Real> non_local_variable;
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH__ */
+#endif /* AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic.cc b/src/model/solid_mechanics/materials/material_elastic.cc
index 9346c939d..af46e94b5 100644
--- a/src/model/solid_mechanics/materials/material_elastic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic.cc
@@ -1,254 +1,257 @@
/**
* @file material_elastic.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jan 29 2018
*
* @brief Specialization of the material class for the elastic material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElastic<dim>::MaterialElastic(SolidMechanicsModel & model,
const ID & id)
: Parent(model, id), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElastic<dim>::MaterialElastic(SolidMechanicsModel & model,
UInt /*a_dim*/,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id)
: Parent(model, dim, mesh, fe_engine, id), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::initialize() {
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Parent::initMaterial();
- if (dim == 1)
+ if (dim == 1) {
this->nu = 0.;
+ }
this->updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::updateInternalParameters() {
MaterialThermal<dim>::updateInternalParameters();
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - 2 * this->nu));
this->mu = this->E / (2 * (1 + this->nu));
this->kpa = this->lambda + 2. / 3. * this->mu;
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <> void MaterialElastic<2>::updateInternalParameters() {
MaterialThermal<2>::updateInternalParameters();
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - 2 * this->nu));
this->mu = this->E / (2 * (1 + this->nu));
- if (this->plane_stress)
+ if (this->plane_stress) {
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - this->nu));
+ }
this->kpa = this->lambda + 2. / 3. * this->mu;
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElastic<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator sigma_th_it =
this->sigma_th(el_type, ghost_type).begin();
if (!this->finite_deformation) {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
const Real & sigma_th = *sigma_th_it;
this->computeStressOnQuad(grad_u, sigma, sigma_th);
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
/// finite gradus
Matrix<Real> E(dim, dim);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
/// compute E
this->template gradUToE<dim>(grad_u, E);
const Real & sigma_th = *sigma_th_it;
/// compute second Piola-Kirchhoff stress tensor
this->computeStressOnQuad(E, sigma, sigma_th);
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
-void MaterialElastic<dim>::computeTangentModuli(const ElementType & el_type,
+void MaterialElastic<dim>::computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
-Real MaterialElastic<dim>::getPushWaveSpeed(const Element &) const {
+Real MaterialElastic<dim>::getPushWaveSpeed(const Element & /*unused*/) const {
return sqrt((lambda + 2 * mu) / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
-Real MaterialElastic<dim>::getShearWaveSpeed(const Element &) const {
+Real MaterialElastic<dim>::getShearWaveSpeed(const Element & /*unused*/) const {
return sqrt(mu / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElastic<dim>::computePotentialEnergy(ElementType el_type) {
AKANTU_DEBUG_IN();
// MaterialThermal<dim>::computePotentialEnergy(ElementType)
// needs to be implemented
// MaterialThermal<dim>::computePotentialEnergy(el_type);
auto epot = this->potential_energy(el_type, _not_ghost).begin();
if (!this->finite_deformation) {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
this->computePotentialEnergyOnQuad(grad_u, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
auto E = this->template gradUToE<dim>(grad_u);
this->computePotentialEnergyOnQuad(E, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElastic<dim>::computePotentialEnergyByElement(
ElementType type, UInt index, Vector<Real> & epot_on_quad_points) {
auto gradu_it = this->gradu(type).begin(dim, dim);
auto gradu_end = this->gradu(type).begin(dim, dim);
auto stress_it = this->stress(type).begin(dim, dim);
- if (this->finite_deformation)
+ if (this->finite_deformation) {
stress_it = this->piola_kirchhoff_2(type).begin(dim, dim);
+ }
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
gradu_it += index * nb_quadrature_points;
gradu_end += (index + 1) * nb_quadrature_points;
stress_it += index * nb_quadrature_points;
Real * epot_quad = epot_on_quad_points.storage();
Matrix<Real> grad_u(dim, dim);
if (this->finite_deformation) {
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
auto E = this->template gradUToE<dim>(*gradu_it);
this->computePotentialEnergyOnQuad(E, *stress_it, *epot_quad);
}
} else {
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
this->computePotentialEnergyOnQuad(*gradu_it, *stress_it, *epot_quad);
}
}
}
/* -------------------------------------------------------------------------- */
template <>
Real MaterialElastic<1>::getPushWaveSpeed(const Element & /*element*/) const {
return std::sqrt(this->E / this->rho);
}
template <>
Real MaterialElastic<1>::getShearWaveSpeed(const Element & /*element*/) const {
AKANTU_EXCEPTION("There is no shear wave speed in 1D");
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(elastic, MaterialElastic);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic.hh b/src/model/solid_mechanics/materials/material_elastic.hh
index 3ee992ff6..dcde5ccbe 100644
--- a/src/model/solid_mechanics/materials/material_elastic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic.hh
@@ -1,158 +1,158 @@
/**
* @file material_elastic.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Nov 17 2017
*
* @brief Material isotropic elastic
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_thermal.hh"
#include "plane_stress_toolbox.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ELASTIC_HH__
-#define __AKANTU_MATERIAL_ELASTIC_HH__
+#ifndef AKANTU_MATERIAL_ELASTIC_HH_
+#define AKANTU_MATERIAL_ELASTIC_HH_
namespace akantu {
/**
* Material elastic isotropic
*
* parameters in the material files :
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - Plane_Stress : if 0: plane strain, else: plane stress (default: 0)
*/
template <UInt spatial_dimension>
class MaterialElastic
: public PlaneStressToolbox<spatial_dimension,
MaterialThermal<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
using Parent =
PlaneStressToolbox<spatial_dimension, MaterialThermal<spatial_dimension>>;
public:
MaterialElastic(SolidMechanicsModel & model, const ID & id = "");
MaterialElastic(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
~MaterialElastic() override = default;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
- void computeTangentModuli(const ElementType & el_type,
+ void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type) override;
void
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) override;
/// compute the p-wave speed in the material
Real getPushWaveSpeed(const Element & element) const override;
/// compute the s-wave speed in the material
Real getShearWaveSpeed(const Element & element) const override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
- const Real sigma_th = 0) const;
+ Real sigma_th = 0) const;
/// compute the tangent stiffness matrix for an element
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent) const;
/// recompute the lame coefficient if E or nu changes
void updateInternalParameters() override;
static inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot);
bool hasStiffnessMatrixChanged() override {
return (not was_stiffness_assembled);
}
MatrixType getTangentType() override {
return _symmetric;
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get first Lame constant
AKANTU_GET_MACRO(Lambda, lambda, Real);
/// get second Lame constant
AKANTU_GET_MACRO(Mu, mu, Real);
/// get bulk modulus
AKANTU_GET_MACRO(Kappa, kpa, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// Bulk modulus
Real kpa;
/// defines if the stiffness was computed
bool was_stiffness_assembled;
};
} // namespace akantu
#include "material_elastic_inline_impl.hh"
-#endif /* __AKANTU_MATERIAL_ELASTIC_HH__ */
+#endif /* AKANTU_MATERIAL_ELASTIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_inline_impl.hh b/src/model/solid_mechanics/materials/material_elastic_inline_impl.hh
index 673544380..be93c1d7a 100644
--- a/src/model/solid_mechanics/materials/material_elastic_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_inline_impl.hh
@@ -1,119 +1,120 @@
/**
* @file material_elastic_inline_impl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Fri Dec 16 2016
*
* @brief Implementation of the inline functions of the material elastic
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_HH__
-#define __AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_HH__
+#ifndef AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_HH_
+#define AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialElastic<spatial_dimension>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma,
- const Real sigma_th) const {
+ Real sigma_th) const {
Real trace = grad_u.trace(); // trace = (\nabla u)_{kk}
// \sigma_{ij} = \lambda * (\nabla u)_{kk} * \delta_{ij} + \mu * (\nabla
// u_{ij} + \nabla u_{ji})
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
- sigma(i, j) = (i == j) * lambda * trace +
- mu * (grad_u(i, j) + grad_u(j, i)) + (i == j) * sigma_th;
+ sigma(i, j) = Math::kronecker(i, j) * lambda * trace +
+ mu * (grad_u(i, j) + grad_u(j, i)) + Math::kronecker(i, j) * sigma_th;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void MaterialElastic<1>::computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
Real sigma_th) const {
sigma(0, 0) = this->E * grad_u(0, 0) + sigma_th;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialElastic<spatial_dimension>::computeTangentModuliOnQuad(
Matrix<Real> & tangent) const {
UInt n = tangent.cols();
// Real Ep = E/((1+nu)*(1-2*nu));
Real Miiii = lambda + 2 * mu;
Real Miijj = lambda;
Real Mijij = mu;
- if (spatial_dimension == 1)
+ if (spatial_dimension == 1) {
tangent(0, 0) = this->E;
- else
+ } else {
tangent(0, 0) = Miiii;
+ }
// test of dimension should by optimized out by the compiler due to the
// template
if (spatial_dimension >= 2) {
tangent(1, 1) = Miiii;
tangent(0, 1) = Miijj;
tangent(1, 0) = Miijj;
tangent(n - 1, n - 1) = Mijij;
}
if (spatial_dimension == 3) {
tangent(2, 2) = Miiii;
tangent(0, 2) = Miijj;
tangent(1, 2) = Miijj;
tangent(2, 0) = Miijj;
tangent(2, 1) = Miijj;
tangent(3, 3) = Mijij;
tangent(4, 4) = Mijij;
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElastic<dim>::computePotentialEnergyOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & sigma, Real & epot) {
epot = .5 * sigma.doubleDot(grad_u);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
MaterialElastic<1>::computeTangentModuliOnQuad(Matrix<Real> & tangent) const {
tangent(0, 0) = E;
}
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_HH__ */
+#endif /* AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
index c35211725..f3e97931b 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
@@ -1,262 +1,264 @@
/**
* @file material_elastic_linear_anisotropic.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 25 2013
* @date last modification: Tue Feb 20 2018
*
* @brief Anisotropic elastic material
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "material_elastic_linear_anisotropic.hh"
#include "solid_mechanics_model.hh"
#include <algorithm>
#include <sstream>
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElasticLinearAnisotropic<dim>::MaterialElasticLinearAnisotropic(
SolidMechanicsModel & model, const ID & id, bool symmetric)
: Material(model, id), rot_mat(dim, dim), Cprime(dim * dim, dim * dim),
C(voigt_h::size, voigt_h::size), eigC(voigt_h::size),
symmetric(symmetric), alpha(0), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->dir_vecs.push_back(std::make_unique<Vector<Real>>(dim));
(*this->dir_vecs.back())[0] = 1.;
this->registerParam("n1", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of main material axis");
if (dim > 1) {
this->dir_vecs.push_back(std::make_unique<Vector<Real>>(dim));
(*this->dir_vecs.back())[1] = 1.;
this->registerParam("n2", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of secondary material axis");
}
if (dim > 2) {
this->dir_vecs.push_back(std::make_unique<Vector<Real>>(dim));
(*this->dir_vecs.back())[2] = 1.;
this->registerParam("n3", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of tertiary material axis");
}
for (UInt i = 0; i < voigt_h::size; ++i) {
UInt start = 0;
if (this->symmetric) {
start = i;
}
for (UInt j = start; j < voigt_h::size; ++j) {
std::stringstream param("C");
param << "C" << i + 1 << j + 1;
this->registerParam(param.str(), this->Cprime(i, j), Real(0.),
_pat_parsmod, "Coefficient " + param.str());
}
}
this->registerParam("alpha", this->alpha, _pat_parsmod,
"Proportion of viscous stress");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElasticLinearAnisotropic<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::updateInternalParameters() {
Material::updateInternalParameters();
if (this->symmetric) {
for (UInt i = 0; i < voigt_h::size; ++i) {
for (UInt j = i + 1; j < voigt_h::size; ++j) {
this->Cprime(j, i) = this->Cprime(i, j);
}
}
}
this->rotateCprime();
this->C.eig(this->eigC);
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <UInt Dim> void MaterialElasticLinearAnisotropic<Dim>::rotateCprime() {
// start by filling the empty parts fo Cprime
UInt diff = Dim * Dim - voigt_h::size;
for (UInt i = voigt_h::size; i < Dim * Dim; ++i) {
for (UInt j = 0; j < Dim * Dim; ++j) {
this->Cprime(i, j) = this->Cprime(i - diff, j);
}
}
for (UInt i = 0; i < Dim * Dim; ++i) {
for (UInt j = voigt_h::size; j < Dim * Dim; ++j) {
this->Cprime(i, j) = this->Cprime(i, j - diff);
}
}
// construction of rotator tensor
// normalise rotation matrix
for (UInt j = 0; j < Dim; ++j) {
Vector<Real> rot_vec = this->rot_mat(j);
rot_vec = *this->dir_vecs[j];
rot_vec.normalize();
}
// make sure the vectors form a right-handed base
Vector<Real> test_axis(3);
- Vector<Real> v1(3), v2(3), v3(3, 0.);
+ Vector<Real> v1(3);
+ Vector<Real> v2(3);
+ Vector<Real> v3(3, 0.);
if (Dim == 2) {
for (UInt i = 0; i < Dim; ++i) {
v1[i] = this->rot_mat(0, i);
v2[i] = this->rot_mat(1, i);
}
v3.crossProduct(v1, v2);
if (v3.norm() < 8 * std::numeric_limits<Real>::epsilon()) {
AKANTU_ERROR("The axis vectors parallel.");
}
v3.normalize();
} else if (Dim == 3) {
v1 = this->rot_mat(0);
v2 = this->rot_mat(1);
v3 = this->rot_mat(2);
}
test_axis.crossProduct(v1, v2);
test_axis -= v3;
if (test_axis.norm() > 8 * std::numeric_limits<Real>::epsilon()) {
AKANTU_ERROR("The axis vectors do not form a right-handed coordinate "
<< "system. I. e., ||n1 x n2 - n3|| should be zero, but "
<< "it is " << test_axis.norm() << ".");
}
// create the rotator and the reverse rotator
Matrix<Real> rotator(Dim * Dim, Dim * Dim);
Matrix<Real> revrotor(Dim * Dim, Dim * Dim);
for (UInt i = 0; i < Dim; ++i) {
for (UInt j = 0; j < Dim; ++j) {
for (UInt k = 0; k < Dim; ++k) {
for (UInt l = 0; l < Dim; ++l) {
UInt I = voigt_h::mat[i][j];
UInt J = voigt_h::mat[k][l];
rotator(I, J) = this->rot_mat(k, i) * this->rot_mat(l, j);
revrotor(I, J) = this->rot_mat(i, k) * this->rot_mat(j, l);
}
}
}
}
// create the full rotated matrix
Matrix<Real> Cfull(Dim * Dim, Dim * Dim);
Cfull = rotator * Cprime * revrotor;
for (UInt i = 0; i < voigt_h::size; ++i) {
for (UInt j = 0; j < voigt_h::size; ++j) {
this->C(i, j) = Cfull(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computeStress(
ElementType el_type, GhostType ghost_type) {
// Wikipedia convention:
// 2*eps_ij (i!=j) = voigt_eps_I
// http://en.wikipedia.org/wiki/Voigt_notation
AKANTU_DEBUG_IN();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computeTangentModuli(
- const ElementType & el_type, Array<Real> & tangent_matrix,
+ ElementType el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computePotentialEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(!this->finite_deformation,
"finite deformation not possible in material anisotropic "
"(TO BE IMPLEMENTED)");
Array<Real>::scalar_iterator epot =
this->potential_energy(el_type, _not_ghost).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
computePotentialEnergyOnQuad(grad_u, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialElasticLinearAnisotropic<dim>::getCelerity(
__attribute__((unused)) const Element & element) const {
return std::sqrt(this->eigC(0) / rho);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(elastic_anisotropic, MaterialElasticLinearAnisotropic);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
index fc977fb04..5663fdd8d 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
@@ -1,142 +1,142 @@
/**
* @file material_elastic_linear_anisotropic.hh
*
* @author Till Junge <till.junge@epfl.ch>
* @author Enrico Milanese <enrico.milanese@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 16 2018
*
* @brief Orthotropic elastic material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH__
-#define __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH__
+#ifndef AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH_
+#define AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH_
namespace akantu {
/**
* General linear anisotropic elastic material
* The only constraint on the elastic tensor is that it can be represented
* as a symmetric 6x6 matrix (3D) or 3x3 (2D).
*
* parameters in the material files :
* - rho : density (default: 0)
* - C_ij : entry on the stiffness
*/
template <UInt Dim> class MaterialElasticLinearAnisotropic : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialElasticLinearAnisotropic(SolidMechanicsModel & model,
const ID & id = "", bool symmetric = true);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
- void computeTangentModuli(const ElementType & el_type,
+ void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type) override;
void updateInternalParameters() override;
bool hasStiffnessMatrixChanged() override {
return (not was_stiffness_assembled);
}
MatrixType getTangentType() override {
return _symmetric;
}
protected:
// compute C from Cprime
void rotateCprime();
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma) const;
/// tangent matrix for a given quadrature point
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent) const;
inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// compute max wave celerity
Real getCelerity(const Element & element) const override;
AKANTU_GET_MACRO(VoigtStiffness, C, Matrix<Real>);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
using voigt_h = VoigtHelper<Dim>;
/// direction matrix and vectors
std::vector<std::unique_ptr<Vector<Real>>> dir_vecs;
Matrix<Real> rot_mat;
/// Elastic stiffness tensor in material frame and full vectorised notation
Matrix<Real> Cprime;
/// Elastic stiffness tensor in voigt notation
Matrix<Real> C;
/// eigenvalues of stiffness tensor
Vector<Real> eigC;
bool symmetric;
/// viscous proportion
Real alpha;
/// defines if the stiffness was computed
bool was_stiffness_assembled;
};
} // namespace akantu
#include "material_elastic_linear_anisotropic_inline_impl.hh"
-#endif /* __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH__ */
+#endif /* AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.hh b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.hh
index dd2f362d1..3f0204d5f 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.hh
@@ -1,72 +1,72 @@
/**
* @file material_elastic_linear_anisotropic_inline_impl.hh
*
* @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 16 2018
* @date last modification: Fri Feb 16 2018
*
* @brief Implementation of the inline functions of the material elastic linear
* anisotropic
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic_linear_anisotropic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_HH__
-#define __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_HH__
+#ifndef AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_HH_
+#define AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElasticLinearAnisotropic<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma) const {
auto voigt_strain = strainToVoigt<dim>(gradUToEpsilon<dim>(grad_u));
auto voigt_stress = this->C * voigt_strain;
voigtToStress<dim>(voigt_stress, sigma);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElasticLinearAnisotropic<dim>::computeTangentModuliOnQuad(
Matrix<Real> & tangent) const {
tangent.copy(this->C);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElasticLinearAnisotropic<dim>::computePotentialEnergyOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & sigma, Real & epot) {
AKANTU_DEBUG_ASSERT(this->symmetric,
"The elastic constants matrix is not symmetric,"
"energy is not path independent.");
epot = .5 * sigma.doubleDot(grad_u);
}
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_HH__ */
+#endif /* AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc b/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
index a1490e46e..12c24f420 100644
--- a/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
@@ -1,171 +1,175 @@
/**
* @file material_elastic_orthotropic.cc
*
* @author Till Junge <till.junge@epfl.ch>
* @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Orthotropic elastic material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "material_elastic_orthotropic.hh"
#include "solid_mechanics_model.hh"
#include <algorithm>
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt Dim>
MaterialElasticOrthotropic<Dim>::MaterialElasticOrthotropic(
SolidMechanicsModel & model, const ID & id)
: MaterialElasticLinearAnisotropic<Dim>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("E1", E1, Real(0.), _pat_parsmod, "Young's modulus (n1)");
this->registerParam("E2", E2, Real(0.), _pat_parsmod, "Young's modulus (n2)");
this->registerParam("nu12", nu12, Real(0.), _pat_parsmod,
"Poisson's ratio (12)");
this->registerParam("G12", G12, Real(0.), _pat_parsmod, "Shear modulus (12)");
if (Dim > 2) {
this->registerParam("E3", E3, Real(0.), _pat_parsmod,
"Young's modulus (n3)");
this->registerParam("nu13", nu13, Real(0.), _pat_parsmod,
"Poisson's ratio (13)");
this->registerParam("nu23", nu23, Real(0.), _pat_parsmod,
"Poisson's ratio (23)");
this->registerParam("G13", G13, Real(0.), _pat_parsmod,
"Shear modulus (13)");
this->registerParam("G23", G23, Real(0.), _pat_parsmod,
"Shear modulus (23)");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt Dim> void MaterialElasticOrthotropic<Dim>::initMaterial() {
AKANTU_DEBUG_IN();
- Material::initMaterial();
+ MaterialElasticLinearAnisotropic<Dim>::initMaterial();
AKANTU_DEBUG_ASSERT(not this->finite_deformation,
"finite deformation not possible in material orthotropic "
"(TO BE IMPLEMENTED)");
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt Dim>
void MaterialElasticOrthotropic<Dim>::updateInternalParameters() {
- this->C.clear();
- this->Cprime.clear();
+ this->C.zero();
+ this->Cprime.zero();
/* 1) construction of temporary material frame stiffness tensor------------ */
// http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real nu31 = nu13 * E3 / E1;
Real nu32 = nu23 * E3 / E2;
// Full (i.e. dim^2 by dim^2) stiffness tensor in material frame
if (Dim == 1) {
AKANTU_ERROR("Dimensions 1 not implemented: makes no sense to have "
"orthotropy for 1D");
}
Real Gamma;
- if (Dim == 3)
+ if (Dim == 3) {
Gamma = 1 / (1 - nu12 * nu21 - nu23 * nu32 - nu31 * nu13 -
2 * nu21 * nu32 * nu13);
+ }
- if (Dim == 2)
+ if (Dim == 2) {
Gamma = 1 / (1 - nu12 * nu21);
+ }
// Lamé's first parameters
this->Cprime(0, 0) = E1 * (1 - nu23 * nu32) * Gamma;
this->Cprime(1, 1) = E2 * (1 - nu13 * nu31) * Gamma;
- if (Dim == 3)
+ if (Dim == 3) {
this->Cprime(2, 2) = E3 * (1 - nu12 * nu21) * Gamma;
+ }
// normalised poisson's ratio's
this->Cprime(1, 0) = this->Cprime(0, 1) = E1 * (nu21 + nu31 * nu23) * Gamma;
if (Dim == 3) {
this->Cprime(2, 0) = this->Cprime(0, 2) = E1 * (nu31 + nu21 * nu32) * Gamma;
this->Cprime(2, 1) = this->Cprime(1, 2) = E2 * (nu32 + nu12 * nu31) * Gamma;
}
// Lamé's second parameters (shear moduli)
if (Dim == 3) {
this->Cprime(3, 3) = G23;
this->Cprime(4, 4) = G13;
this->Cprime(5, 5) = G12;
- } else
+ } else {
this->Cprime(2, 2) = G12;
+ }
/* 1) rotation of C into the global frame */
this->rotateCprime();
this->C.eig(this->eigC);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElasticOrthotropic<spatial_dimension>::
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) {
Array<Real>::matrix_iterator gradu_it =
this->gradu(type).begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator gradu_end =
this->gradu(type).begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator stress_it =
this->stress(type).begin(spatial_dimension, spatial_dimension);
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
gradu_it += index * nb_quadrature_points;
gradu_end += (index + 1) * nb_quadrature_points;
stress_it += index * nb_quadrature_points;
Real * epot_quad = epot_on_quad_points.storage();
Matrix<Real> grad_u(spatial_dimension, spatial_dimension);
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
grad_u.copy(*gradu_it);
this->computePotentialEnergyOnQuad(grad_u, *stress_it, *epot_quad);
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(elastic_orthotropic, MaterialElasticOrthotropic);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh b/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
index de1019b6f..c0a1fe800 100644
--- a/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
@@ -1,135 +1,135 @@
/**
* @file material_elastic_orthotropic.hh
*
* @author Till Junge <till.junge@epfl.ch>
* @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Feb 16 2018
*
* @brief Orthotropic elastic material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic_linear_anisotropic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH__
-#define __AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH__
+#ifndef AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH_
+#define AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH_
namespace akantu {
/**
* Orthotropic elastic material
*
* parameters in the material files :
* - n1 : direction of x-axis in material base, normalisation not necessary
* (default: {1, 0, 0})
* - n2 : direction of y-axis in material base, normalisation not necessary
* (default: {0, 1, 0})
* - n3 : direction of z-axis in material base, normalisation not necessary
* (default: {0, 0, 1})
* - rho : density (default: 0)
* - E1 : Young's modulus along n1 (default: 0)
* - E2 : Young's modulus along n2 (default: 0)
* - E3 : Young's modulus along n3 (default: 0)
* - nu12 : Poisson's ratio along 12 (default: 0)
* - nu13 : Poisson's ratio along 13 (default: 0)
* - nu23 : Poisson's ratio along 23 (default: 0)
* - G12 : Shear modulus along 12 (default: 0)
* - G13 : Shear modulus along 13 (default: 0)
* - G23 : Shear modulus along 23 (default: 0)
*/
template <UInt Dim>
class MaterialElasticOrthotropic
: public MaterialElasticLinearAnisotropic<Dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialElasticOrthotropic(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
void updateInternalParameters() override;
void
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(E1, E1, Real);
AKANTU_GET_MACRO(E2, E2, Real);
AKANTU_GET_MACRO(E3, E3, Real);
AKANTU_GET_MACRO(Nu12, nu12, Real);
AKANTU_GET_MACRO(Nu13, nu13, Real);
AKANTU_GET_MACRO(Nu23, nu23, Real);
AKANTU_GET_MACRO(G12, G12, Real);
AKANTU_GET_MACRO(G13, G13, Real);
AKANTU_GET_MACRO(G23, G23, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the n1 young modulus
Real E1{0.};
/// the n2 young modulus
Real E2{0.};
/// the n3 young modulus
Real E3{0.};
/// 12 Poisson coefficient
Real nu12{0.};
/// 13 Poisson coefficient
Real nu13{0.};
/// 23 Poisson coefficient
Real nu23{0.};
/// 12 shear modulus
Real G12{0.};
/// 13 shear modulus
Real G13{0.};
/// 23 shear modulus
Real G23{0.};
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH__ */
+#endif /* AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
index 88ca54496..ae493cc19 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
@@ -1,208 +1,208 @@
/**
* @file material_reinforcement.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Fri Feb 09 2018
*
* @brief Reinforcement material
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_REINFORCEMENT_HH__
-#define __AKANTU_MATERIAL_REINFORCEMENT_HH__
+#ifndef AKANTU_MATERIAL_REINFORCEMENT_HH_
+#define AKANTU_MATERIAL_REINFORCEMENT_HH_
#include "aka_common.hh"
#include "embedded_interface_model.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Material used to represent embedded reinforcements
*
* This class is used for computing the reinforcement stiffness matrix
* along with the reinforcement residual. Room is made for constitutive law,
* but actual use of contitutive laws is made in MaterialReinforcementTemplate.
*
* Be careful with the dimensions in this class :
* - this->spatial_dimension is always 1
* - the template parameter dim is the dimension of the problem
*/
template <class Mat, UInt dim> class MaterialReinforcement : public Mat {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/// Constructor
MaterialReinforcement(EmbeddedInterfaceModel & model, const ID & id = "");
/// Destructor
~MaterialReinforcement() override;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Init the material
void initMaterial() override;
/// Init the filters for background elements
void initFilters();
/// Init the background shape derivatives
void initBackgroundShapeDerivatives();
/// Init the cosine matrices
void initDirectingCosines();
/// Assemble stiffness matrix
void assembleStiffnessMatrix(GhostType ghost_type) override;
/// Compute all the stresses !
void computeAllStresses(GhostType ghost_type) override;
/// Compute energy
Real getEnergy(const std::string & id) override;
/// Assemble the residual of one type of element (typically _segment_2)
void assembleInternalForces(GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Protected methods */
/* ------------------------------------------------------------------------ */
protected:
/// Allocate the background shape derivatives
void allocBackgroundShapeDerivatives();
/// Compute the directing cosines matrix for one element type
- void computeDirectingCosines(const ElementType & type, GhostType ghost_type);
+ void computeDirectingCosines(ElementType type, GhostType ghost_type);
/// Compute the directing cosines matrix on quadrature points.
inline void computeDirectingCosinesOnQuad(const Matrix<Real> & nodes,
Matrix<Real> & cosines);
/// Add the prestress to the computed stress
- void addPrestress(const ElementType & type, GhostType ghost_type);
+ void addPrestress(ElementType type, GhostType ghost_type);
/// Compute displacement gradient in reinforcement
- void computeGradU(const ElementType & interface_type, GhostType ghost_type);
+ void computeGradU(ElementType interface_type, GhostType ghost_type);
/// Assemble the stiffness matrix for an element type (typically _segment_2)
- void assembleStiffnessMatrix(const ElementType & type, GhostType ghost_type);
+ void assembleStiffnessMatrix(ElementType type, GhostType ghost_type);
/// Assemble the stiffness matrix for background & interface types
- void assembleStiffnessMatrixInterface(const ElementType & interface_type,
- const ElementType & background_type,
+ void assembleStiffnessMatrixInterface(ElementType interface_type,
+ ElementType background_type,
GhostType ghost_type);
/// Compute the background shape derivatives for a type
- void computeBackgroundShapeDerivatives(const ElementType & type,
+ void computeBackgroundShapeDerivatives(ElementType type,
GhostType ghost_type);
/// Compute the background shape derivatives for a type pair
- void computeBackgroundShapeDerivatives(const ElementType & interface_type,
- const ElementType & bg_type,
+ void computeBackgroundShapeDerivatives(ElementType interface_type,
+ ElementType bg_type,
GhostType ghost_type,
const Array<UInt> & filter);
/// Filter elements crossed by interface of a type
void filterInterfaceBackgroundElements(Array<UInt> & foreground,
Array<UInt> & background,
- const ElementType & type,
- const ElementType & interface_type,
+ ElementType type,
+ ElementType interface_type,
GhostType ghost_type);
/// Assemble the residual of one type of element (typically _segment_2)
- void assembleInternalForces(const ElementType & type, GhostType ghost_type);
+ void assembleInternalForces(ElementType type, GhostType ghost_type);
/// Assemble the residual for a pair of elements
- void assembleInternalForcesInterface(const ElementType & interface_type,
- const ElementType & background_type,
+ void assembleInternalForcesInterface(ElementType interface_type,
+ ElementType background_type,
GhostType ghost_type);
// TODO figure out why voigt size is 4 in 2D
inline void stressTensorToVoigtVector(const Matrix<Real> & tensor,
Vector<Real> & vector);
inline void strainTensorToVoigtVector(const Matrix<Real> & tensor,
Vector<Real> & vector);
/// Get background filter
- Array<UInt> & getBackgroundFilter(const ElementType & fg_type,
- const ElementType & bg_type,
+ Array<UInt> & getBackgroundFilter(ElementType fg_type,
+ ElementType bg_type,
GhostType ghost_type) {
return (*background_filter(fg_type, ghost_type))(bg_type, ghost_type);
}
/// Get foreground filter
- Array<UInt> & getForegroundFilter(const ElementType & fg_type,
- const ElementType & bg_type,
+ Array<UInt> & getForegroundFilter(ElementType fg_type,
+ ElementType bg_type,
GhostType ghost_type) {
return (*foreground_filter(fg_type, ghost_type))(bg_type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Embedded model
EmbeddedInterfaceModel & emodel;
/// Gradu of concrete on reinforcement
InternalField<Real> gradu_embedded;
/// C matrix on quad
InternalField<Real> directing_cosines;
/// Prestress on quad
InternalField<Real> pre_stress;
/// Cross-sectional area
Real area;
template <typename T>
using CrossMap = ElementTypeMap<std::unique_ptr<ElementTypeMapArray<T>>>;
/// Background mesh shape derivatives
CrossMap<Real> shape_derivatives;
/// Foreground mesh filter (contains segment ids)
CrossMap<UInt> foreground_filter;
/// Background element filter (contains bg ids)
CrossMap<UInt> background_filter;
};
} // namespace akantu
#include "material_reinforcement_tmpl.hh"
-#endif // __AKANTU_MATERIAL_REINFORCEMENT_HH__
+#endif // AKANTU_MATERIAL_REINFORCEMENT_HH_
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
index 692f7372a..d3dcd411b 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
@@ -1,779 +1,780 @@
/**
* @file material_reinforcement_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Mar 25 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Reinforcement material
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_reinforcement.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
MaterialReinforcement<Mat, dim>::MaterialReinforcement(
EmbeddedInterfaceModel & model, const ID & id)
: Mat(model, 1, model.getInterfaceMesh(),
model.getFEEngine("EmbeddedInterfaceFEEngine"), id),
emodel(model),
gradu_embedded("gradu_embedded", *this, 1,
model.getFEEngine("EmbeddedInterfaceFEEngine"),
this->element_filter),
directing_cosines("directing_cosines", *this, 1,
model.getFEEngine("EmbeddedInterfaceFEEngine"),
this->element_filter),
pre_stress("pre_stress", *this, 1,
model.getFEEngine("EmbeddedInterfaceFEEngine"),
this->element_filter),
- area(1.0), shape_derivatives() {
+ area(1.0) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initialize() {
AKANTU_DEBUG_IN();
this->registerParam("area", area, _pat_parsable | _pat_modifiable,
"Reinforcement cross-sectional area");
this->registerParam("pre_stress", pre_stress, _pat_parsable | _pat_modifiable,
"Uniform pre-stress");
// this->unregisterInternal(this->stress);
// Fool the AvgHomogenizingFunctor
// stress.initialize(dim * dim);
// Reallocate the element filter
this->element_filter.initialize(this->emodel.getInterfaceMesh(),
_spatial_dimension = 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
MaterialReinforcement<Mat, dim>::~MaterialReinforcement() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initMaterial() {
Mat::initMaterial();
gradu_embedded.initialize(dim * dim);
pre_stress.initialize(1);
/// We initialise the stuff that is not going to change during the simulation
this->initFilters();
this->allocBackgroundShapeDerivatives();
this->initBackgroundShapeDerivatives();
this->initDirectingCosines();
}
/* -------------------------------------------------------------------------- */
/// Initialize the filter for background elements
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initFilters() {
for (auto gt : ghost_types) {
for (auto && type : emodel.getInterfaceMesh().elementTypes(1, gt)) {
std::string shaped_id = "filter";
- if (gt == _ghost)
+ if (gt == _ghost) {
shaped_id += ":ghost";
-
+ }
auto & background =
background_filter(std::make_unique<ElementTypeMapArray<UInt>>(
"bg_" + shaped_id, this->name),
type, gt);
auto & foreground = foreground_filter(
std::make_unique<ElementTypeMapArray<UInt>>(shaped_id, this->name),
type, gt);
foreground->initialize(emodel.getMesh(), _nb_component = 1,
_ghost_type = gt);
background->initialize(emodel.getMesh(), _nb_component = 1,
_ghost_type = gt);
// Computing filters
for (auto && bg_type : background->elementTypes(dim, gt)) {
filterInterfaceBackgroundElements(
(*foreground)(bg_type), (*background)(bg_type), bg_type, type, gt);
}
}
}
}
/* -------------------------------------------------------------------------- */
/// Construct a filter for a (interface_type, background_type) pair
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::filterInterfaceBackgroundElements(
- Array<UInt> & foreground, Array<UInt> & background,
- const ElementType & type, const ElementType & interface_type,
- GhostType ghost_type) {
+ Array<UInt> & foreground, Array<UInt> & background, ElementType type,
+ ElementType interface_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
foreground.resize(0);
background.resize(0);
Array<Element> & elements =
emodel.getInterfaceAssociatedElements(interface_type, ghost_type);
Array<UInt> & elem_filter = this->element_filter(interface_type, ghost_type);
for (auto & elem_id : elem_filter) {
Element & elem = elements(elem_id);
if (elem.type == type) {
background.push_back(elem.element);
foreground.push_back(elem_id);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
namespace detail {
class BackgroundShapeDInitializer : public ElementTypeMapArrayInitializer {
public:
BackgroundShapeDInitializer(UInt spatial_dimension, FEEngine & engine,
- const ElementType & foreground_type,
+ ElementType foreground_type,
const ElementTypeMapArray<UInt> & filter,
- const GhostType & ghost_type)
+ GhostType ghost_type)
: ElementTypeMapArrayInitializer(
- [](const ElementType & bgtype, const GhostType &) {
+ [](ElementType bgtype, GhostType /*unused*/) {
return ShapeFunctions::getShapeDerivativesSize(bgtype);
},
spatial_dimension, ghost_type, _ek_regular) {
auto nb_quad = engine.getNbIntegrationPoints(foreground_type);
// Counting how many background elements are affected by elements of
// interface_type
for (auto type : filter.elementTypes(this->spatial_dimension)) {
// Inserting size
array_size_per_bg_type(filter(type).size() * nb_quad, type,
this->ghost_type);
}
}
auto elementTypes() const -> decltype(auto) {
return array_size_per_bg_type.elementTypes();
}
- UInt size(const ElementType & bgtype) const {
+ UInt size(ElementType bgtype) const {
return array_size_per_bg_type(bgtype, this->ghost_type);
}
protected:
ElementTypeMap<UInt> array_size_per_bg_type;
};
} // namespace detail
/**
* Background shape derivatives need to be stored per background element
* types but also per embedded element type, which is why they are stored
* in an ElementTypeMap<ElementTypeMapArray<Real> *>. The outer ElementTypeMap
* refers to the embedded types, and the inner refers to the background types.
*/
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::allocBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
for (auto gt : ghost_types) {
for (auto && type : emodel.getInterfaceMesh().elementTypes(1, gt)) {
std::string shaped_id = "embedded_shape_derivatives";
- if (gt == _ghost)
+ if (gt == _ghost) {
shaped_id += ":ghost";
+ }
auto & shaped_etma = shape_derivatives(
std::make_unique<ElementTypeMapArray<Real>>(shaped_id, this->name),
type, gt);
shaped_etma->initialize(
detail::BackgroundShapeDInitializer(
emodel.getSpatialDimension(),
emodel.getFEEngine("EmbeddedInterfaceFEEngine"), type,
*background_filter(type, gt), gt),
0, true);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
for (auto interface_type :
this->element_filter.elementTypes(this->spatial_dimension)) {
for (auto type : background_filter(interface_type)->elementTypes(dim)) {
computeBackgroundShapeDerivatives(interface_type, type, _not_ghost,
this->element_filter(interface_type));
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeBackgroundShapeDerivatives(
- const ElementType & interface_type, const ElementType & bg_type,
- GhostType ghost_type, const Array<UInt> & filter) {
+ ElementType interface_type, ElementType bg_type, GhostType ghost_type,
+ const Array<UInt> & filter) {
auto & interface_engine = emodel.getFEEngine("EmbeddedInterfaceFEEngine");
auto & engine = emodel.getFEEngine();
auto & interface_mesh = emodel.getInterfaceMesh();
const auto nb_nodes_elem_bg = Mesh::getNbNodesPerElement(bg_type);
// const auto nb_strss = VoigtHelper<dim>::size;
const auto nb_quads_per_elem =
interface_engine.getNbIntegrationPoints(interface_type);
Array<Real> quad_pos(0, dim, "interface_quad_pos");
interface_engine.interpolateOnIntegrationPoints(interface_mesh.getNodes(),
quad_pos, dim, interface_type,
ghost_type, filter);
auto & background_shapesd =
(*shape_derivatives(interface_type, ghost_type))(bg_type, ghost_type);
auto & background_elements =
(*background_filter(interface_type, ghost_type))(bg_type, ghost_type);
auto & foreground_elements =
(*foreground_filter(interface_type, ghost_type))(bg_type, ghost_type);
auto shapesd_begin =
background_shapesd.begin(dim, nb_nodes_elem_bg, nb_quads_per_elem);
auto quad_begin = quad_pos.begin(dim, nb_quads_per_elem);
for (auto && tuple : zip(background_elements, foreground_elements)) {
- UInt bg = std::get<0>(tuple), fg = std::get<1>(tuple);
+ auto bg = std::get<0>(tuple);
+ auto fg = std::get<1>(tuple);
for (UInt i = 0; i < nb_quads_per_elem; ++i) {
Matrix<Real> shapesd = Tensor3<Real>(shapesd_begin[fg])(i);
Vector<Real> quads = Matrix<Real>(quad_begin[fg])(i);
engine.computeShapeDerivatives(quads, bg, bg_type, shapesd, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initDirectingCosines() {
AKANTU_DEBUG_IN();
Mesh & mesh = emodel.getInterfaceMesh();
const UInt voigt_size = VoigtHelper<dim>::size;
directing_cosines.initialize(voigt_size);
for (auto && type : mesh.elementTypes(1, _not_ghost)) {
computeDirectingCosines(type, _not_ghost);
// computeDirectingCosines(*type_it, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleStiffnessMatrix(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
for (auto && type : interface_mesh.elementTypes(1, _not_ghost)) {
assembleStiffnessMatrix(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleInternalForces(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
for (auto && type : interface_mesh.elementTypes(1, _not_ghost)) {
this->assembleInternalForces(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeAllStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
for (auto && type : interface_mesh.elementTypes(_ghost_type = ghost_type)) {
computeGradU(type, ghost_type);
this->computeStress(type, ghost_type);
addPrestress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
-void MaterialReinforcement<Mat, dim>::addPrestress(const ElementType & type,
+void MaterialReinforcement<Mat, dim>::addPrestress(ElementType type,
GhostType ghost_type) {
auto & stress = this->stress(type, ghost_type);
auto & sigma_p = this->pre_stress(type, ghost_type);
for (auto && tuple : zip(stress, sigma_p)) {
std::get<0>(tuple) += std::get<1>(tuple);
}
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleInternalForces(
- const ElementType & type, GhostType ghost_type) {
+ ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = emodel.getMesh();
for (auto && mesh_type : mesh.elementTypes(dim, ghost_type)) {
assembleInternalForcesInterface(type, mesh_type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Computes and assemble the residual. Residual in reinforcement is computed as:
*
* \f[
* \vec{r} = A_s \int_S{\mathbf{B}^T\mathbf{C}^T \vec{\sigma_s}\,\mathrm{d}s}
* \f]
*/
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleInternalForcesInterface(
- const ElementType & interface_type, const ElementType & background_type,
+ ElementType interface_type, ElementType background_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt voigt_size = VoigtHelper<dim>::size;
FEEngine & interface_engine = emodel.getFEEngine("EmbeddedInterfaceFEEngine");
Array<UInt> & elem_filter = this->element_filter(interface_type, ghost_type);
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points =
interface_engine.getNbIntegrationPoints(interface_type, ghost_type);
UInt nb_element = elem_filter.size();
UInt back_dof = dim * nodes_per_background_e;
Array<Real> & shapesd = (*shape_derivatives(interface_type, ghost_type))(
background_type, ghost_type);
Array<Real> integrant(nb_quadrature_points * nb_element, back_dof,
"integrant");
auto integrant_it = integrant.begin(back_dof);
auto integrant_end = integrant.end(back_dof);
Array<Real>::matrix_iterator B_it =
shapesd.begin(dim, nodes_per_background_e);
auto C_it = directing_cosines(interface_type, ghost_type).begin(voigt_size);
auto sigma_it = this->stress(interface_type, ghost_type).begin();
Matrix<Real> Bvoigt(voigt_size, back_dof);
for (; integrant_it != integrant_end;
++integrant_it, ++B_it, ++C_it, ++sigma_it) {
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(*B_it, Bvoigt,
nodes_per_background_e);
Vector<Real> & C = *C_it;
Vector<Real> & BtCt_sigma = *integrant_it;
BtCt_sigma.mul<true>(Bvoigt, C);
BtCt_sigma *= *sigma_it * area;
}
Array<Real> residual_interface(nb_element, back_dof, "residual_interface");
interface_engine.integrate(integrant, residual_interface, back_dof,
interface_type, ghost_type, elem_filter);
integrant.resize(0);
Array<UInt> background_filter(nb_element, 1, "background_filter");
auto & filter =
getBackgroundFilter(interface_type, background_type, ghost_type);
emodel.getDOFManager().assembleElementalArrayLocalArray(
residual_interface, emodel.getInternalForce(), background_type,
ghost_type, -1., filter);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeDirectingCosines(
- const ElementType & type, GhostType ghost_type) {
+ ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const UInt steel_dof = dim * nb_nodes_per_element;
const UInt voigt_size = VoigtHelper<dim>::size;
const UInt nb_quad_points = emodel.getFEEngine("EmbeddedInterfaceFEEngine")
.getNbIntegrationPoints(type, ghost_type);
Array<Real> node_coordinates(this->element_filter(type, ghost_type).size(),
steel_dof);
this->emodel.getFEEngine().template extractNodalToElementField<Real>(
interface_mesh, interface_mesh.getNodes(), node_coordinates, type,
ghost_type, this->element_filter(type, ghost_type));
Array<Real>::matrix_iterator directing_cosines_it =
directing_cosines(type, ghost_type).begin(1, voigt_size);
Array<Real>::matrix_iterator node_coordinates_it =
node_coordinates.begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator node_coordinates_end =
node_coordinates.end(dim, nb_nodes_per_element);
for (; node_coordinates_it != node_coordinates_end; ++node_coordinates_it) {
for (UInt i = 0; i < nb_quad_points; i++, ++directing_cosines_it) {
Matrix<Real> & nodes = *node_coordinates_it;
Matrix<Real> & cosines = *directing_cosines_it;
computeDirectingCosinesOnQuad(nodes, cosines);
}
}
// Mauro: the directing_cosines internal is defined on the quadrature points
// of each element
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleStiffnessMatrix(
- const ElementType & type, GhostType ghost_type) {
+ ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = emodel.getMesh();
for (auto && mesh_type : mesh.elementTypes(dim, ghost_type)) {
assembleStiffnessMatrixInterface(type, mesh_type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Computes the reinforcement stiffness matrix (Gomes & Awruch, 2001)
* \f[
* \mathbf{K}_e = \sum_{i=1}^R{A_i\int_{S_i}{\mathbf{B}^T
* \mathbf{C}_i^T \mathbf{D}_{s, i} \mathbf{C}_i \mathbf{B}\,\mathrm{d}s}}
* \f]
*/
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleStiffnessMatrixInterface(
- const ElementType & interface_type, const ElementType & background_type,
+ ElementType interface_type, ElementType background_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt voigt_size = VoigtHelper<dim>::size;
FEEngine & interface_engine = emodel.getFEEngine("EmbeddedInterfaceFEEngine");
Array<UInt> & elem_filter = this->element_filter(interface_type, ghost_type);
Array<Real> & grad_u = gradu_embedded(interface_type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points =
interface_engine.getNbIntegrationPoints(interface_type, ghost_type);
UInt back_dof = dim * nodes_per_background_e;
UInt integrant_size = back_dof;
grad_u.resize(nb_quadrature_points * nb_element);
Array<Real> tangent_moduli(nb_element * nb_quadrature_points, 1,
"interface_tangent_moduli");
this->computeTangentModuli(interface_type, tangent_moduli, ghost_type);
Array<Real> & shapesd = (*shape_derivatives(interface_type, ghost_type))(
background_type, ghost_type);
Array<Real> integrant(nb_element * nb_quadrature_points,
integrant_size * integrant_size, "B^t*C^t*D*C*B");
/// Temporary matrices for integrant product
Matrix<Real> Bvoigt(voigt_size, back_dof);
Matrix<Real> DCB(1, back_dof);
Matrix<Real> CtDCB(voigt_size, back_dof);
Array<Real>::scalar_iterator D_it = tangent_moduli.begin();
Array<Real>::scalar_iterator D_end = tangent_moduli.end();
Array<Real>::matrix_iterator C_it =
directing_cosines(interface_type, ghost_type).begin(1, voigt_size);
Array<Real>::matrix_iterator B_it =
shapesd.begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator integrant_it =
integrant.begin(integrant_size, integrant_size);
for (; D_it != D_end; ++D_it, ++C_it, ++B_it, ++integrant_it) {
Real & D = *D_it;
Matrix<Real> & C = *C_it;
Matrix<Real> & B = *B_it;
Matrix<Real> & BtCtDCB = *integrant_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(B, Bvoigt,
nodes_per_background_e);
DCB.mul<false, false>(C, Bvoigt);
DCB *= D * area;
CtDCB.mul<true, false>(C, DCB);
BtCtDCB.mul<true, false>(Bvoigt, CtDCB);
}
tangent_moduli.resize(0);
Array<Real> K_interface(nb_element, integrant_size * integrant_size,
"K_interface");
interface_engine.integrate(integrant, K_interface,
integrant_size * integrant_size, interface_type,
ghost_type, elem_filter);
integrant.resize(0);
// Mauro: Here K_interface contains the local stiffness matrices,
// directing_cosines contains the information about the orientation
// of the reinforcements, any rotation of the local stiffness matrix
// can be done here
auto & filter =
getBackgroundFilter(interface_type, background_type, ghost_type);
emodel.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", K_interface, background_type, ghost_type, _symmetric,
filter);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
Real MaterialReinforcement<Mat, dim>::getEnergy(const std::string & id) {
AKANTU_DEBUG_IN();
if (id == "potential") {
Real epot = 0.;
this->computePotentialEnergyByElements();
for (auto && type :
this->element_filter.elementTypes(this->spatial_dimension)) {
FEEngine & interface_engine =
emodel.getFEEngine("EmbeddedInterfaceFEEngine");
epot += interface_engine.integrate(
this->potential_energy(type, _not_ghost), type, _not_ghost,
this->element_filter(type, _not_ghost));
epot *= area;
}
return epot;
}
AKANTU_DEBUG_OUT();
return 0;
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
-void MaterialReinforcement<Mat, dim>::computeGradU(
- const ElementType & interface_type, GhostType ghost_type) {
+void MaterialReinforcement<Mat, dim>::computeGradU(ElementType interface_type,
+ GhostType ghost_type) {
// Looping over background types
for (auto && bg_type :
background_filter(interface_type, ghost_type)->elementTypes(dim)) {
const UInt nodes_per_background_e = Mesh::getNbNodesPerElement(bg_type);
const UInt voigt_size = VoigtHelper<dim>::size;
auto & bg_shapesd =
(*shape_derivatives(interface_type, ghost_type))(bg_type, ghost_type);
auto & filter = getBackgroundFilter(interface_type, bg_type, ghost_type);
Array<Real> disp_per_element(0, dim * nodes_per_background_e, "disp_elem");
FEEngine::extractNodalToElementField(
emodel.getMesh(), emodel.getDisplacement(), disp_per_element, bg_type,
ghost_type, filter);
Matrix<Real> concrete_du(dim, dim);
Matrix<Real> epsilon(dim, dim);
Vector<Real> evoigt(voigt_size);
for (auto && tuple :
zip(make_view(disp_per_element, dim, nodes_per_background_e),
make_view(bg_shapesd, dim, nodes_per_background_e),
this->gradu(interface_type, ghost_type),
make_view(this->directing_cosines(interface_type, ghost_type),
voigt_size))) {
auto & u = std::get<0>(tuple);
auto & B = std::get<1>(tuple);
auto & du = std::get<2>(tuple);
auto & C = std::get<3>(tuple);
concrete_du.mul<false, true>(u, B);
auto epsilon = 0.5 * (concrete_du + concrete_du.transpose());
strainTensorToVoigtVector(epsilon, evoigt);
du = C.dot(evoigt);
}
}
}
/* -------------------------------------------------------------------------- */
/**
* The structure of the directing cosines matrix is :
* \f{eqnarray*}{
* C_{1,\cdot} & = & (l^2, m^2, n^2, mn, ln, lm) \\
* C_{i,j} & = & 0
* \f}
*
* with :
* \f[
* (l, m, n) = \frac{1}{\|\frac{\mathrm{d}\vec{r}(s)}{\mathrm{d}s}\|} \cdot
* \frac{\mathrm{d}\vec{r}(s)}{\mathrm{d}s}
* \f]
*/
template <class Mat, UInt dim>
inline void MaterialReinforcement<Mat, dim>::computeDirectingCosinesOnQuad(
const Matrix<Real> & nodes, Matrix<Real> & cosines) {
AKANTU_DEBUG_IN();
-
AKANTU_DEBUG_ASSERT(nodes.cols() == 2,
"Higher order reinforcement elements not implemented");
- const Vector<Real> a = nodes(0), b = nodes(1);
+ const Vector<Real> a = nodes(0);
+ const Vector<Real> b = nodes(1);
Vector<Real> delta = b - a;
Real sq_length = 0.;
for (UInt i = 0; i < dim; i++) {
sq_length += delta(i) * delta(i);
}
if (dim == 2) {
cosines(0, 0) = delta(0) * delta(0); // l^2
cosines(0, 1) = delta(1) * delta(1); // m^2
cosines(0, 2) = delta(0) * delta(1); // lm
} else if (dim == 3) {
cosines(0, 0) = delta(0) * delta(0); // l^2
cosines(0, 1) = delta(1) * delta(1); // m^2
cosines(0, 2) = delta(2) * delta(2); // n^2
cosines(0, 3) = delta(1) * delta(2); // mn
cosines(0, 4) = delta(0) * delta(2); // ln
cosines(0, 5) = delta(0) * delta(1); // lm
}
cosines /= sq_length;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
inline void MaterialReinforcement<Mat, dim>::stressTensorToVoigtVector(
const Matrix<Real> & tensor, Vector<Real> & vector) {
AKANTU_DEBUG_IN();
for (UInt i = 0; i < dim; i++) {
vector(i) = tensor(i, i);
}
if (dim == 2) {
vector(2) = tensor(0, 1);
} else if (dim == 3) {
vector(3) = tensor(1, 2);
vector(4) = tensor(0, 2);
vector(5) = tensor(0, 1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
inline void MaterialReinforcement<Mat, dim>::strainTensorToVoigtVector(
const Matrix<Real> & tensor, Vector<Real> & vector) {
AKANTU_DEBUG_IN();
for (UInt i = 0; i < dim; i++) {
vector(i) = tensor(i, i);
}
if (dim == 2) {
vector(2) = 2 * tensor(0, 1);
} else if (dim == 3) {
vector(3) = 2 * tensor(1, 2);
vector(4) = 2 * tensor(0, 2);
vector(5) = 2 * tensor(0, 1);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
index 7d73ed426..cd288dcbf 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
@@ -1,270 +1,272 @@
/**
* @file material_neohookean.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Mon Apr 08 2013
* @date last modification: Wed Nov 08 2017
*
* @brief Specialization of the material class for finite deformation
* neo-hookean material
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_neohookean.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialNeohookean<spatial_dimension>::MaterialNeohookean(
SolidMechanicsModel & model, const ID & id)
: PlaneStressToolbox<spatial_dimension>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("E", E, Real(0.), _pat_parsable | _pat_modifiable,
"Young's modulus");
this->registerParam("nu", nu, Real(0.5), _pat_parsable | _pat_modifiable,
"Poisson's ratio");
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
this->finite_deformation = true;
this->initialize_third_axis_deformation = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
PlaneStressToolbox<spatial_dimension>::initMaterial();
- if (spatial_dimension == 1)
+ if (spatial_dimension == 1) {
nu = 0.;
+ }
this->updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <> void MaterialNeohookean<2>::initMaterial() {
AKANTU_DEBUG_IN();
PlaneStressToolbox<2>::initMaterial();
this->updateInternalParameters();
- if (this->plane_stress)
+ if (this->plane_stress) {
this->third_axis_deformation.setDefaultValue(1.);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::updateInternalParameters() {
lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
mu = E / (2 * (1 + nu));
kpa = lambda + 2. / 3. * mu;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeCauchyStressPlaneStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
PlaneStressToolbox<dim>::computeCauchyStressPlaneStress(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeCauchyStressPlaneStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto gradu_it = this->gradu(el_type, ghost_type).begin(2, 2);
auto gradu_end = this->gradu(el_type, ghost_type).end(2, 2);
auto piola_it = this->piola_kirchhoff_2(el_type, ghost_type).begin(2, 2);
auto stress_it = this->stress(el_type, ghost_type).begin(2, 2);
auto c33_it = this->third_axis_deformation(el_type, ghost_type).begin();
for (; gradu_it != gradu_end; ++gradu_it, ++piola_it, ++stress_it, ++c33_it) {
Matrix<Real> & grad_u = *gradu_it;
Matrix<Real> & piola = *piola_it;
Matrix<Real> & sigma = *stress_it;
StoCauchy<2>(gradUToF<2>(grad_u), piola, sigma, *c33_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
PlaneStressToolbox<2>::computeStress(el_type, ghost_type);
auto c33_it = this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma, *c33_it);
++c33_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeThirdAxisDeformation(
ElementType /*el_type*/, GhostType /*ghost_type*/) {}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeThirdAxisDeformation(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(this->plane_stress, "The third component of the strain "
"can only be computed for 2D "
"problems in Plane Stress!!");
Array<Real>::scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeThirdAxisDeformationOnQuad(grad_u, *c33_it);
++c33_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::computePotentialEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
Material::computePotentialEnergy(el_type);
Array<Real>::scalar_iterator epot = this->potential_energy(el_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
computePotentialEnergyOnQuad(grad_u, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::computeTangentModuli(
- __attribute__((unused)) const ElementType & el_type,
+ __attribute__((unused)) ElementType el_type,
Array<Real> & tangent_matrix,
__attribute__((unused)) GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeTangentModuli(__attribute__((unused))
- const ElementType & el_type,
+ ElementType el_type,
Array<Real> & tangent_matrix,
__attribute__((unused))
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
PlaneStressToolbox<2>::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u, *c33_it);
++c33_it;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialNeohookean<spatial_dimension>::getPushWaveSpeed(
__attribute__((unused)) const Element & element) const {
return sqrt((this->lambda + 2 * this->mu) / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialNeohookean<spatial_dimension>::getShearWaveSpeed(
__attribute__((unused)) const Element & element) const {
return sqrt(this->mu / this->rho);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(neohookean, MaterialNeohookean);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
index 7ae5bf6da..0bca79512 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
@@ -1,169 +1,169 @@
/**
* @file material_neohookean.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 29 2017
*
* @brief Material isotropic elastic
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "plane_stress_toolbox.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_NEOHOOKEAN_HH__
-#define __AKANTU_MATERIAL_NEOHOOKEAN_HH__
+#ifndef AKANTU_MATERIAL_NEOHOOKEAN_HH_
+#define AKANTU_MATERIAL_NEOHOOKEAN_HH_
namespace akantu {
/**
* Material elastic isotropic
*
* parameters in the material files :
* - rho : density (default: 0)
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - Plane_Stress : if 0: plane strain, else: plane stress (default: 0)
*/
template <UInt spatial_dimension>
class MaterialNeohookean : public PlaneStressToolbox<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialNeohookean(SolidMechanicsModel & model, const ID & id = "");
~MaterialNeohookean() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// Computation of the cauchy stress for plane strain materials
void
computeCauchyStressPlaneStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// Non linear computation of the third direction strain in 2D plane stress
/// case
void computeThirdAxisDeformation(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type) override;
/// compute the tangent stiffness matrix for an element type
- void computeTangentModuli(const ElementType & el_type,
+ void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the p-wave speed in the material
Real getPushWaveSpeed(const Element & element) const override;
/// compute the s-wave speed in the material
Real getShearWaveSpeed(const Element & element) const override;
MatrixType getTangentType() override {
return _symmetric;
}
protected:
/// constitutive law for a given quadrature point
inline void computePiolaKirchhoffOnQuad(const Matrix<Real> & E,
Matrix<Real> & S);
/// constitutive law for a given quadrature point (first piola)
inline void computeFirstPiolaKirchhoffOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & S,
Matrix<Real> & P);
/// constitutive law for a given quadrature point
inline void computeDeltaStressOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & grad_delta_u,
Matrix<Real> & delta_S);
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & S,
const Real & C33 = 1.0);
/// constitutive law for a given quadrature point
inline void computeThirdAxisDeformationOnQuad(Matrix<Real> & grad_u,
Real & c33_value);
/// constitutive law for a given quadrature point
// inline void updateStressOnQuad(const Matrix<Real> & sigma,
// Matrix<Real> & cauchy_sigma);
/// compute the potential energy for a quadrature point
inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
Real & epot);
/// compute the tangent stiffness matrix for an element
void computeTangentModuliOnQuad(Matrix<Real> & tangent, Matrix<Real> & grad_u,
const Real & C33 = 1.0);
/// recompute the lame coefficient if E or nu changes
void updateInternalParameters() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// Bulk modulus
Real kpa;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_neohookean_inline_impl.hh"
-#endif /* __AKANTU_MATERIAL_NEOHOOKEAN_HH__ */
+#endif /* AKANTU_MATERIAL_NEOHOOKEAN_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.hh b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.hh
index 1ae0ebb1b..8a0b473ea 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.hh
@@ -1,193 +1,197 @@
/**
* @file material_neohookean_inline_impl.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Mon Apr 08 2013
* @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the inline functions of the material elastic
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_neohookean.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <iostream>
#include <utility>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeDeltaStressOnQuad(
__attribute__((unused)) const Matrix<Real> & grad_u,
__attribute__((unused)) const Matrix<Real> & grad_delta_u,
__attribute__((unused)) Matrix<Real> & delta_S) {}
//! computes the second piola kirchhoff stress, called S
template <UInt dim>
inline void MaterialNeohookean<dim>::computeStressOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & S,
const Real & C33) {
// Neo hookean book
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
Matrix<Real> Cminus(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Real J = F.det() * sqrt(C33); // the term sqrt(C33) corresponds to the off
// plane strain (2D plane stress)
// std::cout<<"det(F) -> "<<J<<std::endl;
Cminus.inverse(C);
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
- S(i, j) = (i == j) * mu + (lambda * log(J) - mu) * Cminus(i, j);
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
+ S(i, j) = Math::kronecker(i, j) * mu + (lambda * log(J) - mu) * Cminus(i, j);
+ }
+ }
}
/* -------------------------------------------------------------------------- */
class C33_NR : public Math::NewtonRaphsonFunctor {
public:
C33_NR(std::string name, const Real & lambda, const Real & mu,
const Matrix<Real> & C)
: NewtonRaphsonFunctor(std::move(name)), lambda(lambda), mu(mu), C(C) {}
inline Real f(Real x) const override {
return (this->lambda / 2. *
(std::log(x) + std::log(this->C(0, 0) * this->C(1, 1) -
Math::pow<2>(this->C(0, 1)))) +
this->mu * (x - 1.));
}
inline Real f_prime(Real x) const override {
AKANTU_DEBUG_ASSERT(std::abs(x) > Math::getTolerance(),
"x is zero (x should be the off plane right Cauchy"
<< " measure in this function so you made a mistake"
<< " somewhere else that lead to a zero here!!!");
return (this->lambda / (2. * x) + this->mu);
}
private:
const Real & lambda;
const Real & mu;
const Matrix<Real> & C;
};
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeThirdAxisDeformationOnQuad(
Matrix<Real> & grad_u, Real & c33_value) {
// Neo hookean book
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Math::NewtonRaphson nr(1e-5, 100);
c33_value = nr.solve(
C33_NR("Neohookean_plan_stress", this->lambda, this->mu, C), c33_value);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void
MaterialNeohookean<dim>::computePiolaKirchhoffOnQuad(const Matrix<Real> & E,
Matrix<Real> & S) {
Real trace = E.trace(); /// \f$ trace = (\nabla u)_{kk} \f$
/// \f$ \sigma_{ij} = \lambda * (\nabla u)_{kk} * \delta_{ij} + \mu * (\nabla
/// u_{ij} + \nabla u_{ji}) \f$
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
- S(i, j) = (i == j) * lambda * trace + 2.0 * mu * E(i, j);
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
+ S(i, j) = Math::kronecker(i, j) * lambda * trace + 2.0 * mu * E(i, j);
+ }
+ }
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeFirstPiolaKirchhoffOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & S, Matrix<Real> & P) {
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
// first Piola-Kirchhoff is computed as the product of the deformation
// gracient
// tensor and the second Piola-Kirchhoff stress tensor
P = F * S;
}
/**************************************************************************************/
/* Computation of the potential energy for a this neo hookean material */
template <UInt dim>
inline void MaterialNeohookean<dim>::computePotentialEnergyOnQuad(
const Matrix<Real> & grad_u, Real & epot) {
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Real J = F.det();
// std::cout<<"det(F) -> "<<J<<std::endl;
epot =
0.5 * lambda * pow(log(J), 2.) + mu * (-log(J) + 0.5 * (C.trace() - dim));
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, Matrix<Real> & grad_u, const Real & C33) {
// Neo hookean book
UInt cols = tangent.cols();
UInt rows = tangent.rows();
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim);
Matrix<Real> Cminus(dim, dim);
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Real J = F.det() * sqrt(C33);
// std::cout<<"det(F) -> "<<J<<std::endl;
Cminus.inverse(C);
for (UInt m = 0; m < rows; m++) {
UInt i = VoigtHelper<dim>::vec[m][0];
UInt j = VoigtHelper<dim>::vec[m][1];
for (UInt n = 0; n < cols; n++) {
UInt k = VoigtHelper<dim>::vec[n][0];
UInt l = VoigtHelper<dim>::vec[n][1];
// book belytchko
tangent(m, n) = lambda * Cminus(i, j) * Cminus(k, l) +
(mu - lambda * log(J)) * (Cminus(i, k) * Cminus(j, l) +
Cminus(i, l) * Cminus(k, j));
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_non_local.hh b/src/model/solid_mechanics/materials/material_non_local.hh
index 8d2e2858f..fb983cb5a 100644
--- a/src/model/solid_mechanics/materials/material_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_non_local.hh
@@ -1,118 +1,118 @@
/**
* @file material_non_local.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Sep 11 2017
*
* @brief Material class that handle the non locality of a law for example
* damage.
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_NON_LOCAL_HH__
-#define __AKANTU_MATERIAL_NON_LOCAL_HH__
+#ifndef AKANTU_MATERIAL_NON_LOCAL_HH_
+#define AKANTU_MATERIAL_NON_LOCAL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
class MaterialNonLocalInterface {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material the non local parts of the material
void initMaterialNonLocal() {
this->registerNeighborhood();
this->registerNonLocalVariables();
};
/// insert the quadrature points in the neighborhoods of the non-local manager
virtual void insertIntegrationPointsInNeighborhoods(
- const GhostType & ghost_type,
+ GhostType ghost_type,
const ElementTypeMapReal & quadrature_points_coordinates) = 0;
/// update the values in the non-local internal fields
virtual void updateNonLocalInternals(ElementTypeMapReal & non_local_flattened,
const ID & field_id,
- const GhostType & ghost_type,
- const ElementKind & kind) = 0;
+ GhostType ghost_type,
+ ElementKind kind) = 0;
/// constitutive law
virtual void computeNonLocalStresses(GhostType ghost_type = _not_ghost) = 0;
protected:
/// get the name of the neighborhood for this material
virtual ID getNeighborhoodName() = 0;
/// register the neighborhoods for the material
virtual void registerNeighborhood() = 0;
/// register the non local internal variable
virtual void registerNonLocalVariables() = 0;
- virtual inline void onElementsAdded(const Array<Element> &,
- const NewElementsEvent &) {}
+ virtual inline void onElementsAdded(const Array<Element> & /*unused*/,
+ const NewElementsEvent & /*unused*/) {}
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
class MaterialNonLocal : public MaterialNonLocalInterface, public LocalParent {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit MaterialNonLocal(SolidMechanicsModel & model, const ID & id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// insert the quadrature points in the neighborhoods of the non-local manager
void insertIntegrationPointsInNeighborhoods(
- const GhostType & ghost_type,
+ GhostType ghost_type,
const ElementTypeMapReal & quadrature_points_coordinates) override;
/// update the values in the non-local internal fields
void updateNonLocalInternals(ElementTypeMapReal & non_local_flattened,
const ID & field_id,
- const GhostType & ghost_type,
- const ElementKind & kind) override;
+ GhostType ghost_type,
+ ElementKind kind) override;
/// register the neighborhoods for the material
void registerNeighborhood() override;
protected:
/// get the name of the neighborhood for this material
ID getNeighborhoodName() override { return this->name; }
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "material_non_local_tmpl.hh"
-#endif /* __AKANTU_MATERIAL_NON_LOCAL_HH__ */
+#endif /* AKANTU_MATERIAL_NON_LOCAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_non_local_tmpl.hh b/src/model/solid_mechanics/materials/material_non_local_tmpl.hh
index 3608a2b56..241f63a2b 100644
--- a/src/model/solid_mechanics/materials/material_non_local_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_non_local_tmpl.hh
@@ -1,127 +1,127 @@
/**
* @file material_non_local_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 06 2017
* @date last modification: Tue Nov 07 2017
*
* @brief Implementation of material non-local
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "material_non_local.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
MaterialNonLocal<dim, LocalParent>::MaterialNonLocal(
SolidMechanicsModel & model, const ID & id)
: LocalParent(model, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
void MaterialNonLocal<dim, LocalParent>::insertIntegrationPointsInNeighborhoods(
- const GhostType & ghost_type,
+ GhostType ghost_type,
const ElementTypeMapReal & quadrature_points_coordinates) {
IntegrationPoint q;
q.ghost_type = ghost_type;
auto & neighborhood = this->model.getNonLocalManager().getNeighborhood(
this->getNeighborhoodName());
for (auto & type :
this->element_filter.elementTypes(dim, ghost_type, _ek_regular)) {
q.type = type;
const auto & elem_filter = this->element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
- if (nb_element) {
+ if (nb_element != 0U) {
UInt nb_quad =
this->getFEEngine().getNbIntegrationPoints(type, ghost_type);
const auto & quads = quadrature_points_coordinates(type, ghost_type);
auto nb_total_element =
this->model.getMesh().getNbElement(type, ghost_type);
auto quads_it = quads.begin_reinterpret(dim, nb_quad, nb_total_element);
for (auto & elem : elem_filter) {
Matrix<Real> quads = quads_it[elem];
q.element = elem;
for (UInt nq = 0; nq < nb_quad; ++nq) {
q.num_point = nq;
q.global_num = q.element * nb_quad + nq;
neighborhood.insertIntegrationPoint(q, quads(nq));
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
void MaterialNonLocal<dim, LocalParent>::updateNonLocalInternals(
ElementTypeMapReal & non_local_flattened, const ID & field_id,
- const GhostType & ghost_type, const ElementKind & kind) {
+ GhostType ghost_type, ElementKind kind) {
/// loop over all types in the material
for (auto & el_type :
this->element_filter.elementTypes(dim, ghost_type, kind)) {
Array<Real> & internal =
this->template getInternal<Real>(field_id)(el_type, ghost_type);
auto & internal_flat = non_local_flattened(el_type, ghost_type);
auto nb_component = internal_flat.getNbComponent();
auto internal_it = internal.begin(nb_component);
auto internal_flat_it = internal_flat.begin(nb_component);
/// loop all elements for the given type
const auto & filter = this->element_filter(el_type, ghost_type);
UInt nb_quads =
this->getFEEngine().getNbIntegrationPoints(el_type, ghost_type);
for (auto & elem : filter) {
for (UInt q = 0; q < nb_quads; ++q, ++internal_it) {
UInt global_quad = elem * nb_quads + q;
*internal_it = internal_flat_it[global_quad];
}
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
void MaterialNonLocal<dim, LocalParent>::registerNeighborhood() {
ID name = this->getNeighborhoodName();
this->model.getNonLocalManager().registerNeighborhood(name, name);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
index 864b4f320..7d5b4bc9f 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
@@ -1,201 +1,203 @@
/**
* @file material_linear_isotropic_hardening.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
* @date last modification: Sat Dec 02 2017
*
* @brief Specialization of the material class for isotropic finite deformation
* linear hardening plasticity
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_linear_isotropic_hardening.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialLinearIsotropicHardening<dim>::MaterialLinearIsotropicHardening(
SolidMechanicsModel & model, const ID & id)
: MaterialPlastic<dim>(model, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialLinearIsotropicHardening<spatial_dimension>::
MaterialLinearIsotropicHardening(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id)
: MaterialPlastic<spatial_dimension>(model, dim, mesh, fe_engine, id) {}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialLinearIsotropicHardening<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
+ // NOLINTNEXTLINE(bugprone-parent-virtual-call)
MaterialThermal<spatial_dimension>::computeStress(el_type, ghost_type);
+
// infinitesimal and finite deformation
auto sigma_th_it = this->sigma_th(el_type, ghost_type).begin();
auto previous_sigma_th_it =
this->sigma_th.previous(el_type, ghost_type).begin();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto inelastic_strain_it = this->inelastic_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto iso_hardening_it = this->iso_hardening(el_type, ghost_type).begin();
auto previous_iso_hardening_it =
this->iso_hardening.previous(el_type, ghost_type).begin();
//
// Finite Deformations
//
if (this->finite_deformation) {
auto previous_piola_kirchhoff_2_it =
this->piola_kirchhoff_2.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto green_strain_it = this->green_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_piola_kirchhoff_2_it;
auto & green_strain = *green_strain_it;
this->template gradUToE<spatial_dimension>(grad_u, green_strain);
Matrix<Real> previous_green_strain(spatial_dimension, spatial_dimension);
this->template gradUToE<spatial_dimension>(previous_grad_u,
previous_green_strain);
Matrix<Real> F_tensor(spatial_dimension, spatial_dimension);
this->template gradUToF<spatial_dimension>(grad_u, F_tensor);
computeStressOnQuad(green_strain, previous_green_strain, sigma,
previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it,
*previous_sigma_th_it, F_tensor);
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
//++previous_stress_it;
++previous_gradu_it;
++green_strain_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
++previous_piola_kirchhoff_2_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
// Infinitesimal deformations
else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_stress_it;
computeStressOnQuad(
grad_u, previous_grad_u, sigma, previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it, *previous_sigma_th_it);
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
++previous_stress_it;
++previous_gradu_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialLinearIsotropicHardening<spatial_dimension>::computeTangentModuli(
- const ElementType & el_type, Array<Real> & tangent_matrix,
+ ElementType el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto iso_hardening = this->iso_hardening(el_type, ghost_type).begin();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u, *previous_gradu_it, sigma,
*previous_stress_it, *iso_hardening);
++previous_gradu_it;
++previous_stress_it;
++iso_hardening;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(plastic_linear_isotropic_hardening,
MaterialLinearIsotropicHardening);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
index d3447f563..9f9d9f920 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
@@ -1,112 +1,114 @@
/**
* @file material_linear_isotropic_hardening.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sat Dec 02 2017
*
* @brief Specialization of the material class for isotropic finite deformation
* linear hardening plasticity
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH__
-#define __AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH__
+#ifndef AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH_
+#define AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH_
namespace akantu {
/**
* Material plastic with a linear evolution of the yielding stress
*/
template <UInt spatial_dimension>
class MaterialLinearIsotropicHardening
: public MaterialPlastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialLinearIsotropicHardening(SolidMechanicsModel & model,
const ID & id = "");
MaterialLinearIsotropicHardening(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
- void computeTangentModuli(const ElementType & el_type,
+ void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
protected:
/// Infinitesimal deformations
- inline void computeStressOnQuad(
- const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
- Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
- Matrix<Real> & inelas_strain, const Matrix<Real> & previous_inelas_strain,
- Real & iso_hardening, const Real & previous_iso_hardening,
- const Real & sigma_th, const Real & previous_sigma_th);
+ inline void
+ computeStressOnQuad(const Matrix<Real> & grad_u,
+ const Matrix<Real> & previous_grad_u,
+ Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
+ Matrix<Real> & inelastic_strain,
+ const Matrix<Real> & previous_inelastic_strain,
+ Real & iso_hardening, const Real & previous_iso_hardening,
+ const Real & sigma_th, const Real & previous_sigma_th);
/// Finite deformations
inline void computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
- Matrix<Real> & inelas_strain, const Matrix<Real> & previous_inelas_strain,
- Real & iso_hardening, const Real & previous_iso_hardening,
- const Real & sigma_th, const Real & previous_sigma_th,
- const Matrix<Real> & F_tensor);
+ Matrix<Real> & inelastic_strain,
+ const Matrix<Real> & previous_inelastic_strain, Real & iso_hardening,
+ const Real & previous_iso_hardening, const Real & sigma_th,
+ const Real & previous_sigma_th, const Matrix<Real> & F_tensor);
inline void computeTangentModuliOnQuad(
Matrix<Real> & tangent, const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u, const Matrix<Real> & sigma_tensor,
const Matrix<Real> & previous_sigma_tensor,
const Real & iso_hardening) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "material_linear_isotropic_hardening_inline_impl.hh"
-#endif /* __AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH__ */
+#endif /* AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.hh b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.hh
index 6d7a12f5e..f4cdaf146 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.hh
@@ -1,296 +1,300 @@
/**
* @file material_linear_isotropic_hardening_inline_impl.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
* @date last modification: Thu Nov 30 2017
*
* @brief Implementation of the inline functions of the material plasticity
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "material_linear_isotropic_hardening.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/// Infinitesimal deformations
template <UInt dim>
inline void MaterialLinearIsotropicHardening<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain, Real & iso_hardening,
const Real & previous_iso_hardening, const Real & sigma_th,
const Real & previous_sigma_th) {
Real delta_sigma_th = sigma_th - previous_sigma_th;
Matrix<Real> grad_delta_u(grad_u);
grad_delta_u -= previous_grad_u;
// Compute trial stress, sigma_tr
Matrix<Real> sigma_tr(dim, dim);
MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr,
delta_sigma_th);
sigma_tr += previous_sigma;
// We need a full stress tensor, otherwise the VM stress is messed up
Matrix<Real> sigma_tr_dev(3, 3, 0);
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
sigma_tr_dev(i, j) = sigma_tr(i, j);
+ }
+ }
sigma_tr_dev -= Matrix<Real>::eye(3, sigma_tr.trace() / 3.0);
// Compute effective deviatoric trial stress
Real s = sigma_tr_dev.doubleDot(sigma_tr_dev);
Real sigma_tr_dev_eff = std::sqrt(3. / 2. * s);
bool initial_yielding =
((sigma_tr_dev_eff - iso_hardening - this->sigma_y) > 0);
Real dp = (initial_yielding)
? (sigma_tr_dev_eff - this->sigma_y - previous_iso_hardening) /
(3 * this->mu + this->h)
: 0;
iso_hardening = previous_iso_hardening + this->h * dp;
// Compute inelastic strain (ignore last components in 1-2D)
Matrix<Real> delta_inelastic_strain(dim, dim, 0.);
if (std::abs(sigma_tr_dev_eff) >
sigma_tr_dev.norm<L_inf>() * Math::getTolerance()) {
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
delta_inelastic_strain(i, j) = sigma_tr_dev(i, j);
+ }
+ }
delta_inelastic_strain *= 3. / 2. * dp / sigma_tr_dev_eff;
}
MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
grad_delta_u, sigma, previous_sigma, inelastic_strain,
previous_inelastic_strain, delta_inelastic_strain);
}
/* -------------------------------------------------------------------------- */
/// Finite deformations
template <UInt dim>
inline void MaterialLinearIsotropicHardening<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain, Real & iso_hardening,
const Real & previous_iso_hardening, const Real & sigma_th,
const Real & previous_sigma_th, const Matrix<Real> & F_tensor) {
// Finite plasticity
Real dp = 0.0;
Real d_dp = 0.0;
UInt n = 0;
Real delta_sigma_th = sigma_th - previous_sigma_th;
Matrix<Real> grad_delta_u(grad_u);
grad_delta_u -= previous_grad_u;
// Compute trial stress, sigma_tr
Matrix<Real> sigma_tr(dim, dim);
MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr,
delta_sigma_th);
sigma_tr += previous_sigma;
// Compute deviatoric trial stress, sigma_tr_dev
Matrix<Real> sigma_tr_dev(sigma_tr);
sigma_tr_dev -= Matrix<Real>::eye(dim, sigma_tr.trace() / 3.0);
// Compute effective deviatoric trial stress
Real s = sigma_tr_dev.doubleDot(sigma_tr_dev);
Real sigma_tr_dev_eff = std::sqrt(3. / 2. * s);
// compute the cauchy stress to apply the Von-Mises criterion
Matrix<Real> cauchy_stress(dim, dim);
Material::StoCauchy<dim>(F_tensor, sigma_tr, cauchy_stress);
Matrix<Real> cauchy_stress_dev(cauchy_stress);
cauchy_stress_dev -= Matrix<Real>::eye(dim, cauchy_stress.trace() / 3.0);
Real c = cauchy_stress_dev.doubleDot(cauchy_stress_dev);
Real cauchy_stress_dev_eff = std::sqrt(3. / 2. * c);
const Real iso_hardening_t = previous_iso_hardening;
iso_hardening = iso_hardening_t;
// Loop for correcting stress based on yield function
// F is written in terms of S
// bool initial_yielding = ( (sigma_tr_dev_eff - iso_hardening -
// this->sigma_y) > 0) ;
// while ( initial_yielding && std::abs(sigma_tr_dev_eff - iso_hardening -
// this->sigma_y) > Math::getTolerance() ) {
// d_dp = (sigma_tr_dev_eff - 3. * this->mu *dp - iso_hardening -
// this->sigma_y)
// / (3. * this->mu + this->h);
// //r = r + h * dp;
// dp = dp + d_dp;
// iso_hardening = iso_hardening_t + this->h * dp;
// ++n;
// /// TODO : explicit this criterion with an error message
// if ((std::abs(d_dp) < 1e-9) || (n>50)){
// AKANTU_DEBUG_INFO("convergence of increment of plastic strain. d_dp:"
// << d_dp << "\tNumber of iteration:"<<n);
// break;
// }
// }
// F is written in terms of cauchy stress
bool initial_yielding =
((cauchy_stress_dev_eff - iso_hardening - this->sigma_y) > 0);
while (initial_yielding && std::abs(cauchy_stress_dev_eff - iso_hardening -
this->sigma_y) > Math::getTolerance()) {
d_dp = (cauchy_stress_dev_eff - 3. * this->mu * dp - iso_hardening -
this->sigma_y) /
(3. * this->mu + this->h);
// r = r + h * dp;
dp = dp + d_dp;
iso_hardening = iso_hardening_t + this->h * dp;
++n;
/// TODO : explicit this criterion with an error message
if ((d_dp < 1e-5) || (n > 50)) {
AKANTU_DEBUG_INFO("convergence of increment of plastic strain. d_dp:"
<< d_dp << "\tNumber of iteration:" << n);
break;
}
}
// Update internal variable
Matrix<Real> delta_inelastic_strain(dim, dim, 0.);
if (std::abs(sigma_tr_dev_eff) >
sigma_tr_dev.norm<L_inf>() * Math::getTolerance()) {
// /// compute the direction of the plastic strain as \frac{\partial
// F}{\partial S} = \frac{3}{2J\sigma_{effective}}} Ft \sigma_{dev} F
Matrix<Real> cauchy_dev_F(dim, dim);
cauchy_dev_F.mul<false, false>(F_tensor, cauchy_stress_dev);
Real J = F_tensor.det();
- Real constant = J ? 1. / J : 0;
+ Real constant = not Math::are_float_equal(J, 0.) ? 1. / J : 0;
constant *= 3. * dp / (2. * cauchy_stress_dev_eff);
delta_inelastic_strain.mul<true, false>(F_tensor, cauchy_dev_F, constant);
// Direction given by the piola kirchhoff deviatoric tensor \frac{\partial
// F}{\partial S} = \frac{3}{2\sigma_{effective}}}S_{dev}
// delta_inelastic_strain.copy(sigma_tr_dev);
// delta_inelastic_strain *= 3./2. * dp / sigma_tr_dev_eff;
}
MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
grad_delta_u, sigma, previous_sigma, inelastic_strain,
previous_inelastic_strain, delta_inelastic_strain);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialLinearIsotropicHardening<dim>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, __attribute__((unused)) const Matrix<Real> & grad_u,
__attribute__((unused)) const Matrix<Real> & previous_grad_u,
__attribute__((unused)) const Matrix<Real> & sigma_tensor,
__attribute__((unused)) const Matrix<Real> & previous_sigma_tensor,
__attribute__((unused)) const Real & iso_hardening) const {
// Real r=iso_hardening;
// Matrix<Real> grad_delta_u(grad_u);
// grad_delta_u -= previous_grad_u;
// //Compute trial stress, sigma_tr
// Matrix<Real> sigma_tr(dim, dim);
// MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr);
// sigma_tr += previous_sigma_tensor;
// // Compute deviatoric trial stress, sigma_tr_dev
// Matrix<Real> sigma_tr_dev(sigma_tr);
// sigma_tr_dev -= Matrix<Real>::eye(dim, sigma_tr.trace() / 3.0);
// // Compute effective deviatoric trial stress
// Real s = sigma_tr_dev.doubleDot(sigma_tr_dev);
// Real sigma_tr_dev_eff=std::sqrt(3./2. * s);
// // Compute deviatoric stress, sigma_dev
// Matrix<Real> sigma_dev(sigma_tensor);
// sigma_dev -= Matrix<Real>::eye(dim, sigma_tensor.trace() / 3.0);
// // Compute effective deviatoric stress
// s = sigma_dev.doubleDot(sigma_dev);
// Real sigma_dev_eff = std::sqrt(3./2. * s);
// Real xr = 0.0;
// if(sigma_tr_dev_eff > sigma_dev_eff * Math::getTolerance())
// xr = sigma_dev_eff / sigma_tr_dev_eff;
// Real __attribute__((unused)) q = 1.5 * (1. / (1. + 3. * this->mu /
// this->h) - xr);
/*
UInt cols = tangent.cols();
UInt rows = tangent.rows();
for (UInt m = 0; m < rows; ++m) {
UInt i = VoigtHelper<dim>::vec[m][0];
UInt j = VoigtHelper<dim>::vec[m][1];
for (UInt n = 0; n < cols; ++n) {
UInt k = VoigtHelper<dim>::vec[n][0];
UInt l = VoigtHelper<dim>::vec[n][1];
*/
// This section of the code is commented
// There were some problems with the convergence of plastic-coupled
// simulations with thermal expansion
// XXX: DO NOT REMOVE
/*if (((sigma_tr_dev_eff-iso_hardening-sigmay) > 0) && (xr > 0)) {
tangent(m,n) =
2. * this->mu * q * (sigma_tr_dev (i,j) / sigma_tr_dev_eff) * (sigma_tr_dev
(k,l) / sigma_tr_dev_eff) +
(i==k) * (j==l) * 2. * this->mu * xr +
(i==j) * (k==l) * (this->kpa - 2./3. * this->mu * xr);
if ((m == n) && (m>=dim))
tangent(m, n) = tangent(m, n) - this->mu * xr;
} else {*/
/*
tangent(m,n) = (i==k) * (j==l) * 2. * this->mu +
(i==j) * (k==l) * this->lambda;
tangent(m,n) -= (m==n) * (m>=dim) * this->mu;
*/
//}
// correct tangent stiffness for shear component
//}
//}
MaterialElastic<dim>::computeTangentModuliOnQuad(tangent);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc b/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
index a475795da..059a710d5 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
@@ -1,201 +1,199 @@
/**
* @file material_plastic.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
* @date last modification: Sun Dec 03 2017
*
* @brief Implemantation of the akantu::MaterialPlastic class
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialPlastic<spatial_dimension>::MaterialPlastic(SolidMechanicsModel & model,
const ID & id)
: MaterialElastic<spatial_dimension>(model, id),
iso_hardening("iso_hardening", *this),
inelastic_strain("inelastic_strain", *this),
plastic_energy("plastic_energy", *this),
d_plastic_energy("d_plastic_energy", *this) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
template <UInt spatial_dimension>
MaterialPlastic<spatial_dimension>::MaterialPlastic(SolidMechanicsModel & model,
UInt dim, const Mesh & mesh,
FEEngine & fe_engine,
const ID & id)
: MaterialElastic<spatial_dimension>(model, dim, mesh, fe_engine, id),
iso_hardening("iso_hardening", *this, dim, fe_engine,
this->element_filter),
inelastic_strain("inelastic_strain", *this, dim, fe_engine,
this->element_filter),
plastic_energy("plastic_energy", *this, dim, fe_engine,
this->element_filter),
d_plastic_energy("d_plastic_energy", *this, dim, fe_engine,
this->element_filter) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::initialize() {
this->registerParam("h", h, Real(0.), _pat_parsable | _pat_modifiable,
"Hardening modulus");
this->registerParam("sigma_y", sigma_y, Real(0.),
_pat_parsable | _pat_modifiable, "Yield stress");
this->iso_hardening.initialize(1);
this->iso_hardening.initializeHistory();
this->plastic_energy.initialize(1);
this->d_plastic_energy.initialize(1);
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->use_previous_stress_thermal = true;
this->inelastic_strain.initialize(spatial_dimension * spatial_dimension);
this->inelastic_strain.initializeHistory();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialPlastic<spatial_dimension>::getEnergy(const std::string & type) {
- if (type == "plastic")
+ if (type == "plastic") {
return getPlasticEnergy();
- else
- return MaterialElastic<spatial_dimension>::getEnergy(type);
-
- return 0.;
+ }
+ return MaterialElastic<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialPlastic<spatial_dimension>::getPlasticEnergy() {
AKANTU_DEBUG_IN();
Real penergy = 0.;
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
penergy +=
this->fem.integrate(plastic_energy(type, _not_ghost), type, _not_ghost,
this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return penergy;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::computePotentialEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
Array<Real>::scalar_iterator epot = this->potential_energy(el_type).begin();
Array<Real>::const_iterator<Matrix<Real>> inelastic_strain_it =
this->inelastic_strain(el_type).begin(spatial_dimension,
spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
Matrix<Real> elastic_strain(spatial_dimension, spatial_dimension);
elastic_strain.copy(grad_u);
elastic_strain -= *inelastic_strain_it;
MaterialElastic<spatial_dimension>::computePotentialEnergyOnQuad(
elastic_strain, sigma, *epot);
++epot;
++inelastic_strain_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::updateEnergies(ElementType el_type) {
AKANTU_DEBUG_IN();
MaterialElastic<spatial_dimension>::updateEnergies(el_type);
Array<Real>::iterator<> pe_it = this->plastic_energy(el_type).begin();
Array<Real>::iterator<> wp_it = this->d_plastic_energy(el_type).begin();
Array<Real>::iterator<Matrix<Real>> inelastic_strain_it =
this->inelastic_strain(el_type).begin(spatial_dimension,
spatial_dimension);
Array<Real>::iterator<Matrix<Real>> previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type).begin(spatial_dimension,
spatial_dimension);
Array<Real>::matrix_iterator previous_sigma =
this->stress.previous(el_type).begin(spatial_dimension,
spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
Matrix<Real> delta_strain_it(*inelastic_strain_it);
delta_strain_it -= *previous_inelastic_strain_it;
Matrix<Real> sigma_h(sigma);
sigma_h += *previous_sigma;
*wp_it = .5 * sigma_h.doubleDot(delta_strain_it);
*pe_it += *wp_it;
++pe_it;
++wp_it;
++inelastic_strain_it;
++previous_inelastic_strain_it;
++previous_sigma;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL_ONLY(MaterialPlastic);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh b/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
index 61f061a09..de3cad9df 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
@@ -1,127 +1,128 @@
/**
* @file material_plastic.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Dec 07 2017
*
* @brief Common interface for plastic materials
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_PLASTIC_HH__
-#define __AKANTU_MATERIAL_PLASTIC_HH__
+#ifndef AKANTU_MATERIAL_PLASTIC_HH_
+#define AKANTU_MATERIAL_PLASTIC_HH_
namespace akantu {
/**
* Parent class for the plastic constitutive laws
* parameters in the material files :
* - h : Hardening parameter (default: 0)
* - sigmay : Yield stress
*/
template <UInt dim> class MaterialPlastic : public MaterialElastic<dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialPlastic(SolidMechanicsModel & model, const ID & id = "");
MaterialPlastic(SolidMechanicsModel & model, UInt a_dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the energy specifying the type for the time step
Real getEnergy(const std::string & type) override;
/// Compute the plastic energy
void updateEnergies(ElementType el_type) override;
/// Compute the true potential energy
void computePotentialEnergy(ElementType el_type) override;
protected:
/// compute the stress and inelastic strain for the quadrature point
inline void computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
- Matrix<Real> & inelas_strain, const Matrix<Real> & previous_inelas_strain,
+ Matrix<Real> & inelastic_strain,
+ const Matrix<Real> & previous_inelastic_strain,
const Matrix<Real> & delta_inelastic_strain) const;
inline void computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & delta_grad_u, Matrix<Real> & sigma,
- const Matrix<Real> & previous_sigma, Matrix<Real> & inelas_strain,
- const Matrix<Real> & previous_inelas_strain,
+ const Matrix<Real> & previous_sigma, Matrix<Real> & inelastic_strain,
+ const Matrix<Real> & previous_inelastic_strain,
const Matrix<Real> & delta_inelastic_strain) const;
/// get the plastic energy for the time step
Real getPlasticEnergy();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Yield stresss
Real sigma_y;
/// hardening modulus
Real h;
/// isotropic hardening, r
InternalField<Real> iso_hardening;
/// inelastic strain arrays ordered by element types (inelastic deformation)
InternalField<Real> inelastic_strain;
/// Plastic energy
InternalField<Real> plastic_energy;
/// @todo : add a coefficient beta that will multiply the plastic energy
/// increment
/// to compute the energy converted to heat
/// Plastic energy increment
InternalField<Real> d_plastic_energy;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "material_plastic_inline_impl.hh"
-#endif /* __AKANTU_MATERIAL_PLASTIC_HH__ */
+#endif /* AKANTU_MATERIAL_PLASTIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_thermal.cc b/src/model/solid_mechanics/materials/material_thermal.cc
index 52df0f8a9..bda853570 100644
--- a/src/model/solid_mechanics/materials/material_thermal.cc
+++ b/src/model/solid_mechanics/materials/material_thermal.cc
@@ -1,118 +1,118 @@
/**
* @file material_thermal.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jan 29 2018
*
* @brief Specialization of the material class for the thermal material
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_thermal.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialThermal<spatial_dimension>::MaterialThermal(SolidMechanicsModel & model,
const ID & id)
: Material(model, id), delta_T("delta_T", *this),
sigma_th("sigma_th", *this), use_previous_stress_thermal(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialThermal<spatial_dimension>::MaterialThermal(SolidMechanicsModel & model,
UInt dim, const Mesh & mesh,
FEEngine & fe_engine,
const ID & id)
: Material(model, dim, mesh, fe_engine, id),
delta_T("delta_T", *this, dim, fe_engine, this->element_filter),
sigma_th("sigma_th", *this, dim, fe_engine, this->element_filter),
use_previous_stress_thermal(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
template <UInt spatial_dimension>
void MaterialThermal<spatial_dimension>::initialize() {
this->registerParam("E", E, Real(0.), _pat_parsable | _pat_modifiable,
"Young's modulus");
this->registerParam("nu", nu, Real(0.5), _pat_parsable | _pat_modifiable,
"Poisson's ratio");
this->registerParam("alpha", alpha, Real(0.), _pat_parsable | _pat_modifiable,
"Thermal expansion coefficient");
this->registerParam("delta_T", delta_T, _pat_parsable | _pat_modifiable,
"Uniform temperature field");
delta_T.initialize(1);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialThermal<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
sigma_th.initialize(1);
if (use_previous_stress_thermal) {
sigma_th.initializeHistory();
}
Material::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialThermal<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
for (auto && tuple : zip(this->delta_T(el_type, ghost_type),
this->sigma_th(el_type, ghost_type))) {
computeStressOnQuad(std::get<1>(tuple), std::get<0>(tuple));
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
-void MaterialThermal<dim>::computePotentialEnergy(ElementType) {
+void MaterialThermal<dim>::computePotentialEnergy(ElementType /*el_type*/) {
AKANTU_DEBUG_IN();
AKANTU_TO_IMPLEMENT();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL_ONLY(MaterialThermal);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_thermal.hh b/src/model/solid_mechanics/materials/material_thermal.hh
index 19828aea2..1a1c26884 100644
--- a/src/model/solid_mechanics/materials/material_thermal.hh
+++ b/src/model/solid_mechanics/materials/material_thermal.hh
@@ -1,112 +1,112 @@
/**
* @file material_thermal.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jan 29 2018
*
* @brief Material isotropic thermo-elastic
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_THERMAL_HH__
-#define __AKANTU_MATERIAL_THERMAL_HH__
+#ifndef AKANTU_MATERIAL_THERMAL_HH_
+#define AKANTU_MATERIAL_THERMAL_HH_
namespace akantu {
template <UInt spatial_dimension> class MaterialThermal : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialThermal(SolidMechanicsModel & model, const ID & id = "");
MaterialThermal(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
~MaterialThermal() override = default;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type) override;
/// local computation of thermal stress
inline void computeStressOnQuad(Real & sigma, const Real & deltaT);
/// local computation of thermal stress
void computePotentialEnergy(ElementType el_type) override;
/* --------------------------------------------------------------------------
*/
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Young modulus
Real E;
/// Poisson ratio
Real nu;
/// Thermal expansion coefficient
/// TODO : implement alpha as a matrix
Real alpha;
/// Temperature field
InternalField<Real> delta_T;
/// Current thermal stress
InternalField<Real> sigma_th;
/// Tell if we need to use the previous thermal stress
bool use_previous_stress_thermal;
};
/* ------------------------------------------------------------------------ */
/* Inline impl */
/* ------------------------------------------------------------------------ */
template <UInt dim>
inline void MaterialThermal<dim>::computeStressOnQuad(Real & sigma,
const Real & deltaT) {
sigma = -this->E / (1. - 2. * this->nu) * this->alpha * deltaT;
}
template <>
inline void MaterialThermal<1>::computeStressOnQuad(Real & sigma,
const Real & deltaT) {
sigma = -this->E * this->alpha * deltaT;
}
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_THERMAL_HH__ */
+#endif /* AKANTU_MATERIAL_THERMAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
index f965ae044..594535c7f 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
@@ -1,310 +1,316 @@
/**
* @file material_standard_linear_solid_deviatoric.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Vladislav Yastrebov <vladislav.yastrebov@epfl.ch>
*
* @date creation: Wed May 04 2011
* @date last modification: Tue Feb 20 2018
*
* @brief Material Visco-elastic
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_standard_linear_solid_deviatoric.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialStandardLinearSolidDeviatoric<
dim>::MaterialStandardLinearSolidDeviatoric(SolidMechanicsModel & model,
const ID & id)
: MaterialElastic<dim>(model, id), stress_dev("stress_dev", *this),
history_integral("history_integral", *this),
dissipated_energy("dissipated_energy", *this) {
AKANTU_DEBUG_IN();
this->registerParam("Eta", eta, Real(1.), _pat_parsable | _pat_modifiable,
"Viscosity");
this->registerParam("Ev", Ev, Real(1.), _pat_parsable | _pat_modifiable,
"Stiffness of the viscous element");
this->registerParam("Einf", E_inf, Real(1.), _pat_readable,
"Stiffness of the elastic element");
UInt stress_size = dim * dim;
this->stress_dev.initialize(stress_size);
this->history_integral.initialize(stress_size);
this->dissipated_energy.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::initMaterial() {
AKANTU_DEBUG_IN();
updateInternalParameters();
MaterialElastic<dim>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::updateInternalParameters() {
MaterialElastic<dim>::updateInternalParameters();
E_inf = this->E - this->Ev;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::setToSteadyState(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d = stress_dev_vect.begin(dim, dim);
Array<Real>::matrix_iterator history_int = history_int_vect.begin(dim, dim);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
/// Compute the first invariant of strain
Real Theta = grad_u.trace();
- for (UInt i = 0; i < dim; ++i)
+ for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
- dev_s(i, j) =
- 2 * this->mu *
- (.5 * (grad_u(i, j) + grad_u(j, i)) - 1. / 3. * Theta * (i == j));
+ dev_s(i, j) = 2 * this->mu *
+ (.5 * (grad_u(i, j) + grad_u(j, i)) -
+ 1. / 3. * Theta * Math::kronecker(i, j));
h(i, j) = 0.;
}
+ }
/// Save the deviator of stress
++stress_d;
++history_int;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real tau = 0.;
// if(std::abs(Ev) > std::numeric_limits<Real>::epsilon())
tau = eta / Ev;
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d = stress_dev_vect.begin(dim, dim);
Array<Real>::matrix_iterator history_int = history_int_vect.begin(dim, dim);
Matrix<Real> s(dim, dim);
Real dt = this->model.getTimeStep();
Real exp_dt_tau = exp(-dt / tau);
Real exp_dt_tau_2 = exp(-.5 * dt / tau);
Matrix<Real> epsilon_v(dim, dim);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
- s.clear();
- sigma.clear();
+ s.zero();
+ sigma.zero();
/// Compute the first invariant of strain
Real gamma_inf = E_inf / this->E;
Real gamma_v = Ev / this->E;
auto epsilon_d = this->template gradUToEpsilon<dim>(grad_u);
Real Theta = epsilon_d.trace();
epsilon_v.eye(Theta / Real(3.));
epsilon_d -= epsilon_v;
Matrix<Real> U_rond_prim(dim, dim);
U_rond_prim.eye(gamma_inf * this->kpa * Theta);
- for (UInt i = 0; i < dim; ++i)
+ for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
s(i, j) = 2 * this->mu * epsilon_d(i, j);
h(i, j) = exp_dt_tau * h(i, j) + exp_dt_tau_2 * (s(i, j) - dev_s(i, j));
dev_s(i, j) = s(i, j);
sigma(i, j) = U_rond_prim(i, j) + gamma_inf * s(i, j) + gamma_v * h(i, j);
}
+ }
/// Save the deviator of stress
++stress_d;
++history_int;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
this->updateDissipatedEnergy(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::updateDissipatedEnergy(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
// if(ghost_type == _ghost) return 0.;
Real tau = 0.;
tau = eta / Ev;
Real * dis_energy = dissipated_energy(el_type, ghost_type).storage();
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d = stress_dev_vect.begin(dim, dim);
Array<Real>::matrix_iterator history_int = history_int_vect.begin(dim, dim);
Matrix<Real> q(dim, dim);
Matrix<Real> q_rate(dim, dim);
Matrix<Real> epsilon_d(dim, dim);
Matrix<Real> epsilon_v(dim, dim);
Real dt = this->model.getTimeStep();
Real gamma_v = Ev / this->E;
Real alpha = 1. / (2. * this->mu * gamma_v);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
/// Compute the first invariant of strain
this->template gradUToEpsilon<dim>(grad_u, epsilon_d);
Real Theta = epsilon_d.trace();
epsilon_v.eye(Theta / Real(3.));
epsilon_d -= epsilon_v;
q.copy(dev_s);
q -= h;
q *= gamma_v;
q_rate.copy(dev_s);
q_rate *= gamma_v;
q_rate -= q;
q_rate /= tau;
- for (UInt i = 0; i < dim; ++i)
- for (UInt j = 0; j < dim; ++j)
+ for (UInt i = 0; i < dim; ++i) {
+ for (UInt j = 0; j < dim; ++j) {
*dis_energy += (epsilon_d(i, j) - alpha * q(i, j)) * q_rate(i, j) * dt;
+ }
+ }
/// Save the deviator of stress
++stress_d;
++history_int;
++dis_energy;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialStandardLinearSolidDeviatoric<dim>::getDissipatedEnergy() const {
AKANTU_DEBUG_IN();
Real de = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type : this->element_filter.elementTypes(dim, _not_ghost)) {
de +=
this->fem.integrate(dissipated_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialStandardLinearSolidDeviatoric<dim>::getDissipatedEnergy(
ElementType type, UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
auto it =
this->dissipated_energy(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->fem.integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialStandardLinearSolidDeviatoric<dim>::getEnergy(
const std::string & type) {
- if (type == "dissipated")
+ if (type == "dissipated") {
return getDissipatedEnergy();
- else if (type == "dissipated_sls_deviatoric")
+ }
+ if (type == "dissipated_sls_deviatoric") {
return getDissipatedEnergy();
- else
- return MaterialElastic<dim>::getEnergy(type);
+ }
+ return MaterialElastic<dim>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialStandardLinearSolidDeviatoric<dim>::getEnergy(
const std::string & energy_id, ElementType type, UInt index) {
- if (energy_id == "dissipated")
+ if (energy_id == "dissipated") {
return getDissipatedEnergy(type, index);
- else if (energy_id == "dissipated_sls_deviatoric")
+ }
+ if (energy_id == "dissipated_sls_deviatoric") {
return getDissipatedEnergy(type, index);
- else
- return MaterialElastic<dim>::getEnergy(energy_id, type, index);
+ }
+ return MaterialElastic<dim>::getEnergy(energy_id, type, index);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(sls_deviatoric, MaterialStandardLinearSolidDeviatoric);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
index f08016f99..855f78c32 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
@@ -1,136 +1,136 @@
/**
* @file material_standard_linear_solid_deviatoric.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Vladislav Yastrebov <vladislav.yastrebov@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Material Visco-elastic, based on Standard Solid rheological model,
* see
* [] J.C. Simo, T.J.R. Hughes, "Computational Inelasticity", Springer (1998),
* see Sections 10.2 and 10.3
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH__
-#define __AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH__
+#ifndef AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH_
+#define AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH_
namespace akantu {
/**
* Material standard linear solid deviatoric
*
*
* @verbatim
E_\inf
------|\/\/\|------
| |
---| |---
| |
----|\/\/\|--[|----
E_v \eta
@endverbatim
*
* keyword : sls_deviatoric
*
* parameters in the material files :
* - E : Initial Young's modulus @f$ E = E_i + E_v @f$
* - eta : viscosity
* - Ev : stiffness of the viscous element
*/
template <UInt spatial_dimension>
class MaterialStandardLinearSolidDeviatoric
: public MaterialElastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialStandardLinearSolidDeviatoric(SolidMechanicsModel & model,
const ID & id = "");
~MaterialStandardLinearSolidDeviatoric() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// update the internal parameters (for modifiable parameters)
void updateInternalParameters() override;
/// set material to steady state
void setToSteadyState(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// update the dissipated energy, is called after the stress have been
/// computed
void updateDissipatedEnergy(ElementType el_type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy for the time step
Real getDissipatedEnergy() const;
Real getDissipatedEnergy(ElementType type, UInt index) const;
/// get the energy using an energy type string for the time step
Real getEnergy(const std::string & type) override;
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// viscosity, viscous elastic modulus
Real eta, Ev, E_inf;
Vector<Real> etas;
/// history of deviatoric stress
InternalField<Real> stress_dev;
/// Internal variable: history integral
InternalField<Real> history_integral;
/// Dissipated energy
InternalField<Real> dissipated_energy;
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH__ */
+#endif /* AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc b/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc
index 025f3087a..49cc92d7f 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc
@@ -1,729 +1,737 @@
/**
* @file material_viscoelastic_maxwell.hh
*
* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
*
* @date creation: Tue May 08 2018
* @date last modification: Tue May 08 2018
*
* @brief Material Visco-elastic, based on Maxwell chain,
* see
* [] R. de Borst and A.H. van den Boogaard "Finite-element modeling of
* deformation and cracking in early-age concrete", J.Eng.Mech., 1994
* as well as
* [] Manual of DIANA FEA Theory manual v.10.2 Section 37.6
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_viscoelastic_maxwell.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialViscoelasticMaxwell<spatial_dimension>::MaterialViscoelasticMaxwell(
SolidMechanicsModel & model, const ID & id)
: MaterialElastic<spatial_dimension>(model, id),
C(voigt_h::size, voigt_h::size), D(voigt_h::size, voigt_h::size),
sigma_v("sigma_v", *this), epsilon_v("epsilon_v", *this),
dissipated_energy("dissipated_energy", *this),
mechanical_work("mechanical_work", *this) {
AKANTU_DEBUG_IN();
this->registerParam("Einf", Einf, Real(1.), _pat_parsable | _pat_modifiable,
"Stiffness of the elastic element");
this->registerParam("previous_dt", previous_dt, Real(0.), _pat_readable,
"Time step of previous solveStep");
this->registerParam("Eta", Eta, _pat_parsable | _pat_modifiable,
"Viscosity of a Maxwell element");
this->registerParam("Ev", Ev, _pat_parsable | _pat_modifiable,
"Stiffness of a Maxwell element");
this->update_variable_flag = true;
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->use_previous_stress_thermal = true;
this->dissipated_energy.initialize(1);
this->mechanical_work.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
this->E = Einf + Ev.norm<L_1>();
// this->E = std::min(this->Einf, this->Ev(0));
MaterialElastic<spatial_dimension>::initMaterial();
AKANTU_DEBUG_ASSERT(this->Eta.size() == this->Ev.size(),
"Eta and Ev have different dimensions! Please correct.");
AKANTU_DEBUG_ASSERT(
!this->finite_deformation,
"Current material works only in infinitesimal deformations.");
UInt stress_size = spatial_dimension * spatial_dimension;
this->sigma_v.initialize(stress_size * this->Ev.size());
this->epsilon_v.initialize(stress_size * this->Ev.size());
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<
spatial_dimension>::updateInternalParameters() {
MaterialElastic<spatial_dimension>::updateInternalParameters();
Real pre_mult = 1 / (1 + this->nu) / (1 - 2 * this->nu);
UInt n = voigt_h::size;
Real Miiii = pre_mult * (1 - this->nu);
Real Miijj = pre_mult * this->nu;
Real Mijij = pre_mult * 0.5 * (1 - 2 * this->nu);
Real Diiii = 1;
Real Diijj = -this->nu;
Real Dijij = (2 + 2 * this->nu);
if (spatial_dimension == 1) {
C(0, 0) = 1;
D(0, 0) = 1;
} else {
C(0, 0) = Miiii;
D(0, 0) = Diiii;
}
if (spatial_dimension >= 2) {
C(1, 1) = Miiii;
C(0, 1) = Miijj;
C(1, 0) = Miijj;
C(n - 1, n - 1) = Mijij;
D(1, 1) = Diiii;
D(0, 1) = Diijj;
D(1, 0) = Diijj;
D(n - 1, n - 1) = Dijij;
}
if (spatial_dimension == 3) {
C(2, 2) = Miiii;
C(0, 2) = Miijj;
C(1, 2) = Miijj;
C(2, 0) = Miijj;
C(2, 1) = Miijj;
C(3, 3) = Mijij;
C(4, 4) = Mijij;
D(2, 2) = Diiii;
D(0, 2) = Diijj;
D(1, 2) = Diijj;
D(2, 0) = Diijj;
D(2, 1) = Diijj;
D(3, 3) = Dijij;
D(4, 4) = Dijij;
}
}
/* -------------------------------------------------------------------------- */
template <> void MaterialViscoelasticMaxwell<2>::updateInternalParameters() {
MaterialElastic<2>::updateInternalParameters();
Real pre_mult = 1 / (1 + this->nu) / (1 - 2 * this->nu);
UInt n = voigt_h::size;
Real Miiii = pre_mult * (1 - this->nu);
Real Miijj = pre_mult * this->nu;
Real Mijij = pre_mult * 0.5 * (1 - 2 * this->nu);
Real Diiii = 1;
Real Diijj = -this->nu;
Real Dijij = (2 + 2 * this->nu);
C(0, 0) = Miiii;
C(1, 1) = Miiii;
C(0, 1) = Miijj;
C(1, 0) = Miijj;
C(n - 1, n - 1) = Mijij;
D(0, 0) = Diiii;
D(1, 1) = Diiii;
D(0, 1) = Diijj;
D(1, 0) = Diijj;
D(n - 1, n - 1) = Dijij;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
+ // NOLINTNEXTLINE(bugprone-parent-virtual-call)
MaterialThermal<spatial_dimension>::computeStress(el_type, ghost_type);
auto sigma_th_it = this->sigma_th(el_type, ghost_type).begin();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto sigma_v_it =
this->sigma_v(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, *previous_gradu_it, sigma, *sigma_v_it,
*sigma_th_it);
++sigma_th_it;
++previous_gradu_it;
++sigma_v_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, Tensor3<Real> & sigma_v, const Real & sigma_th) {
// Wikipedia convention:
// 2*eps_ij (i!=j) = voigt_eps_I
// http://en.wikipedia.org/wiki/Voigt_notation
Vector<Real> voigt_current_strain(voigt_h::size);
Vector<Real> voigt_previous_strain(voigt_h::size);
Vector<Real> voigt_stress(voigt_h::size);
Vector<Real> voigt_sigma_v(voigt_h::size);
for (UInt I = 0; I < voigt_h::size; ++I) {
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_current_strain(I) = voigt_factor * (grad_u(i, j) + grad_u(j, i)) / 2.;
voigt_previous_strain(I) =
voigt_factor * (previous_grad_u(i, j) + previous_grad_u(j, i)) / 2.;
}
voigt_stress = this->Einf * this->C * voigt_current_strain;
Real dt = this->model.getTimeStep();
for (UInt k = 0; k < Eta.size(); ++k) {
Real lambda = this->Eta(k) / this->Ev(k);
Real exp_dt_lambda = exp(-dt / lambda);
Real E_additional;
if (exp_dt_lambda == 1) {
E_additional = this->Ev(k);
} else {
E_additional = (1 - exp_dt_lambda) * this->Ev(k) * lambda / dt;
}
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_sigma_v(I) = sigma_v(i, j, k);
}
voigt_stress += E_additional * this->C *
(voigt_current_strain - voigt_previous_strain) +
exp_dt_lambda * voigt_sigma_v;
}
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
- sigma(i, j) = sigma(j, i) = voigt_stress(I) + (i == j) * sigma_th;
+ sigma(i, j) = sigma(j, i) =
+ voigt_stress(I) + Math::kronecker(i, j) * sigma_th;
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computePotentialEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
+ // NOLINTNEXTLINE(bugprone-parent-virtual-call)
MaterialThermal<spatial_dimension>::computePotentialEnergy(el_type);
auto epot = this->potential_energy(el_type).begin();
auto sigma_v_it = this->sigma_v(el_type).begin(
spatial_dimension, spatial_dimension, this->Eta.size());
auto epsilon_v_it = this->epsilon_v(el_type).begin(
spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
this->computePotentialEnergyOnQuad(grad_u, *epot, *sigma_v_it, *epsilon_v_it);
++epot;
++sigma_v_it;
++epsilon_v_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::
computePotentialEnergyOnQuad(const Matrix<Real> & grad_u, Real & epot,
Tensor3<Real> & sigma_v,
Tensor3<Real> & epsilon_v) {
Vector<Real> voigt_strain(voigt_h::size);
Vector<Real> voigt_stress(voigt_h::size);
Vector<Real> voigt_sigma_v(voigt_h::size);
for (UInt I = 0; I < voigt_h::size; ++I) {
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_strain(I) = voigt_factor * (grad_u(i, j) + grad_u(j, i)) / 2.;
}
voigt_stress = this->Einf * this->C * voigt_strain;
epot = 0.5 * voigt_stress.dot(voigt_strain);
for (UInt k = 0; k < this->Eta.size(); ++k) {
Matrix<Real> stress_v = sigma_v(k);
Matrix<Real> strain_v = epsilon_v(k);
epot += 0.5 * stress_v.doubleDot(strain_v);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
-void MaterialViscoelasticMaxwell<spatial_dimension>::afterSolveStep(bool converged) {
+void MaterialViscoelasticMaxwell<spatial_dimension>::afterSolveStep(
+ bool converged) {
Material::afterSolveStep(converged);
- if(not converged) return;
+ if (not converged) {
+ return;
+ }
for (auto & el_type : this->element_filter.elementTypes(
_all_dimensions, _not_ghost, _ek_not_defined)) {
if (this->update_variable_flag) {
auto previous_gradu_it = this->gradu.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto sigma_v_it =
this->sigma_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
auto epsilon_v_it =
this->epsilon_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
updateIntVarOnQuad(grad_u, *previous_gradu_it, *sigma_v_it,
*epsilon_v_it);
++previous_gradu_it;
++sigma_v_it;
++epsilon_v_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
this->updateDissipatedEnergy(el_type);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::updateIntVarOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Tensor3<Real> & sigma_v, Tensor3<Real> & epsilon_v) {
Matrix<Real> grad_delta_u(grad_u);
grad_delta_u -= previous_grad_u;
Real dt = this->model.getTimeStep();
Vector<Real> voigt_delta_strain(voigt_h::size);
for (UInt I = 0; I < voigt_h::size; ++I) {
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_delta_strain(I) =
voigt_factor * (grad_delta_u(i, j) + grad_delta_u(j, i)) / 2.;
}
for (UInt k = 0; k < this->Eta.size(); ++k) {
Real lambda = this->Eta(k) / this->Ev(k);
Real exp_dt_lambda = exp(-dt / lambda);
Real E_ef_v;
if (exp_dt_lambda == 1) {
E_ef_v = this->Ev(k);
} else {
E_ef_v = (1 - exp_dt_lambda) * this->Ev(k) * lambda / dt;
}
Vector<Real> voigt_sigma_v(voigt_h::size);
Vector<Real> voigt_epsilon_v(voigt_h::size);
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_sigma_v(I) = sigma_v(i, j, k);
}
voigt_sigma_v =
exp_dt_lambda * voigt_sigma_v + E_ef_v * this->C * voigt_delta_strain;
voigt_epsilon_v = 1 / Ev(k) * this->D * voigt_sigma_v;
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
sigma_v(i, j, k) = sigma_v(j, i, k) = voigt_sigma_v(I);
epsilon_v(i, j, k) = epsilon_v(j, i, k) = voigt_epsilon_v(I);
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computeTangentModuli(
- const ElementType & el_type, Array<Real> & tangent_matrix,
- GhostType ghost_type) {
+ ElementType el_type, Array<Real> & tangent_matrix, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real dt = this->model.getTimeStep();
Real E_ef = this->Einf;
for (UInt k = 0; k < Eta.size(); ++k) {
Real lambda = this->Eta(k) / this->Ev(k);
Real exp_dt_lambda = exp(-dt / lambda);
if (exp_dt_lambda == 1) {
E_ef += this->Ev(k);
} else {
E_ef += (1 - exp_dt_lambda) * this->Ev(k) * lambda / dt;
}
}
this->previous_dt = dt;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
tangent_matrix *= E_ef;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computeTangentModuliOnQuad(
Matrix<Real> & tangent) {
tangent.copy(C);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::savePreviousState() {
for (auto & el_type : this->element_filter.elementTypes(
_all_dimensions, _not_ghost, _ek_not_defined)) {
auto sigma_th_it = this->sigma_th(el_type, _not_ghost).begin();
auto previous_sigma_th_it =
this->sigma_th.previous(el_type, _not_ghost).begin();
auto previous_gradu_it = this->gradu.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto previous_sigma_it = this->stress.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto sigma_v_it =
this->sigma_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_sigma_it;
previous_grad_u.copy(grad_u);
previous_sigma.copy(sigma);
*previous_sigma_th_it = *sigma_th_it;
++previous_gradu_it, ++previous_sigma_it, ++previous_sigma_th_it,
++sigma_v_it, ++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::updateIntVariables() {
for (auto & el_type : this->element_filter.elementTypes(
_all_dimensions, _not_ghost, _ek_not_defined)) {
auto previous_gradu_it = this->gradu.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto previous_sigma_it = this->stress.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto sigma_v_it =
this->sigma_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
auto epsilon_v_it =
this->epsilon_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
updateIntVarOnQuad(grad_u, *previous_gradu_it, *sigma_v_it, *epsilon_v_it);
++previous_gradu_it;
++sigma_v_it;
++epsilon_v_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::updateDissipatedEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
this->computePotentialEnergy(el_type);
auto epot = this->potential_energy(el_type).begin();
auto dis_energy = this->dissipated_energy(el_type).begin();
auto mech_work = this->mechanical_work(el_type).begin();
auto sigma_v_it = this->sigma_v(el_type).begin(
spatial_dimension, spatial_dimension, this->Eta.size());
auto epsilon_v_it = this->epsilon_v(el_type).begin(
spatial_dimension, spatial_dimension, this->Eta.size());
auto previous_gradu_it =
this->gradu.previous(el_type).begin(spatial_dimension, spatial_dimension);
auto previous_sigma_it = this->stress.previous(el_type).begin(
spatial_dimension, spatial_dimension);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
updateDissipatedEnergyOnQuad(grad_u, *previous_gradu_it, sigma,
*previous_sigma_it, *dis_energy, *mech_work,
*epot);
++previous_gradu_it;
++previous_sigma_it;
++dis_energy;
++mech_work;
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::
updateDissipatedEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
const Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma,
Real & dis_energy, Real & mech_work,
const Real & pot_energy) {
Real dt = this->model.getTimeStep();
Matrix<Real> strain_rate = grad_u;
strain_rate -= previous_grad_u;
strain_rate /= dt;
Matrix<Real> av_stress = sigma;
av_stress += previous_sigma;
av_stress /= 2;
mech_work += av_stress.doubleDot(strain_rate) * dt;
dis_energy = mech_work - pot_energy;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getDissipatedEnergy()
const {
AKANTU_DEBUG_IN();
Real de = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
de +=
this->fem.integrate(this->dissipated_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getDissipatedEnergy(
ElementType type, UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
auto it =
this->dissipated_energy(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->fem.integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getMechanicalWork() const {
AKANTU_DEBUG_IN();
Real mw = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
mw +=
this->fem.integrate(this->mechanical_work(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return mw;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getMechanicalWork(
ElementType type, UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
auto it = this->mechanical_work(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->fem.integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getPotentialEnergy()
const {
AKANTU_DEBUG_IN();
Real epot = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
epot +=
this->fem.integrate(this->potential_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getPotentialEnergy(
ElementType type, UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
auto it =
this->potential_energy(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->fem.integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getEnergy(
const std::string & type) {
- if (type == "dissipated")
+ if (type == "dissipated") {
return getDissipatedEnergy();
- else if (type == "potential")
+ }
+ if (type == "potential") {
return getPotentialEnergy();
- else if (type == "work")
+ }
+ if (type == "work") {
return getMechanicalWork();
- else
- return MaterialElastic<spatial_dimension>::getEnergy(type);
+ }
+ return MaterialElastic<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getEnergy(
const std::string & energy_id, ElementType type, UInt index) {
- if (energy_id == "dissipated")
+ if (energy_id == "dissipated") {
return getDissipatedEnergy(type, index);
- else if (energy_id == "potential")
+ }
+ if (energy_id == "potential") {
return getPotentialEnergy(type, index);
- else if (energy_id == "work")
+ }
+ if (energy_id == "work") {
return getMechanicalWork(type, index);
- else
- return MaterialElastic<spatial_dimension>::getEnergy(energy_id, type,
- index);
+ }
+ return MaterialElastic<spatial_dimension>::getEnergy(energy_id, type, index);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::forceUpdateVariable() {
update_variable_flag = true;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::forceNotUpdateVariable() {
update_variable_flag = false;
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(viscoelastic_maxwell, MaterialViscoelasticMaxwell);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh b/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh
index 6fef719dc..693bee468 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh
@@ -1,229 +1,229 @@
/**
* @file material_viscoelastic_maxwell.hh
*
* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
*
* @date creation: Tue May 08 2018
* @date last modification: Tue May 08 2018
*
* @brief Material Visco-elastic, based on Maxwell chain,
* see
* [] R. de Borst and A.H. van den Boogaard "Finite-element modeling of
* deformation and cracking in early-age concrete", J.Eng.Mech., 1994
* as well as
* [] Manual of DIANA FEA Theory manual v.10.2 Section 37.6
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_VISCOELASTIC_MAXWELL_HH__
-#define __AKANTU_MATERIAL_VISCOELASTIC_MAXWELL_HH__
+#ifndef AKANTU_MATERIAL_VISCOELASTIC_MAXWELL_HH_
+#define AKANTU_MATERIAL_VISCOELASTIC_MAXWELL_HH_
namespace akantu {
/**
* Material Viscoelastic based on Maxwell chain
*
*
* @verbatim
E_0
------|\/\/\|-------
| |
---| |---
| |
----|\/\/\|--[|-----
| E_v1 \Eta_1|
---| |---
| |
----|\/\/\|--[|-----
| E_v2 \Eta_2 |
---| |---
| |
----|\/\/\|--[|----
E_vN \Eta_N
@endverbatim
*
* keyword : viscoelastic_maxwell
*
* parameters in the material files :
* - N : number of Maxwell elements
* - Einf : one spring element stiffness
* - Ev1 : stiffness of the 1st viscous element
* - Eta1: viscosity of the 1st Maxwell element
* ...
* - Ev<N> : stiffness of the Nst viscous element
* - Eta<N>: viscosity of the Nst Maxwell element
*/
template <UInt spatial_dimension>
class MaterialViscoelasticMaxwell : public MaterialElastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialViscoelasticMaxwell(SolidMechanicsModel & model, const ID & id = "");
~MaterialViscoelasticMaxwell() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// recompute the lame coefficient and effective tangent moduli
void updateInternalParameters() override;
/// update internal variable on a converged Newton
void afterSolveStep(bool converged) override;
/// update internal variable based on previous and current strain values
void updateIntVariables();
/// update the internal variable sigma_v on quadrature point
void updateIntVarOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
Tensor3<Real> & sigma_v, Tensor3<Real> & epsilon_v);
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
- void computeTangentModuli(const ElementType & el_type,
+ void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// save previous stress and strain values into "previous" arrays
void savePreviousState() override;
/// change flag of updateIntVar to true
void forceUpdateVariable();
/// change flag of updateIntVar to false
void forceNotUpdateVariable();
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type) override;
protected:
void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u, Real & epot,
Tensor3<Real> & sigma_v,
Tensor3<Real> & epsilon_v);
/// update the dissipated energy, is called after the stress have been
/// computed
void updateDissipatedEnergy(ElementType el_type);
void updateDissipatedEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
const Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma,
Real & dis_energy, Real & mech_work,
const Real & pot_energy);
/// compute stresses on a quadrature point
void computeStressOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, Tensor3<Real> & sigma_v,
const Real & sigma_th);
/// compute tangent moduli on a quadrature point
void computeTangentModuliOnQuad(Matrix<Real> & tangent);
bool hasStiffnessMatrixChanged() override {
Real dt = this->model.getTimeStep();
return ((this->previous_dt == dt)
? (!(this->previous_dt == dt)) * (this->was_stiffness_assembled)
: (!(this->previous_dt == dt)));
// return (!(this->previous_dt == dt));
}
MatrixType getTangentType() override {
return _symmetric;
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy
Real getDissipatedEnergy() const;
Real getDissipatedEnergy(ElementType type, UInt index) const;
/// get the potential energy
Real getPotentialEnergy() const;
Real getPotentialEnergy(ElementType type, UInt index) const;
/// get the potential energy
Real getMechanicalWork() const;
Real getMechanicalWork(ElementType type, UInt index) const;
/// get the energy using an energy type string for the time step
Real getEnergy(const std::string & type) override;
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
using voigt_h = VoigtHelper<spatial_dimension>;
/// Vectors of viscosity, viscous elastic modulus, one spring element elastic
/// modulus
Vector<Real> Eta;
Vector<Real> Ev;
Real Einf;
/// time step from previous solveStep
Real previous_dt;
/// Stiffness matrix template
Matrix<Real> C;
/// Compliance matrix template
Matrix<Real> D;
/// Internal variable: viscous_stress
InternalField<Real> sigma_v;
/// Internal variable: spring strain in Maxwell element
InternalField<Real> epsilon_v;
/// Dissipated energy
InternalField<Real> dissipated_energy;
/// Mechanical work
InternalField<Real> mechanical_work;
/// Update internal variable after solve step or not
bool update_variable_flag;
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_VISCOELASTIC_MAXWELL_HH__ */
+#endif /* AKANTU_MATERIAL_VISCOELASTIC_MAXWELL_HH_ */
diff --git a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
index 79e8e27cf..27001f495 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
@@ -1,102 +1,103 @@
/**
* @file plane_stress_toolbox.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 16 2014
* @date last modification: Tue Feb 20 2018
*
* @brief Tools to implement the plane stress behavior in a material
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PLANE_STRESS_TOOLBOX_HH__
-#define __AKANTU_PLANE_STRESS_TOOLBOX_HH__
+#ifndef AKANTU_PLANE_STRESS_TOOLBOX_HH_
+#define AKANTU_PLANE_STRESS_TOOLBOX_HH_
namespace akantu {
class SolidMechanicsModel;
class FEEngine;
} // namespace akantu
namespace akantu {
/**
* Empty class in dimensions different from 2
* This class is only specialized for 2D in the tmpl file
*/
template <UInt dim, class ParentMaterial = Material>
class PlaneStressToolbox : public ParentMaterial {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PlaneStressToolbox(SolidMechanicsModel & model, const ID & id = "")
: ParentMaterial(model, id) {}
PlaneStressToolbox(SolidMechanicsModel & model, UInt spatial_dimension,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "")
: ParentMaterial(model, spatial_dimension, mesh, fe_engine, id) {}
~PlaneStressToolbox() override = default;
protected:
void initialize();
public:
void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) override {
ParentMaterial::computeAllCauchyStresses(ghost_type);
}
virtual void computeCauchyStressPlaneStress(ElementType /*el_type*/,
GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
AKANTU_ERROR("The function \"computeCauchyStressPlaneStress\" can "
"only be used in 2D Plane stress problems, which means "
"that you made a mistake somewhere!! ");
AKANTU_DEBUG_OUT();
}
- virtual void computeThirdAxisDeformation(ElementType, GhostType) {}
+ virtual void computeThirdAxisDeformation(ElementType /*unused*/,
+ GhostType /*unused*/) {}
protected:
bool initialize_third_axis_deformation{false};
};
#define AKANTU_PLANE_STRESS_TOOL_SPEC(dim) \
template <> \
inline PlaneStressToolbox<dim, Material>::PlaneStressToolbox( \
SolidMechanicsModel & model, const ID & id) \
: Material(model, id) {}
AKANTU_PLANE_STRESS_TOOL_SPEC(1)
AKANTU_PLANE_STRESS_TOOL_SPEC(3)
} // namespace akantu
#include "plane_stress_toolbox_tmpl.hh"
-#endif /* __AKANTU_PLANE_STRESS_TOOLBOX_HH__ */
+#endif /* AKANTU_PLANE_STRESS_TOOLBOX_HH_ */
diff --git a/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh b/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
index 3462a712c..6c6d3a7f4 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
@@ -1,163 +1,165 @@
/**
* @file plane_stress_toolbox_tmpl.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Tue Sep 16 2014
* @date last modification: Wed Nov 08 2017
*
* @brief 2D specialization of the akantu::PlaneStressToolbox class
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH__
-#define __AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH__
+#ifndef AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH_
+#define AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class ParentMaterial>
class PlaneStressToolbox<2, ParentMaterial> : public ParentMaterial {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PlaneStressToolbox(SolidMechanicsModel & model, const ID & id = "");
PlaneStressToolbox(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
~PlaneStressToolbox() override = default;
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ThirdAxisDeformation,
third_axis_deformation, Real);
protected:
void initialize() {
this->registerParam("Plane_Stress", plane_stress, false, _pat_parsmod,
"Is plane stress");
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
void initMaterial() override {
ParentMaterial::initMaterial();
if (this->plane_stress && this->initialize_third_axis_deformation) {
this->third_axis_deformation.initialize(1);
this->third_axis_deformation.resize();
}
}
/* ------------------------------------------------------------------------ */
void computeStress(ElementType el_type, GhostType ghost_type) override {
ParentMaterial::computeStress(el_type, ghost_type);
- if (this->plane_stress)
+ if (this->plane_stress) {
computeThirdAxisDeformation(el_type, ghost_type);
+ }
}
/* ------------------------------------------------------------------------ */
- virtual void computeThirdAxisDeformation(ElementType, GhostType) {}
+ virtual void computeThirdAxisDeformation(ElementType /*unused*/,
+ GhostType /*unused*/) {}
/// Computation of Cauchy stress tensor in the case of finite deformation
void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) override {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
AKANTU_DEBUG_ASSERT(this->finite_deformation,
"The Cauchy stress can only be computed if you are "
"working in finite deformation.");
for (auto & type : this->fem.getMesh().elementTypes(2, ghost_type)) {
this->computeCauchyStressPlaneStress(type, ghost_type);
}
} else {
ParentMaterial::computeAllCauchyStresses(ghost_type);
}
AKANTU_DEBUG_OUT();
}
virtual void
computeCauchyStressPlaneStress(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost){};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// third axis strain measure value
InternalField<Real> third_axis_deformation;
/// Plane stress or plane strain
bool plane_stress;
/// For non linear materials, the \f[\epsilon_{zz}\f] might be required
bool initialize_third_axis_deformation;
};
template <class ParentMaterial>
inline PlaneStressToolbox<2, ParentMaterial>::PlaneStressToolbox(
SolidMechanicsModel & model, const ID & id)
: ParentMaterial(model, id),
third_axis_deformation("third_axis_deformation", *this),
plane_stress(false), initialize_third_axis_deformation(false) {
/// @todo Plane_Stress should not be possible to be modified after
/// initMaterial (but before)
this->initialize();
}
template <class ParentMaterial>
inline PlaneStressToolbox<2, ParentMaterial>::PlaneStressToolbox(
SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: ParentMaterial(model, dim, mesh, fe_engine, id),
third_axis_deformation("third_axis_deformation", *this, dim, fe_engine,
this->element_filter),
plane_stress(false), initialize_third_axis_deformation(false) {
this->initialize();
}
template <>
inline PlaneStressToolbox<2, Material>::PlaneStressToolbox(
SolidMechanicsModel & model, const ID & id)
: Material(model, id),
third_axis_deformation("third_axis_deformation", *this),
plane_stress(false), initialize_third_axis_deformation(false) {
/// @todo Plane_Stress should not be possible to be modified after
/// initMaterial (but before)
this->registerParam("Plane_Stress", plane_stress, false, _pat_parsmod,
"Is plane stress");
}
} // namespace akantu
-#endif /* __AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH__ */
+#endif /* AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/random_internal_field.hh b/src/model/solid_mechanics/materials/random_internal_field.hh
index f8a2592c7..e615356ac 100644
--- a/src/model/solid_mechanics/materials/random_internal_field.hh
+++ b/src/model/solid_mechanics/materials/random_internal_field.hh
@@ -1,103 +1,103 @@
/**
* @file random_internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Random internal material parameter
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "internal_field.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_RANDOM_INTERNAL_FIELD_HH__
-#define __AKANTU_RANDOM_INTERNAL_FIELD_HH__
+#ifndef AKANTU_RANDOM_INTERNAL_FIELD_HH_
+#define AKANTU_RANDOM_INTERNAL_FIELD_HH_
namespace akantu {
/**
* class for the internal fields of materials with a random
* distribution
*/
template <typename T, template <typename> class BaseField = InternalField,
template <typename> class Generator = RandomGenerator>
class RandomInternalField : public BaseField<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
RandomInternalField(const ID & id, Material & material);
~RandomInternalField() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
RandomInternalField operator=(const RandomInternalField &) = delete;
public:
- AKANTU_GET_MACRO(RandomParameter, random_parameter, const RandomParameter<T>);
+ AKANTU_GET_MACRO(RandomParameter, random_parameter, const RandomParameter<T>&);
/// initialize the field to a given number of component
void initialize(UInt nb_component) override;
/// set the field to a given value
void setDefaultValue(const T & value) override;
/// set the specified random distribution to a given parameter
void setRandomDistribution(const RandomParameter<T> & param);
/// print the content
void printself(std::ostream & stream, int indent = 0) const override;
protected:
void setArrayValues(T * begin, T * end) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline operator Real() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// random parameter containing the distribution and base value
RandomParameter<T> random_parameter;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const RandomInternalField<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AKANTU_RANDOM_INTERNAL_FIELD_HH__ */
+#endif /* AKANTU_RANDOM_INTERNAL_FIELD_HH_ */
diff --git a/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh b/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
index 16181587c..2ecbe586b 100644
--- a/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
@@ -1,124 +1,124 @@
/**
* @file random_internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Feb 08 2018
*
* @brief Random internal material parameter implementation
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH__
-#define __AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH__
+#ifndef AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH_
+#define AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
RandomInternalField<T, BaseField, Generator>::RandomInternalField(
const ID & id, Material & material)
: BaseField<T>(id, material), random_parameter(T()) {}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
RandomInternalField<T, BaseField, Generator>::~RandomInternalField() = default;
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::initialize(
UInt nb_component) {
this->internalInitialize(nb_component);
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setDefaultValue(
const T & value) {
random_parameter.setBaseValue(value);
this->reset();
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setRandomDistribution(
const RandomParameter<T> & param) {
random_parameter = param;
this->reset();
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::printself(
std::ostream & stream, int indent [[gnu::unused]]) const {
stream << "RandomInternalField [ ";
random_parameter.printself(stream);
stream << " ]";
#if !defined(AKANTU_NDEBUG)
if (AKANTU_DEBUG_TEST(dblDump)) {
stream << std::endl;
InternalField<T>::printself(stream, indent);
}
#endif
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setArrayValues(T * begin,
T * end) {
random_parameter.template setValues<Generator>(begin, end);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
inline RandomInternalField<T, BaseField, Generator>::operator Real() const {
return random_parameter.getBaseValue();
}
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<RandomInternalField<Real>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH__ */
+#endif /* AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
index 754bf5431..a7fe4da1b 100644
--- a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
@@ -1,79 +1,79 @@
/**
* @file damaged_weight_function.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Damaged weight function for non local materials
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DAMAGED_WEIGHT_FUNCTION_HH__
-#define __AKANTU_DAMAGED_WEIGHT_FUNCTION_HH__
+#ifndef AKANTU_DAMAGED_WEIGHT_FUNCTION_HH_
+#define AKANTU_DAMAGED_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Damage weight function */
/* -------------------------------------------------------------------------- */
class DamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
DamagedWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "damaged"), damage(nullptr) {
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
/// set the pointers of internals to the right flattend version
void init() override;
inline Real operator()(Real r,
const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2);
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// internal pointer to the current damage vector
ElementTypeMapReal * damage;
};
} // namespace akantu
#include "damaged_weight_function_inline_impl.hh"
-#endif /* __AKANTU_DAMAGED_WEIGHT_FUNCTION_HH__ */
+#endif /* AKANTU_DAMAGED_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
index 660f55234..f388bd420 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
@@ -1,95 +1,95 @@
/**
* @file remove_damaged_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Wed Nov 08 2017
*
* @brief Removed damaged weight function for non local materials
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH__
-#define __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH__
+#ifndef AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH_
+#define AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Remove damaged weight function */
/* -------------------------------------------------------------------------- */
class RemoveDamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
RemoveDamagedWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "remove_damaged"), damage(nullptr) {
this->registerParam("damage_limit", this->damage_limit, 1., _pat_parsable,
"Damage Threshold");
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
inline void init() override;
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2);
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// limit at which a point is considered as complitely broken
Real damage_limit;
/// internal pointer to the current damage vector
ElementTypeMapReal * damage;
};
} // namespace akantu
#include "remove_damaged_weight_function_inline_impl.hh"
-#endif /* __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH__ */
+#endif /* AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.hh
index debb5667f..f76ef07f1 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.hh
@@ -1,103 +1,105 @@
/**
* @file remove_damaged_weight_function_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Thu Jul 06 2017
*
* @brief Implementation of inline function of remove damaged weight function
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "remove_damaged_weight_function.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_HH__
-#define __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_HH__
+#ifndef AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_HH_
+#define AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline Real RemoveDamagedWeightFunction::
operator()(Real r, const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2) {
/// compute the weight
UInt quad = q2.global_num;
- if (q1 == q2)
+ if (q1 == q2) {
return 1.;
+ }
Array<Real> & dam_array = (*this->damage)(q2.type, q2.ghost_type);
Real D = dam_array(quad);
Real w = 0.;
if (D < damage_limit * (1 - Math::getTolerance())) {
Real alpha = std::max(0., 1. - r * r / this->R2);
w = alpha * alpha;
}
return w;
}
/* -------------------------------------------------------------------------- */
inline void RemoveDamagedWeightFunction::init() {
this->damage = &(this->manager.registerWeightFunctionInternal("damage"));
}
/* -------------------------------------------------------------------------- */
inline UInt
RemoveDamagedWeightFunction::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
- if (tag == SynchronizationTag::_mnl_weight)
+ if (tag == SynchronizationTag::_mnl_weight) {
return this->manager.getModel().getNbIntegrationPoints(elements) *
sizeof(Real);
+ }
return 0;
}
/* -------------------------------------------------------------------------- */
inline void
RemoveDamagedWeightFunction::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_mnl_weight) {
DataAccessor<Element>::packElementalDataHelper<Real>(
*damage, buffer, elements, true,
this->manager.getModel().getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
inline void
RemoveDamagedWeightFunction::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == SynchronizationTag::_mnl_weight) {
DataAccessor<Element>::unpackElementalDataHelper<Real>(
*damage, buffer, elements, true,
this->manager.getModel().getFEEngine());
}
}
} // namespace akantu
-#endif /* __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_HH__ */
+#endif /* AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
index 07ccb80d3..401660b6d 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
@@ -1,82 +1,82 @@
/**
* @file remove_damaged_with_damage_rate_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Removed damaged weight function for non local materials
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH__
-#define __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH__
+#ifndef AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH_
+#define AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Remove damaged with damage rate weight function */
/* -------------------------------------------------------------------------- */
class RemoveDamagedWithDamageRateWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
RemoveDamagedWithDamageRateWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "remove_damage_with_damage_rate"),
damage_with_damage_rate(nullptr) {
this->registerParam<Real>("damage_limit",
this->damage_limit_with_damage_rate, 1,
_pat_parsable, "Damage Threshold");
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
inline Real operator()(Real r,
const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2);
inline void init() override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// limit at which a point is considered as complitely broken
Real damage_limit_with_damage_rate;
/// internal pointer to the current damage vector
ElementTypeMapReal * damage_with_damage_rate;
};
} // namespace akantu
#include "remove_damaged_with_damage_rate_weight_function_inline_impl.hh"
-#endif /* __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_WEIGHT_FUNCTION_HH__ */
+#endif /* AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.hh
index 2ba79119b..4ff028a57 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.hh
@@ -1,66 +1,67 @@
/**
* @file remove_damaged_with_damage_rate_weight_function_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Wed Feb 03 2016
*
* @brief Implementation of inline function of remove damaged with
* damage rate weight function
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "remove_damaged_with_damage_rate_weight_function.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void RemoveDamagedWithDamageRateWeightFunction::init() {
this->damage_with_damage_rate =
&(this->manager.registerWeightFunctionInternal("damage-rate"));
}
/* -------------------------------------------------------------------------- */
inline Real RemoveDamagedWithDamageRateWeightFunction::operator()(
Real r, const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2) {
/// compute the weight
UInt quad = q2.global_num;
- if (q1.global_num == quad)
+ if (q1.global_num == quad) {
return 1.;
+ }
Array<Real> & dam_array =
(*this->damage_with_damage_rate)(q2.type, q2.ghost_type);
Real D = dam_array(quad);
Real w = 0.;
Real alphaexp = 1.;
Real betaexp = 2.;
if (D < damage_limit_with_damage_rate) {
Real alpha = std::max(0., 1. - pow((r * r / this->R2), alphaexp));
w = pow(alpha, betaexp);
}
return w;
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
index 2e39f8046..9af580897 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
@@ -1,98 +1,98 @@
/**
* @file stress_based_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Wed Nov 08 2017
*
* @brief Removed damaged weight function for non local materials
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__
-#define __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__
+#ifndef AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH_
+#define AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Stress Based Weight */
/* -------------------------------------------------------------------------- */
/// based on based on Giry et al.: Stress-based nonlocal damage model,
/// IJSS, 48, 2011
class StressBasedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
StressBasedWeightFunction(NonLocalManager & manager);
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
void init() override;
inline void updateInternals() override;
void updatePrincipalStress(GhostType ghost_type);
inline void updateQuadraturePointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates);
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2);
/// computation of ellipsoid
inline Real computeRhoSquare(Real r, Vector<Real> & eigs,
Matrix<Real> & eigenvects, Vector<Real> & x_s);
protected:
inline void setInternal();
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// tensile strength
Real ft;
/// prinicipal stresses
ElementTypeMapReal * stress_diag;
/// for preselection of types (optimization)
ElementTypeMapReal * selected_stress_diag;
/// principal directions
ElementTypeMapReal * stress_base;
/// lenght intrinisic to the material
ElementTypeMapReal * characteristic_size;
};
} // namespace akantu
#include "stress_based_weight_function_inline_impl.hh"
-#endif /* __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__ */
+#endif /* AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.hh b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.hh
index f00ac30c4..248b9826e 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.hh
@@ -1,196 +1,194 @@
/**
* @file stress_based_weight_function_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Apr 13 2012
* @date last modification: Wed Feb 03 2016
*
* @brief Implementation of inline function of remove damaged with
* damage rate weight function
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "stress_based_weight_function.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void StressBasedWeightFunction::updateInternals() {
// updatePrincipalStress(_not_ghost);
// updatePrincipalStress(_ghost);
}
/* -------------------------------------------------------------------------- */
// inline void StressBasedWeightFunction::selectType(ElementType type1,
// GhostType ghost_type1,
// ElementType type2,
// GhostType ghost_type2) {
// selected_stress_diag = &stress_diag(type2, ghost_type2);
// selected_stress_base = &stress_base(type2, ghost_type2);
// selected_characteristic_size = &characteristic_size(type1, ghost_type1);
// }
/* -------------------------------------------------------------------------- */
-inline Real StressBasedWeightFunction::computeRhoSquare(
- __attribute__((unused)) Real r, __attribute__((unused)) Vector<Real> & eigs,
- __attribute__((unused)) Matrix<Real> & eigenvects,
- __attribute__((unused)) Vector<Real> & x_s) {
+inline Real StressBasedWeightFunction::
+ computeRhoSquare( // NOLINT(readability-convert-member-functions-to-static)
+ Real /*r*/, Vector<Real> & /*eigs*/, Matrix<Real> & /*eigenvects*/,
+ Vector<Real> & /*x_s*/) {
// if (spatial_dimension == 1)
// return eigs[0];
// else if (spatial_dimension == 2) {
// Vector<Real> u1(eigenvects.storage(), 2);
// Real cos_t = x_s.dot(u1) / (x_s.norm() * u1.norm());
// Real cos_t_2;
// Real sin_t_2;
// Real sigma1_2 = eigs[0]*eigs[0];
// Real sigma2_2 = eigs[1]*eigs[1];
// #ifdef __trick__
// Real zero = std::numeric_limits<Real>::epsilon();
// if(std::abs(cos_t) < zero) {
// cos_t_2 = 0;
// sin_t_2 = 1;
// } else {
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// }
// Real rhop1 = std::max(0., cos_t_2 / sigma1_2);
// Real rhop2 = std::max(0., sin_t_2 / sigma2_2);
// #else
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// Real rhop1 = cos_t_2 / sigma1_2;
// Real rhop2 = sin_t_2 / sigma2_2;
// #endif
// return 1./ (rhop1 + rhop2);
// } else if (spatial_dimension == 3) {
// Vector<Real> u1(eigenvects.storage() + 0*3, 3);
// //Vector<Real> u2(eigenvects.storage() + 1*3, 3);
// Vector<Real> u3(eigenvects.storage() + 2*3, 3);
// Real zero = std::numeric_limits<Real>::epsilon();
// Vector<Real> tmp(3);
// tmp.crossProduct(x_s, u3);
// Vector<Real> u3_C_x_s_C_u3(3);
// u3_C_x_s_C_u3.crossProduct(u3, tmp);
// Real norm_u3_C_x_s_C_u3 = u3_C_x_s_C_u3.norm();
// Real cos_t = 0.;
// if(std::abs(norm_u3_C_x_s_C_u3) > zero) {
// Real inv_norm_u3_C_x_s_C_u3 = 1. / norm_u3_C_x_s_C_u3;
// cos_t = u1.dot(u3_C_x_s_C_u3) * inv_norm_u3_C_x_s_C_u3;
// }
// Real cos_p = u3.dot(x_s) / r;
// Real cos_t_2;
// Real sin_t_2;
// Real cos_p_2;
// Real sin_p_2;
// Real sigma1_2 = eigs[0]*eigs[0];
// Real sigma2_2 = eigs[1]*eigs[1];
// Real sigma3_2 = eigs[2]*eigs[2];
// #ifdef __trick__
// if(std::abs(cos_t) < zero) {
// cos_t_2 = 0;
// sin_t_2 = 1;
// } else {
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// }
// if(std::abs(cos_p) < zero) {
// cos_p_2 = 0;
// sin_p_2 = 1;
// } else {
// cos_p_2 = cos_p * cos_p;
// sin_p_2 = (1 - cos_p_2);
// }
// Real rhop1 = std::max(0., sin_p_2 * cos_t_2 / sigma1_2);
// Real rhop2 = std::max(0., sin_p_2 * sin_t_2 / sigma2_2);
// Real rhop3 = std::max(0., cos_p_2 / sigma3_2);
// #else
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// cos_p_2 = cos_p * cos_p;
// sin_p_2 = (1 - cos_p_2);
// Real rhop1 = sin_p_2 * cos_t_2 / sigma1_2;
// Real rhop2 = sin_p_2 * sin_t_2 / sigma2_2;
// Real rhop3 = cos_p_2 / sigma3_2;
// #endif
// return 1./ (rhop1 + rhop2 + rhop3);
// }
return 0.;
}
/* -------------------------------------------------------------------------- */
-inline Real StressBasedWeightFunction::operator()(__attribute__((unused))
- Real r,
- __attribute__((unused))
- const IntegrationPoint & q1,
- __attribute__((unused))
- const IntegrationPoint & q2) {
+inline Real
+StressBasedWeightFunction::operator()(Real /*r*/,
+ const IntegrationPoint & /*q1*/,
+ const IntegrationPoint & /*q2*/) {
// Real zero = std::numeric_limits<Real>::epsilon();
// if(r < zero) return 1.; // means x and s are the same points
// const Vector<Real> & x = q1.getPosition();
// const Vector<Real> & s = q2.getPosition();
// Vector<Real> eigs =
// selected_stress_diag->begin(spatial_dimension)[q2.global_num];
// Matrix<Real> eigenvects =
// selected_stress_base->begin(spatial_dimension,
// spatial_dimension)[q2.global_num];
// Real min_rho_lc = selected_characteristic_size->begin()[q1.global_num];
// Vector<Real> x_s(spatial_dimension);
// x_s = x;
// x_s -= s;
// Real rho_2 = computeRhoSquare(r, eigs, eigenvects, x_s);
// Real rho_lc_2 = std::max(this->R2 * rho_2, min_rho_lc*min_rho_lc);
// // Real w = std::max(0., 1. - r*r / rho_lc_2);
// // w = w*w;
// Real w = exp(- 2*2*r*r / rho_lc_2);
// return w;
return 0.;
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model.cc b/src/model/solid_mechanics/solid_mechanics_model.cc
index e88c11c08..33fa68ec6 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model.cc
@@ -1,1204 +1,1240 @@
/**
* @file solid_mechanics_model.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the SolidMechanicsModel class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "integrator_gauss.hh"
#include "shape_lagrange.hh"
#include "solid_mechanics_model_tmpl.hh"
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "sparse_matrix.hh"
#include "synchronizer_registry.hh"
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_iohelper_paraview.hh"
#endif
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* A solid mechanics model need a mesh and a dimension to be created. the model
* by it self can not do a lot, the good init functions should be called in
* order to configure the model depending on what we want to do.
*
* @param mesh mesh representing the model we want to simulate
* @param dim spatial dimension of the problem, if dim = 0 (default value) the
* dimension of the problem is assumed to be the on of the mesh
* @param id an id to identify the model
* @param memory_id the id of the memory
* @param model_type this is an internal parameter for inheritance purposes
*/
SolidMechanicsModel::SolidMechanicsModel(Mesh & mesh, UInt dim, const ID & id,
const MemoryID & memory_id,
const ModelType model_type)
: Model(mesh, model_type, dim, id, memory_id),
material_index("material index", id, memory_id),
material_local_numbering("material local numbering", id, memory_id) {
AKANTU_DEBUG_IN();
this->registerFEEngineObject<MyFEEngineType>("SolidMechanicsFEEngine", mesh,
Model::spatial_dimension);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("solid_mechanics_model", id, true);
this->mesh.addDumpMesh(mesh, Model::spatial_dimension, _not_ghost,
_ek_regular);
#endif
material_selector = std::make_shared<DefaultMaterialSelector>(material_index),
this->initDOFManager();
this->registerDataAccessor(*this);
if (this->mesh.isDistributed()) {
auto & synchronizer = this->mesh.getElementSynchronizer();
this->registerSynchronizer(synchronizer, SynchronizationTag::_material_id);
this->registerSynchronizer(synchronizer, SynchronizationTag::_smm_mass);
this->registerSynchronizer(synchronizer, SynchronizationTag::_smm_stress);
this->registerSynchronizer(synchronizer, SynchronizationTag::_for_dump);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModel::~SolidMechanicsModel() = default;
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::setTimeStep(Real time_step, const ID & solver_id) {
Model::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper().setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
/* Initialization */
/* -------------------------------------------------------------------------- */
/**
* This function groups many of the initialization in on function. For most of
* basics case the function should be enough. The functions initialize the
* model, the internal vectors, set them to 0, and depending on the parameters
* it also initialize the explicit or implicit solver.
*
* @param options
* \parblock
* contains the different options to initialize the model
* \li \c analysis_method specify the type of solver to use
* \endparblock
*/
void SolidMechanicsModel::initFullImpl(const ModelOptions & options) {
material_index.initialize(mesh, _element_kind = _ek_not_defined,
_default_value = UInt(-1), _with_nb_element = true);
material_local_numbering.initialize(mesh, _element_kind = _ek_not_defined,
_with_nb_element = true);
Model::initFullImpl(options);
// initialize the materials
- if (this->parser.getLastParsedFile() != "") {
+ if (not this->parser.getLastParsedFile().empty()) {
this->instantiateMaterials();
this->initMaterials();
}
this->initBC(*this, *displacement, *displacement_increment, *external_force);
}
/* -------------------------------------------------------------------------- */
TimeStepSolverType SolidMechanicsModel::getDefaultSolverType() const {
return TimeStepSolverType::_dynamic_lumped;
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions SolidMechanicsModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case TimeStepSolverType::_dynamic_lumped: {
options.non_linear_solver_type = NonLinearSolverType::_lumped;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
break;
}
case TimeStepSolverType::_static: {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_pseudo_time;
options.solution_type["displacement"] = IntegrationScheme::_not_defined;
break;
}
case TimeStepSolverType::_dynamic: {
if (this->method == _explicit_consistent_mass) {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
} else {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_trapezoidal_rule_2;
options.solution_type["displacement"] = IntegrationScheme::_displacement;
}
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
std::tuple<ID, TimeStepSolverType>
SolidMechanicsModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _explicit_lumped_mass: {
return std::make_tuple("explicit_lumped",
TimeStepSolverType::_dynamic_lumped);
}
case _explicit_consistent_mass: {
return std::make_tuple("explicit", TimeStepSolverType::_dynamic);
}
case _static: {
return std::make_tuple("static", TimeStepSolverType::_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
}
default:
return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initSolver(TimeStepSolverType time_step_solver_type,
- NonLinearSolverType) {
+ NonLinearSolverType /*unused*/) {
auto & dof_manager = this->getDOFManager();
/* ------------------------------------------------------------------------ */
// for alloc type of solvers
this->allocNodalField(this->displacement, spatial_dimension, "displacement");
this->allocNodalField(this->previous_displacement, spatial_dimension,
"previous_displacement");
this->allocNodalField(this->displacement_increment, spatial_dimension,
"displacement_increment");
this->allocNodalField(this->internal_force, spatial_dimension,
"internal_force");
this->allocNodalField(this->external_force, spatial_dimension,
"external_force");
this->allocNodalField(this->blocked_dofs, spatial_dimension, "blocked_dofs");
this->allocNodalField(this->current_position, spatial_dimension,
"current_position");
// initialize the current positions
this->current_position->copy(this->mesh.getNodes());
/* ------------------------------------------------------------------------ */
if (!dof_manager.hasDOFs("displacement")) {
dof_manager.registerDOFs("displacement", *this->displacement, _dst_nodal);
dof_manager.registerBlockedDOFs("displacement", *this->blocked_dofs);
dof_manager.registerDOFsIncrement("displacement",
*this->displacement_increment);
dof_manager.registerDOFsPrevious("displacement",
*this->previous_displacement);
}
/* ------------------------------------------------------------------------ */
// for dynamic
if (time_step_solver_type == TimeStepSolverType::_dynamic ||
time_step_solver_type == TimeStepSolverType::_dynamic_lumped) {
this->allocNodalField(this->velocity, spatial_dimension, "velocity");
this->allocNodalField(this->acceleration, spatial_dimension,
"acceleration");
if (!dof_manager.hasDOFsDerivatives("displacement", 1)) {
dof_manager.registerDOFsDerivative("displacement", 1, *this->velocity);
dof_manager.registerDOFsDerivative("displacement", 2,
*this->acceleration);
}
}
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*/
void SolidMechanicsModel::initModel() {
/// \todo add the current position as a parameter to initShapeFunctions for
/// large deformation
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleResidual() {
AKANTU_DEBUG_IN();
/* ------------------------------------------------------------------------ */
// computes the internal forces
this->assembleInternalForces();
/* ------------------------------------------------------------------------ */
this->getDOFManager().assembleToResidual("displacement",
*this->external_force, 1);
this->getDOFManager().assembleToResidual("displacement",
*this->internal_force, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_IN();
if ("external" == residual_part) {
this->getDOFManager().assembleToResidual("displacement",
*this->external_force, 1);
AKANTU_DEBUG_OUT();
return;
}
if ("internal" == residual_part) {
this->assembleInternalForces();
this->getDOFManager().assembleToResidual("displacement",
*this->internal_force, 1);
AKANTU_DEBUG_OUT();
return;
}
AKANTU_CUSTOM_EXCEPTION(
debug::SolverCallbackResidualPartUnknown(residual_part));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MatrixType SolidMechanicsModel::getMatrixType(const ID & matrix_id) {
// \TODO check the materials to know what is the correct answer
- if (matrix_id == "C")
+ if (matrix_id == "C") {
return _mt_not_defined;
+ }
if (matrix_id == "K") {
auto matrix_type = _unsymmetric;
for (auto & material : materials) {
matrix_type = std::max(matrix_type, material->getMatrixType(matrix_id));
}
}
return _symmetric;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleStiffnessMatrix();
} else if (matrix_id == "M") {
this->assembleMass();
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleLumpedMatrix(const ID & matrix_id) {
if (matrix_id == "M") {
this->assembleMassLumped();
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::beforeSolveStep() {
- for (auto & material : materials)
+ for (auto & material : materials) {
material->beforeSolveStep();
+ }
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::afterSolveStep(bool converged) {
- for (auto & material : materials)
+ for (auto & material : materials) {
material->afterSolveStep(converged);
+ }
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::predictor() { ++displacement_release; }
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::corrector() { ++displacement_release; }
/* -------------------------------------------------------------------------- */
/**
* This function computes the internal forces as \f$F_{int} = \int_{\Omega} N
* \sigma d\Omega@\f$
*/
void SolidMechanicsModel::assembleInternalForces() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the internal forces");
- this->internal_force->clear();
+ this->internal_force->zero();
// compute the stresses of local elements
AKANTU_DEBUG_INFO("Compute local stresses");
for (auto & material : materials) {
material->computeAllStresses(_not_ghost);
}
/* ------------------------------------------------------------------------ */
/* Computation of the non local part */
- if (this->non_local_manager)
+ if (this->non_local_manager) {
this->non_local_manager->computeAllNonLocalStresses();
+ }
// communicate the stresses
AKANTU_DEBUG_INFO("Send data for residual assembly");
this->asynchronousSynchronize(SynchronizationTag::_smm_stress);
// assemble the forces due to local stresses
AKANTU_DEBUG_INFO("Assemble residual for local elements");
for (auto & material : materials) {
material->assembleInternalForces(_not_ghost);
}
// finalize communications
AKANTU_DEBUG_INFO("Wait distant stresses");
this->waitEndSynchronize(SynchronizationTag::_smm_stress);
// assemble the stresses due to ghost elements
AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
for (auto & material : materials) {
material->assembleInternalForces(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix.");
// Check if materials need to recompute the matrix
bool need_to_reassemble = false;
for (auto & material : materials) {
need_to_reassemble |= material->hasMatrixChanged("K");
}
if (need_to_reassemble) {
- this->getDOFManager().getMatrix("K").clear();
+ this->getDOFManager().getMatrix("K").zero();
// call compute stiffness matrix on each local elements
for (auto & material : materials) {
material->assembleStiffnessMatrix(_not_ghost);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateCurrentPosition() {
- if (this->current_position_release == this->displacement_release)
+ if (this->current_position_release == this->displacement_release) {
return;
+ }
this->current_position->copy(this->mesh.getNodes());
auto cpos_it = this->current_position->begin(Model::spatial_dimension);
auto cpos_end = this->current_position->end(Model::spatial_dimension);
auto disp_it = this->displacement->begin(Model::spatial_dimension);
for (; cpos_it != cpos_end; ++cpos_it, ++disp_it) {
*cpos_it += *disp_it;
}
this->current_position_release = this->displacement_release;
}
/* -------------------------------------------------------------------------- */
const Array<Real> & SolidMechanicsModel::getCurrentPosition() {
this->updateCurrentPosition();
return *this->current_position;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateDataForNonLocalCriterion(
ElementTypeMapReal & criterion) {
const ID field_name = criterion.getName();
for (auto & material : materials) {
- if (!material->isInternal<Real>(field_name, _ek_regular))
+ if (!material->isInternal<Real>(field_name, _ek_regular)) {
continue;
+ }
for (auto ghost_type : ghost_types) {
material->flattenInternal(field_name, criterion, ghost_type, _ek_regular);
}
}
}
/* -------------------------------------------------------------------------- */
/* Information */
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real min_dt = getStableTimeStep(_not_ghost);
/// reduction min over all processors
mesh.getCommunicator().allReduce(min_dt, SynchronizerOperation::_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
-Real SolidMechanicsModel::getStableTimeStep(const GhostType & ghost_type) {
+Real SolidMechanicsModel::getStableTimeStep(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real min_dt = std::numeric_limits<Real>::max();
this->updateCurrentPosition();
Element elem;
elem.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, _ek_regular)) {
elem.type = type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type);
auto mat_indexes = material_index(type, ghost_type).begin();
auto mat_loc_num = material_local_numbering(type, ghost_type).begin();
Array<Real> X(0, nb_nodes_per_element * Model::spatial_dimension);
FEEngine::extractNodalToElementField(mesh, *current_position, X, type,
_not_ghost);
auto X_el = X.begin(Model::spatial_dimension, nb_nodes_per_element);
for (UInt el = 0; el < nb_element;
++el, ++X_el, ++mat_indexes, ++mat_loc_num) {
elem.element = *mat_loc_num;
Real el_h = getFEEngine().getElementInradius(*X_el, type);
Real el_c = this->materials[*mat_indexes]->getCelerity(elem);
Real el_dt = el_h / el_c;
min_dt = std::min(min_dt, el_dt);
}
}
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy() {
AKANTU_DEBUG_IN();
Real ekin = 0.;
UInt nb_nodes = mesh.getNbNodes();
if (this->getDOFManager().hasLumpedMatrix("M")) {
auto m_it = this->mass->begin(Model::spatial_dimension);
auto m_end = this->mass->end(Model::spatial_dimension);
auto v_it = this->velocity->begin(Model::spatial_dimension);
for (UInt n = 0; m_it != m_end; ++n, ++m_it, ++v_it) {
const auto & v = *v_it;
const auto & m = *m_it;
Real mv2 = 0.;
auto is_local_node = mesh.isLocalOrMasterNode(n);
// bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
auto count_node = is_local_node; // && is_not_pbc_slave_node;
if (count_node) {
for (UInt i = 0; i < Model::spatial_dimension; ++i) {
- if (m(i) > std::numeric_limits<Real>::epsilon())
+ if (m(i) > std::numeric_limits<Real>::epsilon()) {
mv2 += v(i) * v(i) * m(i);
+ }
}
}
ekin += mv2;
}
} else if (this->getDOFManager().hasMatrix("M")) {
Array<Real> Mv(nb_nodes, Model::spatial_dimension);
this->getDOFManager().assembleMatMulVectToArray("displacement", "M",
*this->velocity, Mv);
for (auto && data : zip(arange(nb_nodes), make_view(Mv, spatial_dimension),
make_view(*this->velocity, spatial_dimension))) {
ekin += std::get<2>(data).dot(std::get<1>(data)) *
- mesh.isLocalOrMasterNode(std::get<0>(data));
+ static_cast<Real>(mesh.isLocalOrMasterNode(std::get<0>(data)));
}
} else {
AKANTU_ERROR("No function called to assemble the mass matrix.");
}
mesh.getCommunicator().allReduce(ekin, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return ekin * .5;
}
/* -------------------------------------------------------------------------- */
-Real SolidMechanicsModel::getKineticEnergy(const ElementType & type,
- UInt index) {
+Real SolidMechanicsModel::getKineticEnergy(ElementType type, UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
Array<Real> vel_on_quad(nb_quadrature_points, Model::spatial_dimension);
Array<UInt> filter_element(1, 1, index);
getFEEngine().interpolateOnIntegrationPoints(*velocity, vel_on_quad,
Model::spatial_dimension, type,
_not_ghost, filter_element);
auto vit = vel_on_quad.begin(Model::spatial_dimension);
auto vend = vel_on_quad.end(Model::spatial_dimension);
Vector<Real> rho_v2(nb_quadrature_points);
Real rho = materials[material_index(type)(index)]->getRho();
for (UInt q = 0; vit != vend; ++vit, ++q) {
rho_v2(q) = rho * vit->dot(*vit);
}
AKANTU_DEBUG_OUT();
return .5 * getFEEngine().integrate(rho_v2, type, index);
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getExternalWork() {
AKANTU_DEBUG_IN();
auto ext_force_it = external_force->begin(Model::spatial_dimension);
auto int_force_it = internal_force->begin(Model::spatial_dimension);
auto boun_it = blocked_dofs->begin(Model::spatial_dimension);
decltype(ext_force_it) incr_or_velo_it;
if (this->method == _static) {
incr_or_velo_it =
this->displacement_increment->begin(Model::spatial_dimension);
} else {
incr_or_velo_it = this->velocity->begin(Model::spatial_dimension);
}
Real work = 0.;
UInt nb_nodes = this->mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes;
++n, ++ext_force_it, ++int_force_it, ++boun_it, ++incr_or_velo_it) {
const auto & int_force = *int_force_it;
const auto & ext_force = *ext_force_it;
const auto & boun = *boun_it;
const auto & incr_or_velo = *incr_or_velo_it;
bool is_local_node = this->mesh.isLocalOrMasterNode(n);
// bool is_not_pbc_slave_node = !this->isPBCSlaveNode(n);
bool count_node = is_local_node; // && is_not_pbc_slave_node;
if (count_node) {
for (UInt i = 0; i < Model::spatial_dimension; ++i) {
- if (boun(i))
+ if (boun(i)) {
work -= int_force(i) * incr_or_velo(i);
- else
+ } else {
work += ext_force(i) * incr_or_velo(i);
+ }
}
}
}
mesh.getCommunicator().allReduce(work, SynchronizerOperation::_sum);
- if (this->method != _static)
+ if (this->method != _static) {
work *= this->getTimeStep();
+ }
AKANTU_DEBUG_OUT();
return work;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy();
- } else if (energy_id == "external work") {
+ }
+
+ if (energy_id == "external work") {
return getExternalWork();
}
Real energy = 0.;
- for (auto & material : materials)
+ for (auto & material : materials) {
energy += material->getEnergy(energy_id);
+ }
/// reduction sum over all processors
mesh.getCommunicator().allReduce(energy, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id,
- const ElementType & type, UInt index) {
+ ElementType type, UInt index) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy(type, index);
}
UInt mat_index = this->material_index(type, _not_ghost)(index);
UInt mat_loc_num = this->material_local_numbering(type, _not_ghost)(index);
Real energy =
this->materials[mat_index]->getEnergy(energy_id, type, mat_loc_num);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
this->material_index.initialize(mesh, _element_kind = _ek_not_defined,
_with_nb_element = true,
_default_value = UInt(-1));
this->material_local_numbering.initialize(
mesh, _element_kind = _ek_not_defined, _with_nb_element = true,
_default_value = UInt(-1));
ElementTypeMapArray<UInt> filter("new_element_filter", this->getID(),
this->getMemoryID());
- for (auto & elem : element_list) {
- if (mesh.getSpatialDimension(elem.type) != spatial_dimension)
+ for (const auto & elem : element_list) {
+ if (mesh.getSpatialDimension(elem.type) != spatial_dimension) {
continue;
+ }
- if (!filter.exists(elem.type, elem.ghost_type))
+ if (!filter.exists(elem.type, elem.ghost_type)) {
filter.alloc(0, 1, elem.type, elem.ghost_type);
+ }
filter(elem.type, elem.ghost_type).push_back(elem.element);
}
// this fails in parallel if the event is sent on facet between constructor
// and initFull \todo: to debug...
this->assignMaterialToElements(&filter);
- for (auto & material : materials)
+ for (auto & material : materials) {
material->onElementsAdded(element_list, event);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
for (auto & material : materials) {
material->onElementsRemoved(element_list, new_numbering, event);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
if (displacement) {
displacement->resize(nb_nodes, 0.);
++displacement_release;
}
- if (mass)
+ if (mass) {
mass->resize(nb_nodes, 0.);
- if (velocity)
+ }
+ if (velocity) {
velocity->resize(nb_nodes, 0.);
- if (acceleration)
+ }
+ if (acceleration) {
acceleration->resize(nb_nodes, 0.);
- if (external_force)
+ }
+ if (external_force) {
external_force->resize(nb_nodes, 0.);
- if (internal_force)
+ }
+ if (internal_force) {
internal_force->resize(nb_nodes, 0.);
- if (blocked_dofs)
- blocked_dofs->resize(nb_nodes, 0.);
- if (current_position)
+ }
+ if (blocked_dofs) {
+ blocked_dofs->resize(nb_nodes, false);
+ }
+ if (current_position) {
current_position->resize(nb_nodes, 0.);
+ }
- if (previous_displacement)
+ if (previous_displacement) {
previous_displacement->resize(nb_nodes, 0.);
- if (displacement_increment)
+ }
+ if (displacement_increment) {
displacement_increment->resize(nb_nodes, 0.);
+ }
for (auto & material : materials) {
material->onNodesAdded(nodes_list, event);
}
need_to_reassemble_lumped_mass = true;
need_to_reassemble_mass = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesRemoved(const Array<UInt> & /*element_list*/,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & /*event*/) {
if (displacement) {
mesh.removeNodesFromArray(*displacement, new_numbering);
++displacement_release;
}
- if (mass)
+ if (mass) {
mesh.removeNodesFromArray(*mass, new_numbering);
- if (velocity)
+ }
+ if (velocity) {
mesh.removeNodesFromArray(*velocity, new_numbering);
- if (acceleration)
+ }
+ if (acceleration) {
mesh.removeNodesFromArray(*acceleration, new_numbering);
- if (internal_force)
+ }
+ if (internal_force) {
mesh.removeNodesFromArray(*internal_force, new_numbering);
- if (external_force)
+ }
+ if (external_force) {
mesh.removeNodesFromArray(*external_force, new_numbering);
- if (blocked_dofs)
+ }
+ if (blocked_dofs) {
mesh.removeNodesFromArray(*blocked_dofs, new_numbering);
+ }
// if (increment_acceleration)
// mesh.removeNodesFromArray(*increment_acceleration, new_numbering);
- if (displacement_increment)
+ if (displacement_increment) {
mesh.removeNodesFromArray(*displacement_increment, new_numbering);
+ }
- if (previous_displacement)
+ if (previous_displacement) {
mesh.removeNodesFromArray(*previous_displacement, new_numbering);
+ }
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Solid Mechanics Model [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + spatial dimension : " << Model::spatial_dimension
<< std::endl;
stream << space << " + fem [" << std::endl;
getFEEngine().printself(stream, indent + 2);
stream << space << " ]" << std::endl;
stream << space << " + nodals information [" << std::endl;
displacement->printself(stream, indent + 2);
- if (velocity)
+ if (velocity) {
velocity->printself(stream, indent + 2);
- if (acceleration)
+ }
+ if (acceleration) {
acceleration->printself(stream, indent + 2);
- if (mass)
+ }
+ if (mass) {
mass->printself(stream, indent + 2);
+ }
external_force->printself(stream, indent + 2);
internal_force->printself(stream, indent + 2);
blocked_dofs->printself(stream, indent + 2);
stream << space << " ]" << std::endl;
stream << space << " + material information [" << std::endl;
material_index.printself(stream, indent + 2);
stream << space << " ]" << std::endl;
stream << space << " + materials [" << std::endl;
- for (auto & material : materials)
+ for (const auto & material : materials) {
material->printself(stream, indent + 2);
+ }
stream << space << " ]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initializeNonLocal() {
this->non_local_manager->synchronize(*this, SynchronizationTag::_material_id);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::insertIntegrationPointsInNeighborhoods(
- const GhostType & ghost_type) {
+ GhostType ghost_type) {
for (auto & mat : materials) {
MaterialNonLocalInterface * mat_non_local;
if ((mat_non_local =
- dynamic_cast<MaterialNonLocalInterface *>(mat.get())) == nullptr)
+ dynamic_cast<MaterialNonLocalInterface *>(mat.get())) == nullptr) {
continue;
+ }
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_tmp_nl", this->id, this->memory_id);
quadrature_points_coordinates.initialize(this->getFEEngine(),
_nb_component = spatial_dimension,
_ghost_type = ghost_type);
- for (auto & type : quadrature_points_coordinates.elementTypes(
+ for (const auto & type : quadrature_points_coordinates.elementTypes(
Model::spatial_dimension, ghost_type)) {
this->getFEEngine().computeIntegrationPointsCoordinates(
quadrature_points_coordinates(type, ghost_type), type, ghost_type);
}
mat_non_local->initMaterialNonLocal();
mat_non_local->insertIntegrationPointsInNeighborhoods(
ghost_type, quadrature_points_coordinates);
}
}
/* -------------------------------------------------------------------------- */
-void SolidMechanicsModel::computeNonLocalStresses(
- const GhostType & ghost_type) {
+void SolidMechanicsModel::computeNonLocalStresses(GhostType ghost_type) {
for (auto & mat : materials) {
- if (not aka::is_of_type<MaterialNonLocalInterface>(*mat))
+ if (not aka::is_of_type<MaterialNonLocalInterface>(*mat)) {
continue;
+ }
auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
mat_non_local.computeNonLocalStresses(ghost_type);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateLocalInternal(
- ElementTypeMapReal & internal_flat, const GhostType & ghost_type,
- const ElementKind & kind) {
+ ElementTypeMapReal & internal_flat, GhostType ghost_type,
+ ElementKind kind) {
const ID field_name = internal_flat.getName();
for (auto & material : materials) {
- if (material->isInternal<Real>(field_name, kind))
+ if (material->isInternal<Real>(field_name, kind)) {
material->flattenInternal(field_name, internal_flat, ghost_type, kind);
+ }
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateNonLocalInternal(
- ElementTypeMapReal & internal_flat, const GhostType & ghost_type,
- const ElementKind & kind) {
+ ElementTypeMapReal & internal_flat, GhostType ghost_type,
+ ElementKind kind) {
const ID field_name = internal_flat.getName();
for (auto & mat : materials) {
- if (not aka::is_of_type<MaterialNonLocalInterface>(*mat))
+ if (not aka::is_of_type<MaterialNonLocalInterface>(*mat)) {
continue;
+ }
auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
mat_non_local.updateNonLocalInternals(internal_flat, field_name, ghost_type,
kind);
}
}
/* -------------------------------------------------------------------------- */
FEEngine & SolidMechanicsModel::getFEEngineBoundary(const ID & name) {
return getFEEngineClassBoundary<MyFEEngineType>(name);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::splitElementByMaterial(
const Array<Element> & elements,
std::vector<Array<Element>> & elements_per_mat) const {
for (const auto & el : elements) {
Element mat_el = el;
mat_el.element = this->material_local_numbering(el);
elements_per_mat[this->material_index(el)].push_back(mat_el);
}
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModel::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes_per_element = 0;
for (const Element & el : elements) {
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
switch (tag) {
case SynchronizationTag::_material_id: {
size += elements.size() * sizeof(UInt);
break;
}
case SynchronizationTag::_smm_mass: {
size += nb_nodes_per_element * sizeof(Real) *
Model::spatial_dimension; // mass vector
break;
}
case SynchronizationTag::_smm_for_gradu: {
size += nb_nodes_per_element * Model::spatial_dimension *
sizeof(Real); // displacement
break;
}
case SynchronizationTag::_smm_boundary: {
// force, displacement, boundary
size += nb_nodes_per_element * Model::spatial_dimension *
(2 * sizeof(Real) + sizeof(bool));
break;
}
case SynchronizationTag::_for_dump: {
// displacement, velocity, acceleration, residual, force
size += nb_nodes_per_element * Model::spatial_dimension * sizeof(Real) * 5;
break;
}
default: {
}
}
if (tag != SynchronizationTag::_material_id) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
size += mat.getNbData(elements, tag);
});
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_material_id: {
- this->packElementalDataHelper(material_index, buffer, elements, false,
- getFEEngine());
+ packElementalDataHelper(
+ material_index, buffer, elements, false, getFEEngine());
break;
}
case SynchronizationTag::_smm_mass: {
packNodalDataHelper(*mass, buffer, elements, mesh);
break;
}
case SynchronizationTag::_smm_for_gradu: {
packNodalDataHelper(*displacement, buffer, elements, mesh);
break;
}
case SynchronizationTag::_for_dump: {
packNodalDataHelper(*displacement, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*acceleration, buffer, elements, mesh);
packNodalDataHelper(*internal_force, buffer, elements, mesh);
packNodalDataHelper(*external_force, buffer, elements, mesh);
break;
}
case SynchronizationTag::_smm_boundary: {
packNodalDataHelper(*external_force, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if (tag != SynchronizationTag::_material_id) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.packData(buffer, elements, tag);
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
UInt recv_mat_index;
buffer >> recv_mat_index;
UInt & mat_index = material_index(element);
- if (mat_index != UInt(-1))
+ if (mat_index != UInt(-1)) {
continue;
+ }
// add ghosts element to the correct material
mat_index = recv_mat_index;
UInt index = materials[mat_index]->addElement(element);
material_local_numbering(element) = index;
}
break;
}
case SynchronizationTag::_smm_mass: {
unpackNodalDataHelper(*mass, buffer, elements, mesh);
break;
}
case SynchronizationTag::_smm_for_gradu: {
unpackNodalDataHelper(*displacement, buffer, elements, mesh);
break;
}
case SynchronizationTag::_for_dump: {
unpackNodalDataHelper(*displacement, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*acceleration, buffer, elements, mesh);
unpackNodalDataHelper(*internal_force, buffer, elements, mesh);
unpackNodalDataHelper(*external_force, buffer, elements, mesh);
break;
}
case SynchronizationTag::_smm_boundary: {
unpackNodalDataHelper(*external_force, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if (tag != SynchronizationTag::_material_id) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.unpackData(buffer, elements, tag);
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModel::getNbData(const Array<UInt> & dofs,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
// UInt nb_nodes = mesh.getNbNodes();
switch (tag) {
case SynchronizationTag::_smm_uv: {
size += sizeof(Real) * Model::spatial_dimension * 2;
break;
}
- case SynchronizationTag::_smm_res: {
- size += sizeof(Real) * Model::spatial_dimension;
- break;
- }
+ case SynchronizationTag::_smm_res: /* FALLTHRU */
case SynchronizationTag::_smm_mass: {
size += sizeof(Real) * Model::spatial_dimension;
break;
}
case SynchronizationTag::_for_dump: {
size += sizeof(Real) * Model::spatial_dimension * 5;
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
return size * dofs.size();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
const Array<UInt> & dofs,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_smm_uv: {
packDOFDataHelper(*displacement, buffer, dofs);
packDOFDataHelper(*velocity, buffer, dofs);
break;
}
case SynchronizationTag::_smm_res: {
packDOFDataHelper(*internal_force, buffer, dofs);
break;
}
case SynchronizationTag::_smm_mass: {
packDOFDataHelper(*mass, buffer, dofs);
break;
}
case SynchronizationTag::_for_dump: {
packDOFDataHelper(*displacement, buffer, dofs);
packDOFDataHelper(*velocity, buffer, dofs);
packDOFDataHelper(*acceleration, buffer, dofs);
packDOFDataHelper(*internal_force, buffer, dofs);
packDOFDataHelper(*external_force, buffer, dofs);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
const Array<UInt> & dofs,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_smm_uv: {
unpackDOFDataHelper(*displacement, buffer, dofs);
unpackDOFDataHelper(*velocity, buffer, dofs);
break;
}
case SynchronizationTag::_smm_res: {
unpackDOFDataHelper(*internal_force, buffer, dofs);
break;
}
case SynchronizationTag::_smm_mass: {
unpackDOFDataHelper(*mass, buffer, dofs);
break;
}
case SynchronizationTag::_for_dump: {
unpackDOFDataHelper(*displacement, buffer, dofs);
unpackDOFDataHelper(*velocity, buffer, dofs);
unpackDOFDataHelper(*acceleration, buffer, dofs);
unpackDOFDataHelper(*internal_force, buffer, dofs);
unpackDOFDataHelper(*external_force, buffer, dofs);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model.hh b/src/model/solid_mechanics/solid_mechanics_model.hh
index dfb0cc943..a5d896289 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model.hh
@@ -1,565 +1,581 @@
/**
* @file solid_mechanics_model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Model of Solid Mechanics
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition.hh"
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "model.hh"
#include "non_local_manager_callback.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLID_MECHANICS_MODEL_HH__
-#define __AKANTU_SOLID_MECHANICS_MODEL_HH__
+#ifndef AKANTU_SOLID_MECHANICS_MODEL_HH_
+#define AKANTU_SOLID_MECHANICS_MODEL_HH_
namespace akantu {
class Material;
class MaterialSelector;
class DumperIOHelper;
class NonLocalManager;
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
class SolidMechanicsModel
: public Model,
public DataAccessor<Element>,
public DataAccessor<UInt>,
public BoundaryCondition<SolidMechanicsModel>,
public NonLocalManagerCallback,
public EventHandlerManager<SolidMechanicsModelEventHandler> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
class NewMaterialElementsEvent : public NewElementsEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(MaterialList, material, Array<UInt> &);
AKANTU_GET_MACRO(MaterialList, material, const Array<UInt> &);
protected:
Array<UInt> material;
};
using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
protected:
using EventManager = EventHandlerManager<SolidMechanicsModelEventHandler>;
public:
SolidMechanicsModel(
- Mesh & mesh, UInt spatial_dimension = _all_dimensions,
+ Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "solid_mechanics_model", const MemoryID & memory_id = 0,
- const ModelType model_type = ModelType::_solid_mechanics_model);
+ ModelType model_type = ModelType::_solid_mechanics_model);
~SolidMechanicsModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize completely the model
void initFullImpl(
const ModelOptions & options = SolidMechanicsModelOptions()) override;
public:
/// initialize all internal arrays for materials
virtual void initMaterials();
protected:
/// initialize the model
void initModel() override;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
/* ------------------------------------------------------------------------ */
/* Solver interface */
/* ------------------------------------------------------------------------ */
public:
/// assembles the stiffness matrix,
virtual void assembleStiffnessMatrix();
/// assembles the internal forces in the array internal_forces
virtual void assembleInternalForces();
protected:
/// callback for the solver, this adds f_{ext} - f_{int} to the residual
void assembleResidual() override;
/// callback for the solver, this adds f_{ext} or f_{int} to the residual
void assembleResidual(const ID & residual_part) override;
bool canSplitResidual() override { return true; }
/// get the type of matrix needed
MatrixType getMatrixType(const ID & matrix_id) override;
/// callback for the solver, this assembles different matrices
void assembleMatrix(const ID & matrix_id) override;
/// callback for the solver, this assembles the stiffness matrix
void assembleLumpedMatrix(const ID & matrix_id) override;
/// callback for the solver, this is called at beginning of solve
void predictor() override;
/// callback for the solver, this is called at end of solve
void corrector() override;
/// callback for the solver, this is called at beginning of solve
void beforeSolveStep() override;
/// callback for the solver, this is called at end of solve
- void afterSolveStep(bool converted = true) override;
+ void afterSolveStep(bool converged = true) override;
/// Callback for the model to instantiate the matricees when needed
void initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) override;
protected:
/* ------------------------------------------------------------------------ */
TimeStepSolverType getDefaultSolverType() const override;
/* ------------------------------------------------------------------------ */
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
public:
bool isDefaultSolverExplicit() {
return method == _explicit_lumped_mass ||
method == _explicit_consistent_mass;
}
protected:
/// update the current position vector
void updateCurrentPosition();
/* ------------------------------------------------------------------------ */
/* Materials (solid_mechanics_model_material.cc) */
/* ------------------------------------------------------------------------ */
public:
/// register an empty material of a given type
Material & registerNewMaterial(const ID & mat_name, const ID & mat_type,
const ID & opt_param);
/// reassigns materials depending on the material selector
virtual void reassignMaterial();
/// apply a constant eigen_grad_u on all quadrature points of a given material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const ID & material_name,
- const GhostType ghost_type = _not_ghost);
+ GhostType ghost_type = _not_ghost);
protected:
/// register a material in the dynamic database
Material & registerNewMaterial(const ParserSection & mat_section);
/// read the material files to instantiate all the materials
void instantiateMaterials();
/// set the element_id_by_material and add the elements to the good materials
virtual void
assignMaterialToElements(const ElementTypeMapArray<UInt> * filter = nullptr);
/* ------------------------------------------------------------------------ */
/* Mass (solid_mechanics_model_mass.cc) */
/* ------------------------------------------------------------------------ */
public:
/// assemble the lumped mass matrix
void assembleMassLumped();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
protected:
/// assemble the lumped mass matrix for local and ghost elements
void assembleMassLumped(GhostType ghost_type);
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMass(GhostType ghost_type);
/// fill a vector of rho
void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);
/// compute the kinetic energy
Real getKineticEnergy();
- Real getKineticEnergy(const ElementType & type, UInt index);
+ Real getKineticEnergy(ElementType type, UInt index);
/// compute the external work (for impose displacement, the velocity should be
/// given too)
Real getExternalWork();
/* ------------------------------------------------------------------------ */
/* NonLocalManager inherited members */
/* ------------------------------------------------------------------------ */
protected:
void initializeNonLocal() override;
void updateDataForNonLocalCriterion(ElementTypeMapReal & criterion) override;
- void computeNonLocalStresses(const GhostType & ghost_type) override;
+ void computeNonLocalStresses(GhostType ghost_type) override;
void
- insertIntegrationPointsInNeighborhoods(const GhostType & ghost_type) override;
+ insertIntegrationPointsInNeighborhoods(GhostType ghost_type) override;
/// update the values of the non local internal
void updateLocalInternal(ElementTypeMapReal & internal_flat,
- const GhostType & ghost_type,
- const ElementKind & kind) override;
+ GhostType ghost_type,
+ ElementKind kind) override;
/// copy the results of the averaging in the materials
void updateNonLocalInternal(ElementTypeMapReal & internal_flat,
- const GhostType & ghost_type,
- const ElementKind & kind) override;
+ GhostType ghost_type,
+ ElementKind kind) override;
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override;
UInt getNbData(const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) override;
protected:
void
splitElementByMaterial(const Array<Element> & elements,
std::vector<Array<Element>> & elements_per_mat) const;
template <typename Operation>
void splitByMaterial(const Array<Element> & elements, Operation && op) const;
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
void onNodesRemoved(const Array<UInt> & element_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) override;
- void onElementsAdded(const Array<Element> & nodes_list,
+ void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
- void onElementsChanged(const Array<Element> &, const Array<Element> &,
- const ElementTypeMapArray<UInt> &,
- const ChangedElementsEvent &) override{};
+ void onElementsChanged(const Array<Element> & /*unused*/,
+ const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const ChangedElementsEvent & /*unused*/) override{};
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
public:
virtual void onDump();
//! decide wether a field is a material internal or not
bool isInternal(const std::string & field_name,
- const ElementKind & element_kind);
+ ElementKind element_kind);
//! give the amount of data per element
virtual ElementTypeMap<UInt>
getInternalDataPerElem(const std::string & field_name,
- const ElementKind & kind);
+ ElementKind kind);
//! flatten a given material internal field
ElementTypeMapArray<Real> &
- flattenInternal(const std::string & field_name, const ElementKind & kind,
- const GhostType ghost_type = _not_ghost);
+ flattenInternal(const std::string & field_name, ElementKind kind,
+ GhostType ghost_type = _not_ghost);
//! flatten all the registered material internals
- void flattenAllRegisteredInternals(const ElementKind & kind);
+ void flattenAllRegisteredInternals(ElementKind kind);
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
- const UInt & spatial_dimension,
- const ElementKind & kind) override;
+ UInt spatial_dimension,
+ ElementKind kind) override;
virtual void dump(const std::string & dumper_name);
virtual void dump(const std::string & dumper_name, UInt step);
virtual void dump(const std::string & dumper_name, Real time, UInt step);
void dump() override;
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, Model::spatial_dimension, UInt);
/// set the value of the time step
void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// get the value of the conversion from forces/ mass to acceleration
AKANTU_GET_MACRO(F_M2A, f_m2a, Real);
/// set the value of the conversion from forces/ mass to acceleration
AKANTU_SET_MACRO(F_M2A, f_m2a, Real);
+ /// get the SolidMechanicsModel::displacement array
+ AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Displacement, displacement);
/// get the SolidMechanicsModel::displacement array
AKANTU_GET_MACRO_DEREF_PTR(Displacement, displacement);
/// get the SolidMechanicsModel::previous_displacement array
AKANTU_GET_MACRO_DEREF_PTR(PreviousDisplacement, previous_displacement);
/// get the SolidMechanicsModel::current_position array
const Array<Real> & getCurrentPosition();
/// get the SolidMechanicsModel::displacement_increment array
AKANTU_GET_MACRO_DEREF_PTR(Increment, displacement_increment);
+ /// get the SolidMechanicsModel::displacement_increment array
+ AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Increment, displacement_increment);
/// get the lumped SolidMechanicsModel::mass array
AKANTU_GET_MACRO_DEREF_PTR(Mass, mass);
+ /// get the SolidMechanicsModel::velocity array
+ AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Velocity, velocity);
/// get the SolidMechanicsModel::velocity array
AKANTU_GET_MACRO_DEREF_PTR(Velocity, velocity);
+ /// get the SolidMechanicsModel::acceleration array
+ AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Acceleration, acceleration);
/// get the SolidMechanicsModel::acceleration array
AKANTU_GET_MACRO_DEREF_PTR(Acceleration, acceleration);
+ /// get the SolidMechanicsModel::external_force array
+ AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(ExternalForce, external_force);
/// get the SolidMechanicsModel::external_force array
AKANTU_GET_MACRO_DEREF_PTR(ExternalForce, external_force);
/// get the SolidMechanicsModel::force array (external forces)
[[deprecated("Use getExternalForce instead of this function")]] Array<Real> &
getForce() {
return getExternalForce();
}
+ /// get the SolidMechanicsModel::internal_force array (internal forces)
+ AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(InternalForce, internal_force);
/// get the SolidMechanicsModel::internal_force array (internal forces)
AKANTU_GET_MACRO_DEREF_PTR(InternalForce, internal_force);
+ /// get the SolidMechanicsModel::blocked_dofs array
+ AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(BlockedDOFs, blocked_dofs);
/// get the SolidMechanicsModel::blocked_dofs array
AKANTU_GET_MACRO_DEREF_PTR(BlockedDOFs, blocked_dofs);
/// get an iterable on the materials
inline decltype(auto) getMaterials();
/// get an iterable on the materials
inline decltype(auto) getMaterials() const;
/// get a particular material (by numerical material index)
inline Material & getMaterial(UInt mat_index);
/// get a particular material (by numerical material index)
inline const Material & getMaterial(UInt mat_index) const;
/// get a particular material (by material name)
inline Material & getMaterial(const std::string & name);
/// get a particular material (by material name)
inline const Material & getMaterial(const std::string & name) const;
/// get a particular material id from is name
inline UInt getMaterialIndex(const std::string & name) const;
/// give the number of materials
inline UInt getNbMaterials() const { return materials.size(); }
/// give the material internal index from its id
Int getInternalIndexFromID(const ID & id) const;
/// compute the stable time step
Real getStableTimeStep();
/// get the energies
Real getEnergy(const std::string & energy_id);
/// compute the energy for energy
- Real getEnergy(const std::string & energy_id, const ElementType & type,
+ Real getEnergy(const std::string & energy_id, ElementType type,
UInt index);
AKANTU_GET_MACRO(MaterialByElement, material_index,
const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(MaterialLocalNumbering, material_local_numbering,
const ElementTypeMapArray<UInt> &);
/// vectors containing local material element index for each global element
/// index
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(MaterialByElement, material_index,
UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(MaterialByElement, material_index, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(MaterialLocalNumbering,
material_local_numbering, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(MaterialLocalNumbering,
material_local_numbering, UInt);
AKANTU_GET_MACRO_NOT_CONST(MaterialSelector, *material_selector,
MaterialSelector &);
- AKANTU_SET_MACRO(MaterialSelector, material_selector,
- std::shared_ptr<MaterialSelector>);
+ void setMaterialSelector(std::shared_ptr<MaterialSelector> material_selector) {
+ this->material_selector = std::move(material_selector);
+ }
/// Access the non_local_manager interface
AKANTU_GET_MACRO(NonLocalManager, *non_local_manager, NonLocalManager &);
/// get the FEEngine object to integrate or interpolate on the boundary
FEEngine & getFEEngineBoundary(const ID & name = "") override;
protected:
/// compute the stable time step
- Real getStableTimeStep(const GhostType & ghost_type);
+ Real getStableTimeStep(GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// release version of the displacement array
UInt displacement_release{0};
/// release version of the current_position array
UInt current_position_release{0};
/// Check if materials need to recompute the mass array
bool need_to_reassemble_lumped_mass{true};
/// Check if materials need to recompute the mass matrix
bool need_to_reassemble_mass{true};
/// mapping between material name and material internal id
std::map<std::string, UInt> materials_names_to_id;
protected:
/// conversion coefficient form force/mass to acceleration
Real f_m2a{1.0};
/// displacements array
std::unique_ptr<Array<Real>> displacement;
/// displacements array at the previous time step (used in finite deformation)
std::unique_ptr<Array<Real>> previous_displacement;
/// increment of displacement
std::unique_ptr<Array<Real>> displacement_increment;
/// lumped mass array
std::unique_ptr<Array<Real>> mass;
/// velocities array
std::unique_ptr<Array<Real>> velocity;
/// accelerations array
std::unique_ptr<Array<Real>> acceleration;
/// external forces array
std::unique_ptr<Array<Real>> external_force;
/// internal forces array
std::unique_ptr<Array<Real>> internal_force;
/// array specifing if a degree of freedom is blocked or not
std::unique_ptr<Array<bool>> blocked_dofs;
/// array of current position used during update residual
std::unique_ptr<Array<Real>> current_position;
/// Arrays containing the material index for each element
ElementTypeMapArray<UInt> material_index;
/// Arrays containing the position in the element filter of the material
/// (material's local numbering)
ElementTypeMapArray<UInt> material_local_numbering;
/// list of used materials
std::vector<std::unique_ptr<Material>> materials;
/// class defining of to choose a material
std::shared_ptr<MaterialSelector> material_selector;
using flatten_internal_map =
std::map<std::pair<std::string, ElementKind>,
std::unique_ptr<ElementTypeMapArray<Real>>>;
/// map a registered internals to be flattened for dump purposes
flatten_internal_map registered_internals;
/// non local manager
std::unique_ptr<NonLocalManager> non_local_manager;
/// tells if the material are instantiated
bool are_materials_instantiated{false};
};
/* -------------------------------------------------------------------------- */
namespace BC {
namespace Neumann {
using FromStress = FromHigherDim;
using FromTraction = FromSameDim;
} // namespace Neumann
} // namespace BC
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "parser.hh"
#include "solid_mechanics_model_inline_impl.hh"
#include "solid_mechanics_model_tmpl.hh"
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_SOLID_MECHANICS_MODEL_HH__ */
+#endif /* AKANTU_SOLID_MECHANICS_MODEL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
index cef133656..468b0240f 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
@@ -1,540 +1,545 @@
/**
* @file fragment_manager.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jan 23 2014
* @date last modification: Tue Feb 20 2018
*
* @brief Group manager to handle fragments
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fragment_manager.hh"
#include "aka_iterators.hh"
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "material_cohesive.hh"
#include "mesh_iterators.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <functional>
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
FragmentManager::FragmentManager(SolidMechanicsModelCohesive & model,
bool dump_data, const ID & id,
const MemoryID & memory_id)
: GroupManager(model.getMesh(), id, memory_id), model(model),
mass_center(0, model.getSpatialDimension(), "mass_center"),
mass(0, model.getSpatialDimension(), "mass"),
velocity(0, model.getSpatialDimension(), "velocity"),
inertia_moments(0, model.getSpatialDimension(), "inertia_moments"),
principal_directions(
0, model.getSpatialDimension() * model.getSpatialDimension(),
"principal_directions"),
quad_coordinates("quad_coordinates", id),
mass_density("mass_density", id),
nb_elements_per_fragment(0, 1, "nb_elements_per_fragment"),
dump_data(dump_data) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
/// compute quadrature points' coordinates
quad_coordinates.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(quad_coordinates, spatial_dimension,
// spatial_dimension, _not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getMesh().getNodes(),
quad_coordinates);
/// store mass density per quadrature point
mass_density.initialize(mesh, _spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(mass_density, 1, spatial_dimension,
// _not_ghost);
storeMassDensityPerIntegrationPoint();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
class CohesiveElementFilter : public GroupManager::ClusteringFilter {
public:
CohesiveElementFilter(const SolidMechanicsModelCohesive & model,
const Real max_damage = 1.)
: model(model), is_unbroken(max_damage) {}
bool operator()(const Element & el) const override {
- if (Mesh::getKind(el.type) == _ek_regular)
+ if (Mesh::getKind(el.type) == _ek_regular) {
return true;
+ }
const Array<UInt> & mat_indexes =
model.getMaterialByElement(el.type, el.ghost_type);
const Array<UInt> & mat_loc_num =
model.getMaterialLocalNumbering(el.type, el.ghost_type);
const auto & mat = static_cast<const MaterialCohesive &>(
model.getMaterial(mat_indexes(el.element)));
UInt el_index = mat_loc_num(el.element);
UInt nb_quad_per_element =
model.getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(el.type, el.ghost_type);
const Array<Real> & damage_array = mat.getDamage(el.type, el.ghost_type);
AKANTU_DEBUG_ASSERT(nb_quad_per_element * el_index < damage_array.size(),
"This quadrature point is out of range");
const Real * element_damage =
damage_array.storage() + nb_quad_per_element * el_index;
UInt unbroken_quads = std::count_if(
element_damage, element_damage + nb_quad_per_element, is_unbroken);
- if (unbroken_quads > 0)
- return true;
- return false;
+ return (unbroken_quads > 0);
}
private:
struct IsUnbrokenFunctor {
IsUnbrokenFunctor(const Real & max_damage) : max_damage(max_damage) {}
- bool operator()(const Real & x) { return x < max_damage; }
+ bool operator()(const Real & x) const { return x < max_damage; }
const Real max_damage;
};
const SolidMechanicsModelCohesive & model;
const IsUnbrokenFunctor is_unbroken;
};
/* -------------------------------------------------------------------------- */
void FragmentManager::buildFragments(Real damage_limit) {
AKANTU_DEBUG_IN();
if (mesh.isDistributed()) {
auto & cohesive_synchronizer = model.getCohesiveSynchronizer();
cohesive_synchronizer.synchronize(model, SynchronizationTag::_smmc_damage);
}
auto & mesh_facets = mesh.getMeshFacets();
UInt spatial_dimension = model.getSpatialDimension();
std::string fragment_prefix("fragment");
/// generate fragments
global_nb_fragment =
createClusters(spatial_dimension, mesh_facets, fragment_prefix,
CohesiveElementFilter(model, damage_limit));
nb_fragment = getNbElementGroups(spatial_dimension);
fragment_index.resize(nb_fragment);
/// loop over fragments
for (auto && data : zip(iterateElementGroups(), fragment_index)) {
auto name = std::get<0>(data).getName();
/// get fragment index
std::string fragment_index_string = name.substr(fragment_prefix.size() + 1);
std::get<1>(data) = std::stoul(fragment_index_string);
}
/// compute fragments' mass
computeMass();
if (dump_data) {
createDumpDataArray(fragment_index, "fragments", true);
createDumpDataArray(mass, "fragments mass");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeMass() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// create a unit field per quadrature point, since to compute mass
/// it's neccessary to integrate only density
ElementTypeMapArray<Real> unit_field("unit_field", id);
unit_field.initialize(model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost, _default_value = 1.);
integrateFieldOnFragments(unit_field, mass);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeCenterOfMass() {
AKANTU_DEBUG_IN();
/// integrate position multiplied by density
integrateFieldOnFragments(quad_coordinates, mass_center);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * mass_center_storage = mass_center.storage();
UInt total_components = mass_center.size() * mass_center.getNbComponent();
- for (UInt i = 0; i < total_components; ++i)
+ for (UInt i = 0; i < total_components; ++i) {
mass_center_storage[i] /= mass_storage[i];
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeVelocity() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// compute velocity per quadrature point
ElementTypeMapArray<Real> velocity_field("velocity_field", id);
velocity_field.initialize(
model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension, _ghost_type = _not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getVelocity(),
velocity_field);
/// integrate on fragments
integrateFieldOnFragments(velocity_field, velocity);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * velocity_storage = velocity.storage();
UInt total_components = velocity.size() * velocity.getNbComponent();
- for (UInt i = 0; i < total_components; ++i)
+ for (UInt i = 0; i < total_components; ++i) {
velocity_storage[i] /= mass_storage[i];
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Given the distance @f$ \mathbf{r} @f$ between a quadrature point
* and its center of mass, the moment of inertia is computed as \f[
* I_\mathrm{CM} = \mathrm{tr}(\mathbf{r}\mathbf{r}^\mathrm{T})
* \mathbf{I} - \mathbf{r}\mathbf{r}^\mathrm{T} \f] for more
* information check Wikipedia
* (http://en.wikipedia.org/wiki/Moment_of_inertia#Identities_for_a_skew-symmetric_matrix)
*
*/
void FragmentManager::computeInertiaMoments() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
computeCenterOfMass();
/// compute local coordinates products with respect to the center of match
ElementTypeMapArray<Real> moments_coords("moments_coords", id);
moments_coords.initialize(model.getFEEngine(),
_nb_component =
spatial_dimension * spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost, _default_value = 1.);
/// loop over fragments
for (auto && data :
zip(iterateElementGroups(), make_view(mass_center, spatial_dimension))) {
const auto & el_list = std::get<0>(data).getElements();
auto & mass_center = std::get<1>(data);
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
auto nb_quad_per_element =
model.getFEEngine().getNbIntegrationPoints(type);
auto & moments_coords_array = moments_coords(type);
const auto & quad_coordinates_array = quad_coordinates(type);
const auto & el_list_array = el_list(type);
auto moments_begin =
moments_coords_array.begin(spatial_dimension, spatial_dimension);
auto quad_coordinates_begin =
quad_coordinates_array.begin(spatial_dimension);
Vector<Real> relative_coords(spatial_dimension);
for (UInt el = 0; el < el_list_array.size(); ++el) {
UInt global_el = el_list_array(el);
/// loop over quadrature points
for (UInt q = 0; q < nb_quad_per_element; ++q) {
UInt global_q = global_el * nb_quad_per_element + q;
Matrix<Real> moments_matrix = moments_begin[global_q];
const Vector<Real> & quad_coord_vector =
quad_coordinates_begin[global_q];
/// to understand this read the documentation written just
/// before this function
relative_coords = quad_coord_vector;
relative_coords -= mass_center;
moments_matrix.outerProduct(relative_coords, relative_coords);
Real trace = moments_matrix.trace();
moments_matrix *= -1.;
moments_matrix += Matrix<Real>::eye(spatial_dimension, trace);
}
}
}
}
/// integrate moments
Array<Real> integrated_moments(global_nb_fragment,
spatial_dimension * spatial_dimension);
integrateFieldOnFragments(moments_coords, integrated_moments);
/// compute and store principal moments
inertia_moments.resize(global_nb_fragment);
principal_directions.resize(global_nb_fragment);
auto integrated_moments_it =
integrated_moments.begin(spatial_dimension, spatial_dimension);
auto inertia_moments_it = inertia_moments.begin(spatial_dimension);
auto principal_directions_it =
principal_directions.begin(spatial_dimension, spatial_dimension);
for (UInt frag = 0; frag < global_nb_fragment; ++frag,
++integrated_moments_it, ++inertia_moments_it,
++principal_directions_it) {
integrated_moments_it->eig(*inertia_moments_it, *principal_directions_it);
}
- if (dump_data)
+ if (dump_data) {
createDumpDataArray(inertia_moments, "moments of inertia");
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeAllData() {
AKANTU_DEBUG_IN();
buildFragments();
computeVelocity();
computeInertiaMoments();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::storeMassDensityPerIntegrationPoint() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (auto type : mesh.elementTypes(_spatial_dimension = spatial_dimension,
_element_kind = _ek_regular)) {
Array<Real> & mass_density_array = mass_density(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
mass_density_array.resize(nb_element * nb_quad_per_element);
const Array<UInt> & mat_indexes = model.getMaterialByElement(type);
Real * mass_density_it = mass_density_array.storage();
/// store mass_density for each element and quadrature point
for (UInt el = 0; el < nb_element; ++el) {
Material & mat = model.getMaterial(mat_indexes(el));
- for (UInt q = 0; q < nb_quad_per_element; ++q, ++mass_density_it)
+ for (UInt q = 0; q < nb_quad_per_element; ++q, ++mass_density_it) {
*mass_density_it = mat.getRho();
+ }
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::integrateFieldOnFragments(
ElementTypeMapArray<Real> & field, Array<Real> & output) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
UInt nb_component = output.getNbComponent();
/// integration part
output.resize(global_nb_fragment);
- output.clear();
+ output.zero();
auto output_begin = output.begin(nb_component);
/// loop over fragments
for (auto && data : zip(iterateElementGroups(), fragment_index)) {
const auto & el_list = std::get<0>(data).getElements();
auto fragment_index = std::get<1>(data);
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_quad_per_element =
model.getFEEngine().getNbIntegrationPoints(type);
const Array<Real> & density_array = mass_density(type);
Array<Real> & field_array = field(type);
const Array<UInt> & elements = el_list(type);
/// generate array to be integrated by filtering fragment's elements
Array<Real> integration_array(elements.size() * nb_quad_per_element,
nb_component);
auto field_array_begin = field_array.begin_reinterpret(
nb_quad_per_element, nb_component,
field_array.size() / nb_quad_per_element);
auto density_array_begin = density_array.begin_reinterpret(
nb_quad_per_element, density_array.size() / nb_quad_per_element);
for (auto && data : enumerate(make_view(
integration_array, nb_quad_per_element, nb_component))) {
UInt global_el = elements(std::get<0>(data));
auto & int_array = std::get<1>(data);
int_array = field_array_begin[global_el];
/// multiply field by density
const Vector<Real> & density_vector = density_array_begin[global_el];
for (UInt i = 0; i < nb_quad_per_element; ++i) {
for (UInt j = 0; j < nb_component; ++j) {
int_array(i, j) *= density_vector(i);
}
}
}
/// integrate the field over the fragment
Array<Real> integrated_array(elements.size(), nb_component);
model.getFEEngine().integrate(integration_array, integrated_array,
nb_component, type, _not_ghost, elements);
/// sum over all elements and store the result
Vector<Real> output_tmp(output_begin[fragment_index]);
output_tmp += std::accumulate(integrated_array.begin(nb_component),
integrated_array.end(nb_component),
Vector<Real>(nb_component));
}
}
/// sum output over all processors
const Communicator & comm = mesh.getCommunicator();
comm.allReduce(output, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeNbElementsPerFragment() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
nb_elements_per_fragment.resize(global_nb_fragment);
- nb_elements_per_fragment.clear();
+ nb_elements_per_fragment.zero();
/// loop over fragments
for (auto && data : zip(iterateElementGroups(), fragment_index)) {
const auto & el_list = std::get<0>(data).getElements();
auto fragment_index = std::get<1>(data);
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_element = el_list(type).size();
nb_elements_per_fragment(fragment_index) += nb_element;
}
}
/// sum values over all processors
const auto & comm = mesh.getCommunicator();
comm.allReduce(nb_elements_per_fragment, SynchronizerOperation::_sum);
- if (dump_data)
+ if (dump_data) {
createDumpDataArray(nb_elements_per_fragment, "elements per fragment");
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void FragmentManager::createDumpDataArray(Array<T> & data, std::string name,
bool fragment_index_output) {
AKANTU_DEBUG_IN();
- if (data.size() == 0)
+ if (data.empty()) {
return;
+ }
auto & mesh_not_const = const_cast<Mesh &>(mesh);
auto && spatial_dimension = mesh.getSpatialDimension();
auto && nb_component = data.getNbComponent();
auto && data_begin = data.begin(nb_component);
/// loop over fragments
for (auto && data : zip(iterateElementGroups(), fragment_index)) {
const auto & fragment = std::get<0>(data);
auto fragment_idx = std::get<1>(data);
/// loop over cluster types
- for (auto & type : fragment.elementTypes(spatial_dimension)) {
+ for (auto && type : fragment.elementTypes(spatial_dimension)) {
/// init mesh data
auto & mesh_data = mesh_not_const.getDataPointer<T>(
name, type, _not_ghost, nb_component);
auto mesh_data_begin = mesh_data.begin(nb_component);
/// fill mesh data
for (const auto & elem : fragment.getElements(type)) {
Vector<T> md_tmp = mesh_data_begin[elem];
if (fragment_index_output) {
md_tmp(0) = fragment_idx;
} else {
md_tmp = data_begin[fragment_idx];
}
}
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
index 41c95eb6b..707153d0f 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
@@ -1,168 +1,168 @@
/**
* @file fragment_manager.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jan 23 2014
* @date last modification: Thu Jul 06 2017
*
* @brief Group manager to handle fragments
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "group_manager.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_FRAGMENT_MANAGER_HH__
-#define __AKANTU_FRAGMENT_MANAGER_HH__
+#ifndef AKANTU_FRAGMENT_MANAGER_HH_
+#define AKANTU_FRAGMENT_MANAGER_HH_
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
class FragmentManager : public GroupManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FragmentManager(SolidMechanicsModelCohesive & model, bool dump_data = true,
const ID & id = "fragment_manager",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/// store mass density per integration point
void storeMassDensityPerIntegrationPoint();
/// integrate an elemental field multiplied by density on global
/// fragments
void integrateFieldOnFragments(ElementTypeMapArray<Real> & field,
Array<Real> & output);
/// compute fragments' mass
void computeMass();
/// create dump data for a single array
template <typename T>
void createDumpDataArray(Array<T> & data, std::string name,
bool fragment_index_output = false);
public:
/// build fragment list (cohesive elements are considered broken if
/// damage >= damage_limit)
void buildFragments(Real damage_limit = 1.);
/// compute fragments' center of mass
void computeCenterOfMass();
/// compute fragments' velocity
void computeVelocity();
/// computes principal moments of inertia with respect to the center
/// of mass of each fragment
void computeInertiaMoments();
/// compute all fragments' data
void computeAllData();
/// compute number of elements per fragment
void computeNbElementsPerFragment();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get number of fragments
AKANTU_GET_MACRO(NbFragment, global_nb_fragment, UInt);
/// get fragments' mass
AKANTU_GET_MACRO(Mass, mass, const Array<Real> &);
/// get fragments' center of mass
AKANTU_GET_MACRO(CenterOfMass, mass_center, const Array<Real> &);
/// get fragments' velocity
AKANTU_GET_MACRO(Velocity, velocity, const Array<Real> &);
/// get fragments' principal moments of inertia
AKANTU_GET_MACRO(MomentsOfInertia, inertia_moments, const Array<Real> &);
/// get fragments' principal directions
AKANTU_GET_MACRO(PrincipalDirections, principal_directions,
const Array<Real> &);
/// get number of elements per fragment
AKANTU_GET_MACRO(NbElementsPerFragment, nb_elements_per_fragment,
const Array<UInt> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// local_fragment index
Array<UInt> fragment_index;
/// global number of fragments (parallel simulations)
UInt global_nb_fragment;
/// number of fragments
UInt nb_fragment;
/// cohesive solid mechanics model associated
SolidMechanicsModelCohesive & model;
/// fragments' center of mass
Array<Real> mass_center;
/// fragments' mass
Array<Real> mass;
/// fragments' velocity
Array<Real> velocity;
/// fragments' principal moments of inertia with respect to the
/// center of mass
Array<Real> inertia_moments;
/// fragments' principal directions
Array<Real> principal_directions;
/// quadrature points' coordinates
ElementTypeMapArray<Real> quad_coordinates;
/// mass density per quadrature point
ElementTypeMapArray<Real> mass_density;
/// fragment filter
Array<UInt> nb_elements_per_fragment;
/// dump data
bool dump_data;
};
} // namespace akantu
-#endif /* __AKANTU_FRAGMENT_MANAGER_HH__ */
+#endif /* AKANTU_FRAGMENT_MANAGER_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
index 4523e04ae..ba21f38cf 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
@@ -1,166 +1,166 @@
/**
* @file material_selector_cohesive.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Dec 11 2015
* @date last modification: Mon Dec 18 2017
*
* @brief Material selector for cohesive elements
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_selector_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DefaultMaterialCohesiveSelector::DefaultMaterialCohesiveSelector(
const SolidMechanicsModelCohesive & model)
: facet_material(model.getFacetMaterial()), mesh(model.getMesh()) {
// backward compatibility v3: to get the former behavior back when the user
// creates its own selector
this->fallback_selector =
std::make_shared<DefaultMaterialSelector>(model.getMaterialByElement());
}
/* -------------------------------------------------------------------------- */
UInt DefaultMaterialCohesiveSelector::operator()(const Element & element) {
if (Mesh::getKind(element.type) == _ek_cohesive) {
try {
const Array<Element> & cohesive_el_to_facet =
mesh.getMeshFacets().getSubelementToElement(element.type,
element.ghost_type);
bool third_dimension = (mesh.getSpatialDimension() == 3);
const Element & facet =
- cohesive_el_to_facet(element.element, third_dimension);
+ cohesive_el_to_facet(element.element, UInt(third_dimension));
if (facet_material.exists(facet.type, facet.ghost_type)) {
return facet_material(facet.type, facet.ghost_type)(facet.element);
- } else {
- return fallback_value;
}
+ return fallback_value;
+
} catch (...) {
return fallback_value;
}
} else if (Mesh::getSpatialDimension(element.type) ==
mesh.getSpatialDimension() - 1) {
return facet_material(element.type, element.ghost_type)(element.element);
} else {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
MeshDataMaterialCohesiveSelector::MeshDataMaterialCohesiveSelector(
const SolidMechanicsModelCohesive & model)
: model(model), mesh_facets(model.getMeshFacets()),
material_index(mesh_facets.getData<std::string>("physical_names")) {
third_dimension = (model.getSpatialDimension() == 3);
// backward compatibility v3: to get the former behavior back when the user
// creates its own selector
this->fallback_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
}
/* -------------------------------------------------------------------------- */
UInt MeshDataMaterialCohesiveSelector::operator()(const Element & element) {
if (Mesh::getKind(element.type) == _ek_cohesive or
Mesh::getSpatialDimension(element.type) == mesh_facets.getSpatialDimension() - 1) {
Element facet;
if (Mesh::getKind(element.type) == _ek_cohesive) {
facet = mesh_facets.getSubelementToElement(element.type,
element.ghost_type)(element.element,
- third_dimension);
+ UInt(third_dimension));
} else {
facet = element;
}
try {
std::string material_name = this->material_index(facet);
return this->model.getMaterialIndex(material_name);
} catch (...) {
return fallback_value;
}
}
return MaterialSelector::operator()(element);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
MaterialCohesiveRulesSelector::MaterialCohesiveRulesSelector(
const SolidMechanicsModelCohesive & model,
const MaterialCohesiveRules & rules,
ID mesh_data_id) // what we have here is the name of model and also
// the name of different materials
: model(model), mesh_data_id(std::move(mesh_data_id)),
mesh(model.getMesh()), mesh_facets(model.getMeshFacets()),
spatial_dimension(model.getSpatialDimension()), rules(rules) {
// cohesive fallback
this->fallback_selector =
std::make_shared<DefaultMaterialCohesiveSelector>(model);
// non cohesive fallback
this->fallback_selector->setFallback(
std::make_shared<MeshDataMaterialSelector<std::string>>(mesh_data_id,
model));
}
/* -------------------------------------------------------------------------- */
UInt MaterialCohesiveRulesSelector::operator()(const Element & element) {
if (mesh_facets.getSpatialDimension(element.type) ==
(spatial_dimension - 1)) {
const std::vector<Element> & element_to_subelement =
mesh_facets.getElementToSubelement(element.type,
element.ghost_type)(element.element);
// Array<bool> & facets_check = model.getFacetsCheck();
const Element & el1 = element_to_subelement[0];
const Element & el2 = element_to_subelement[1];
ID id1 = mesh.getData<std::string>(mesh_data_id, el1.type,
el1.ghost_type)(el1.element);
ID id2 = id1;
if (el2 != ElementNull) {
id2 = mesh.getData<std::string>(mesh_data_id, el2.type,
el2.ghost_type)(el2.element);
}
auto rit = rules.find(std::make_pair(id1, id2));
if (rit == rules.end()) {
rit = rules.find(std::make_pair(id2, id1));
}
if (rit != rules.end()) {
return model.getMaterialIndex(rit->second);
}
}
return MaterialSelector::operator()(element);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
index 65c31fdad..ecb618f63 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
@@ -1,98 +1,98 @@
/**
* @file material_selector_cohesive.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Dec 11 2015
* @date last modification: Mon Dec 18 2017
*
* @brief Material selectors for cohesive elements
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_selector.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
-#ifndef __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__
-#define __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__
+#ifndef AKANTU_MATERIAL_SELECTOR_COHESIVE_HH_
+#define AKANTU_MATERIAL_SELECTOR_COHESIVE_HH_
/* -------------------------------------------------------------------------- */
/**
* class that assigns the first cohesive material by default to the
* cohesive elements
*/
class DefaultMaterialCohesiveSelector : public MaterialSelector {
public:
DefaultMaterialCohesiveSelector(const SolidMechanicsModelCohesive & model);
UInt operator()(const Element & element) override;
private:
const ElementTypeMapArray<UInt> & facet_material;
const Mesh & mesh;
};
/* -------------------------------------------------------------------------- */
/// To be used with intrinsic elements inserted along mesh physical surfaces
class MeshDataMaterialCohesiveSelector : public MaterialSelector {
public:
MeshDataMaterialCohesiveSelector(const SolidMechanicsModelCohesive & model);
UInt operator()(const Element & element) override;
protected:
const SolidMechanicsModelCohesive & model;
const Mesh & mesh_facets;
const ElementTypeMapArray<std::string> & material_index;
bool third_dimension;
};
/// bulk1, bulk2 -> cohesive
using MaterialCohesiveRules = std::map<std::pair<ID, ID>, ID>;
/* -------------------------------------------------------------------------- */
class MaterialCohesiveRulesSelector : public MaterialSelector {
public:
MaterialCohesiveRulesSelector(const SolidMechanicsModelCohesive & model,
const MaterialCohesiveRules & rules,
ID mesh_data_id = "physical_names");
- UInt operator()(const Element & element);
+ UInt operator()(const Element & element) override;
private:
const SolidMechanicsModelCohesive & model;
ID mesh_data_id;
const Mesh & mesh;
const Mesh & mesh_facets;
UInt spatial_dimension;
MaterialCohesiveRules rules;
};
-#endif /* __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__ */
+#endif /* AKANTU_MATERIAL_SELECTOR_COHESIVE_HH_ */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
index 876075cff..c78ded4b1 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
@@ -1,66 +1,66 @@
/**
* @file cohesive_internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Internal field for cohesive elements
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "internal_field.hh"
-#ifndef __AKANTU_COHESIVE_INTERNAL_FIELD_HH__
-#define __AKANTU_COHESIVE_INTERNAL_FIELD_HH__
+#ifndef AKANTU_COHESIVE_INTERNAL_FIELD_HH_
+#define AKANTU_COHESIVE_INTERNAL_FIELD_HH_
namespace akantu {
/// internal field class for cohesive materials
template <typename T> class CohesiveInternalField : public InternalField<T> {
public:
CohesiveInternalField(const ID & id, Material & material);
~CohesiveInternalField() override;
/// initialize the field to a given number of component
void initialize(UInt nb_component) override;
private:
CohesiveInternalField operator=(__attribute__((unused))
const CohesiveInternalField & other){};
};
/* -------------------------------------------------------------------------- */
/* Facet Internal Field */
/* -------------------------------------------------------------------------- */
template <typename T> class FacetInternalField : public InternalField<T> {
public:
FacetInternalField(const ID & id, Material & material);
~FacetInternalField() override;
/// initialize the field to a given number of component
void initialize(UInt nb_component) override;
};
} // namespace akantu
-#endif /* __AKANTU_COHESIVE_INTERNAL_FIELD_HH__ */
+#endif /* AKANTU_COHESIVE_INTERNAL_FIELD_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
index daae7aaf6..5a677f252 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
@@ -1,94 +1,94 @@
/**
* @file cohesive_internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Wed Nov 08 2017
*
* @brief implementation of the cohesive internal field
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH__
-#define __AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH__
+#ifndef AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH_
+#define AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH_
namespace akantu {
template <typename T>
CohesiveInternalField<T>::CohesiveInternalField(const ID & id,
Material & material)
: InternalField<T>(
id, material, material.getModel().getFEEngine("CohesiveFEEngine"),
aka::as_type<MaterialCohesive>(material).getElementFilter()) {
this->element_kind = _ek_cohesive;
}
template <typename T>
CohesiveInternalField<T>::~CohesiveInternalField() = default;
template <typename T>
void CohesiveInternalField<T>::initialize(UInt nb_component) {
this->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T>
FacetInternalField<T>::FacetInternalField(const ID & id, Material & material)
: InternalField<T>(
id, material, material.getModel().getFEEngine("FacetsFEEngine"),
aka::as_type<MaterialCohesive>(material).getFacetFilter()) {
this->spatial_dimension -= 1;
this->element_kind = _ek_regular;
}
template <typename T> FacetInternalField<T>::~FacetInternalField() = default;
template <typename T>
void FacetInternalField<T>::initialize(UInt nb_component) {
this->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<RandomInternalField<Real, FacetInternalField>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<RandomInternalField<Real, CohesiveInternalField>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
} // namespace akantu
-#endif /* __AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH__ */
+#endif /* AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
index ef37602f5..50a7782fa 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
@@ -1,208 +1,213 @@
/**
* @file material_cohesive_bilinear.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
* @date last modification: Tue Feb 20 2018
*
* @brief Bilinear cohesive constitutive law
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_bilinear.hh"
//#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveBilinear<spatial_dimension>::MaterialCohesiveBilinear(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesiveLinear<spatial_dimension>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("delta_0", delta_0, Real(0.),
_pat_parsable | _pat_readable,
"Elastic limit displacement");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
this->sigma_c_eff.setRandomDistribution(this->sigma_c.getRandomParameter());
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
this->delta_max.setDefaultValue(delta_0);
this->insertion_stress.setDefaultValue(0);
this->delta_max.reset();
this->insertion_stress.reset();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::onElementsAdded(
const Array<Element> & element_list, const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::onElementsAdded(element_list,
event);
bool scale_traction = false;
// don't scale sigma_c if volume_s hasn't been specified by the user
- if (!Math::are_float_equal(this->volume_s, 0.))
+ if (!Math::are_float_equal(this->volume_s, 0.)) {
scale_traction = true;
+ }
Array<Element>::const_scalar_iterator el_it = element_list.begin();
Array<Element>::const_scalar_iterator el_end = element_list.end();
for (; el_it != el_end; ++el_it) {
// filter not ghost cohesive elements
- if (el_it->ghost_type != _not_ghost ||
- Mesh::getKind(el_it->type) != _ek_cohesive)
+ if ((el_it->ghost_type != _not_ghost) or
+ (Mesh::getKind(el_it->type) != _ek_cohesive)) {
continue;
+ }
UInt index = el_it->element;
ElementType type = el_it->type;
UInt nb_element = this->model->getMesh().getNbElement(type);
UInt nb_quad_per_element = this->fem_cohesive.getNbIntegrationPoints(type);
auto sigma_c_begin = this->sigma_c_eff(type).begin_reinterpret(
nb_quad_per_element, nb_element);
Vector<Real> sigma_c_vec = sigma_c_begin[index];
auto delta_c_begin = this->delta_c_eff(type).begin_reinterpret(
nb_quad_per_element, nb_element);
Vector<Real> delta_c_vec = delta_c_begin[index];
- if (scale_traction)
+ if (scale_traction) {
scaleTraction(*el_it, sigma_c_vec);
+ }
/**
* Recompute sigma_c as
* @f$ {\sigma_c}_\textup{new} =
* \frac{{\sigma_c}_\textup{old} \delta_c} {\delta_c - \delta_0} @f$
*/
for (UInt q = 0; q < nb_quad_per_element; ++q) {
delta_c_vec(q) = 2 * this->G_c / sigma_c_vec(q);
- if (delta_c_vec(q) - delta_0 < Math::getTolerance())
+ if (delta_c_vec(q) - delta_0 < Math::getTolerance()) {
AKANTU_ERROR("delta_0 = " << delta_0 << " must be lower than delta_c = "
<< delta_c_vec(q)
<< ", modify your material file");
+ }
sigma_c_vec(q) *= delta_c_vec(q) / (delta_c_vec(q) - delta_0);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::scaleTraction(
const Element & el, Vector<Real> & sigma_c_vec) {
AKANTU_DEBUG_IN();
Real base_sigma_c = this->sigma_c_eff;
const Mesh & mesh_facets = this->model->getMeshFacets();
const FEEngine & fe_engine = this->model->getFEEngine();
auto coh_element_to_facet_begin =
mesh_facets.getSubelementToElement(el.type).begin(2);
const Vector<Element> & coh_element_to_facet =
coh_element_to_facet_begin[el.element];
// compute bounding volume
Real volume = 0;
// loop over facets
for (UInt f = 0; f < 2; ++f) {
const Element & facet = coh_element_to_facet(f);
const Array<std::vector<Element>> & facet_to_element =
mesh_facets.getElementToSubelement(facet.type, facet.ghost_type);
const std::vector<Element> & element_list = facet_to_element(facet.element);
auto elem = element_list.begin();
auto elem_end = element_list.end();
// loop over elements connected to each facet
for (; elem != elem_end; ++elem) {
// skip cohesive elements and dummy elements
- if (*elem == ElementNull || Mesh::getKind(elem->type) == _ek_cohesive)
+ if (*elem == ElementNull || Mesh::getKind(elem->type) == _ek_cohesive) {
continue;
+ }
// unit vector for integration in order to obtain the volume
UInt nb_quadrature_points = fe_engine.getNbIntegrationPoints(elem->type);
Vector<Real> unit_vector(nb_quadrature_points, 1);
volume += fe_engine.integrate(unit_vector, elem->type, elem->element,
elem->ghost_type);
}
}
// scale sigma_c
sigma_c_vec -= base_sigma_c;
sigma_c_vec *= std::pow(this->volume_s / volume, 1. / this->m_s);
sigma_c_vec += base_sigma_c;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::computeTraction(normal, el_type,
ghost_type);
// adjust damage
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto delta_max_it = this->delta_max(el_type, ghost_type).begin();
auto damage_it = this->damage(el_type, ghost_type).begin();
auto damage_end = this->damage(el_type, ghost_type).end();
for (; damage_it != damage_end; ++damage_it, ++delta_max_it, ++delta_c_it) {
*damage_it =
std::max((*delta_max_it - delta_0) / (*delta_c_it - delta_0), Real(0.));
*damage_it = std::min(*damage_it, Real(1.));
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_bilinear, MaterialCohesiveBilinear);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
index e6ff32652..b55fe0911 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
@@ -1,104 +1,104 @@
/**
* @file material_cohesive_bilinear.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Bilinear cohesive constitutive law
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
-#ifndef __AKANTU_MATERIAL_COHESIVE_BILINEAR_HH__
-#define __AKANTU_MATERIAL_COHESIVE_BILINEAR_HH__
+#ifndef AKANTU_MATERIAL_COHESIVE_BILINEAR_HH_
+#define AKANTU_MATERIAL_COHESIVE_BILINEAR_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material bilinear
*
* parameters in the material files :
* - delta_0 : elastic limit displacement (default: 0)
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default:
* 0)
* - G_cI : fracture energy for mode I (default: 0)
* - G_cII : fracture energy for mode II (default: 0)
* - penalty : stiffness in compression to prevent penetration
*/
template <UInt spatial_dimension>
class MaterialCohesiveBilinear
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveBilinear(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// set material parameters for new elements
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/**
* Scale traction sigma_c according to the volume of the
* two elements surrounding an element
*/
void scaleTraction(const Element & el, Vector<Real> & sigma_c_vec);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// elastic limit displacement
Real delta_0;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "material_cohesive_elastic_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_COHESIVE_BILINEAR_HH__ */
+#endif /* AKANTU_MATERIAL_COHESIVE_BILINEAR_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
index 25b519626..9732044eb 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
@@ -1,340 +1,343 @@
/**
* @file material_cohesive_exponential.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Mon Jul 09 2012
* @date last modification: Tue Feb 20 2018
*
* @brief Exponential irreversible cohesive law of mixed mode loading
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_exponential.hh"
#include "dof_synchronizer.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveExponential<spatial_dimension>::MaterialCohesiveExponential(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesive(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("beta", beta, Real(0.), _pat_parsable, "Beta parameter");
this->registerParam("exponential_penalty", exp_penalty, true, _pat_parsable,
"Is contact penalty following the exponential law?");
this->registerParam(
"contact_tangent", contact_tangent, Real(1.0), _pat_parsable,
"Ratio of contact tangent over the initial exponential tangent");
// this->initInternalArray(delta_max, 1, _ek_cohesive);
use_previous_delta_max = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesive::initMaterial();
if ((exp_penalty) && (contact_tangent != 1)) {
contact_tangent = 1;
AKANTU_DEBUG_WARNING("The parsed paramter <contact_tangent> is forced to "
"1.0 when the contact penalty follows the exponential "
"law");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto traction_it = tractions(el_type, ghost_type).begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto traction_end = tractions(el_type, ghost_type).end(spatial_dimension);
auto delta_max_it = delta_max(el_type, ghost_type).begin();
auto delta_max_prev_it = delta_max.previous(el_type, ghost_type).begin();
/// compute scalars
Real beta2 = beta * beta;
/// loop on each quadrature point
for (; traction_it != traction_end; ++traction_it, ++opening_it, ++normal_it,
++delta_max_it, ++delta_max_prev_it) {
/// compute normal and tangential opening vectors
Real normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening(spatial_dimension);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \beta^2 \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta = tangential_opening_norm;
delta *= delta * beta2;
delta += normal_opening_norm * normal_opening_norm;
delta = sqrt(delta);
if ((normal_opening_norm < 0) &&
(std::abs(normal_opening_norm) > Math::getTolerance())) {
Vector<Real> op_n(*normal_it);
op_n *= normal_opening_norm;
Vector<Real> delta_s(*opening_it);
delta_s -= op_n;
delta = tangential_opening_norm * beta;
computeCoupledTraction(*traction_it, *normal_it, delta, delta_s,
*delta_max_it, *delta_max_prev_it);
computeCompressiveTraction(*traction_it, *normal_it, normal_opening_norm,
*opening_it);
- } else
+ } else {
computeCoupledTraction(*traction_it, *normal_it, delta, *opening_it,
*delta_max_it, *delta_max_prev_it);
+ }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCoupledTraction(
Vector<Real> & tract, const Vector<Real> & normal, Real delta,
const Vector<Real> & opening, Real & delta_max_new, Real delta_max) {
AKANTU_DEBUG_IN();
/// full damage case
if (std::abs(delta) < Math::getTolerance()) {
/// set traction to zero
- tract.clear();
+ tract.zero();
} else { /// element not fully damaged
/**
* Compute traction loading @f$ \mathbf{T} =
* e \sigma_c \frac{\delta}{\delta_c} e^{-\delta/ \delta_c}@f$
*/
/**
* Compute traction unloading @f$ \mathbf{T} =
* \frac{t_{max}}{\delta_{max}} \delta @f$
*/
Real beta2 = beta * beta;
Real normal_open_norm = opening.dot(normal);
Vector<Real> op_n_n(spatial_dimension);
op_n_n = normal;
op_n_n *= (1 - beta2);
op_n_n *= normal_open_norm;
tract = beta2 * opening;
tract += op_n_n;
delta_max_new = std::max(delta_max, delta);
tract *=
std::exp(1.) * sigma_c * std::exp(-delta_max_new / delta_c) / delta_c;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCompressiveTraction(
Vector<Real> & tract, const Vector<Real> & normal, Real delta_n,
__attribute__((unused)) const Vector<Real> & opening) {
Vector<Real> temp_tract(normal);
if (exp_penalty) {
temp_tract *= delta_n * std::exp(1) * sigma_c *
std::exp(-delta_n / delta_c) / delta_c;
} else {
Real initial_tg =
contact_tangent * std::exp(1.) * sigma_c * delta_n / delta_c;
temp_tract *= initial_tg;
}
tract += temp_tract;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeTangentTraction(
- const ElementType & el_type, Array<Real> & tangent_matrix,
+ ElementType el_type, Array<Real> & tangent_matrix,
const Array<Real> & normal, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
auto delta_max_it = delta_max.previous(el_type, ghost_type).begin();
Real beta2 = beta * beta;
/**
* compute tangent matrix @f$ \frac{\partial \mathbf{t}}
* {\partial \delta} = \hat{\mathbf{t}} \otimes
* \frac{\partial (t/\delta)}{\partial \delta}
* \frac{\hat{\mathbf{t}}}{\delta}+ \frac{t}{\delta} [ \beta^2 \mathbf{I} +
* (1-\beta^2) (\mathbf{n} \otimes \mathbf{n})] @f$
**/
/**
* In which @f$
* \frac{\partial(t/ \delta)}{\partial \delta} =
* \left\{\begin{array} {l l}
* -e \frac{\sigma_c}{\delta_c^2 }e^{-\delta / \delta_c} & \quad if
* \delta \geq \delta_{max} \\
* 0 & \quad if \delta < \delta_{max}, \delta_n > 0
* \end{array}\right. @f$
**/
for (; tangent_it != tangent_end;
++tangent_it, ++normal_it, ++opening_it, ++delta_max_it) {
Real normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening(spatial_dimension);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
Real delta = tangential_opening_norm;
delta *= delta * beta2;
delta += normal_opening_norm * normal_opening_norm;
delta = sqrt(delta);
if ((normal_opening_norm < 0) &&
(std::abs(normal_opening_norm) > Math::getTolerance())) {
Vector<Real> op_n(*normal_it);
op_n *= normal_opening_norm;
Vector<Real> delta_s(*opening_it);
delta_s -= op_n;
delta = tangential_opening_norm * beta;
computeCoupledTangent(*tangent_it, *normal_it, delta, delta_s,
*delta_max_it);
computeCompressivePenalty(*tangent_it, *normal_it, normal_opening_norm);
- } else
+ } else {
computeCoupledTangent(*tangent_it, *normal_it, delta, *opening_it,
*delta_max_it);
+ }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCoupledTangent(
Matrix<Real> & tangent, const Vector<Real> & normal, Real delta,
- const Vector<Real> & opening, Real) {
+ const Vector<Real> & opening, Real /*unused*/) {
AKANTU_DEBUG_IN();
Real beta2 = beta * beta;
Matrix<Real> J(spatial_dimension, spatial_dimension);
J.eye(beta2);
if (std::abs(delta) < Math::getTolerance()) {
delta = Math::getTolerance();
}
Real opening_normal;
opening_normal = opening.dot(normal);
Vector<Real> delta_e(normal);
delta_e *= opening_normal;
delta_e *= (1. - beta2);
delta_e += (beta2 * opening);
Real exponent = std::exp(1. - delta / delta_c) * sigma_c / delta_c;
Matrix<Real> first_term(spatial_dimension, spatial_dimension);
first_term.outerProduct(normal, normal);
first_term *= (1. - beta2);
first_term += J;
Matrix<Real> second_term(spatial_dimension, spatial_dimension);
second_term.outerProduct(delta_e, delta_e);
second_term /= delta;
second_term /= delta_c;
Matrix<Real> diff(first_term);
diff -= second_term;
tangent = diff;
tangent *= exponent;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCompressivePenalty(
Matrix<Real> & tangent, const Vector<Real> & normal, Real delta_n) {
- if (!exp_penalty)
+ if (!exp_penalty) {
delta_n = 0.;
+ }
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(normal, normal);
Real normal_tg = contact_tangent * std::exp(1.) * sigma_c *
std::exp(-delta_n / delta_c) * (1. - delta_n / delta_c) /
delta_c;
n_outer_n *= normal_tg;
tangent += n_outer_n;
}
INSTANTIATE_MATERIAL(cohesive_exponential, MaterialCohesiveExponential);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
index 7817a8d42..24495057c 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
@@ -1,121 +1,121 @@
/**
* @file material_cohesive_exponential.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Exponential irreversible cohesive law of mixed mode loading
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH__
-#define __AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH__
+#ifndef AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH_
+#define AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material Exponential damage
*
* parameters in the material files :
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default:
* 0)
* - delta_c : critical opening (default: 0)
*/
template <UInt spatial_dimension>
class MaterialCohesiveExponential : public MaterialCohesive {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveExponential(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// Initialization
void initMaterial() override;
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
- void computeTangentTraction(const ElementType & el_type,
+ void computeTangentTraction(ElementType el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type = _not_ghost) override;
private:
void computeCoupledTraction(Vector<Real> & tract, const Vector<Real> & normal,
Real delta, const Vector<Real> & opening,
Real & delta_max_new, Real delta_max);
void computeCompressiveTraction(Vector<Real> & tract,
const Vector<Real> & normal, Real delta_n,
const Vector<Real> & opening);
void computeCoupledTangent(Matrix<Real> & tangent,
const Vector<Real> & normal, Real delta,
const Vector<Real> & opening, Real delta_max_new);
void computeCompressivePenalty(Matrix<Real> & tangent,
const Vector<Real> & normal, Real delta_n);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// beta parameter
Real beta;
/// contact penalty = initial slope ?
bool exp_penalty;
/// Ratio of contact tangent over the initial exponential tangent
Real contact_tangent;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
// #include "material_cohesive_exponential_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH__ */
+#endif /* AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
index 17b79f9ee..d3aadeb8c 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
@@ -1,421 +1,431 @@
/**
* @file material_cohesive_linear.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
* @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#include "dof_synchronizer.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinear<spatial_dimension>::MaterialCohesiveLinear(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesive(model, id), sigma_c_eff("sigma_c_eff", *this),
delta_c_eff("delta_c_eff", *this),
insertion_stress("insertion_stress", *this) {
AKANTU_DEBUG_IN();
this->registerParam("beta", beta, Real(0.), _pat_parsable | _pat_readable,
"Beta parameter");
this->registerParam("G_c", G_c, Real(0.), _pat_parsable | _pat_readable,
"Mode I fracture energy");
this->registerParam("penalty", penalty, Real(0.),
_pat_parsable | _pat_readable, "Penalty coefficient");
this->registerParam("volume_s", volume_s, Real(0.),
_pat_parsable | _pat_readable,
"Reference volume for sigma_c scaling");
this->registerParam("m_s", m_s, Real(1.), _pat_parsable | _pat_readable,
"Weibull exponent for sigma_c scaling");
this->registerParam("kappa", kappa, Real(1.), _pat_parsable | _pat_readable,
"Kappa parameter");
this->registerParam(
"contact_after_breaking", contact_after_breaking, false,
_pat_parsable | _pat_readable,
"Activation of contact when the elements are fully damaged");
this->registerParam("max_quad_stress_insertion", max_quad_stress_insertion,
false, _pat_parsable | _pat_readable,
"Insertion of cohesive element when stress is high "
"enough just on one quadrature point");
this->registerParam("recompute", recompute, false,
_pat_parsable | _pat_modifiable, "recompute solution");
this->use_previous_delta_max = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesive::initMaterial();
sigma_c_eff.initialize(1);
delta_c_eff.initialize(1);
insertion_stress.initialize(spatial_dimension);
- if (not Math::are_float_equal(delta_c, 0.))
+ if (not Math::are_float_equal(delta_c, 0.)) {
delta_c_eff.setDefaultValue(delta_c);
- else
+ } else {
delta_c_eff.setDefaultValue(2 * G_c / sigma_c);
+ }
- if (model->getIsExtrinsic())
+ if (model->getIsExtrinsic()) {
scaleInsertionTraction();
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::updateInternalParameters() {
/// compute scalars
beta2_kappa2 = beta * beta / kappa / kappa;
beta2_kappa = beta * beta / kappa;
- if (Math::are_float_equal(beta, 0))
+ if (Math::are_float_equal(beta, 0)) {
beta2_inv = 0;
- else
+ } else {
beta2_inv = 1. / beta / beta;
+ }
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::scaleInsertionTraction() {
AKANTU_DEBUG_IN();
// do nothing if volume_s hasn't been specified by the user
- if (Math::are_float_equal(volume_s, 0.))
+ if (Math::are_float_equal(volume_s, 0.)) {
return;
+ }
const Mesh & mesh_facets = model->getMeshFacets();
const auto & fe_engine = model->getFEEngine();
const auto & fe_engine_facet = model->getFEEngine("FacetsFEEngine");
Real base_sigma_c = sigma_c;
for (auto && type_facet : mesh_facets.elementTypes(spatial_dimension - 1)) {
const Array<std::vector<Element>> & facet_to_element =
mesh_facets.getElementToSubelement(type_facet);
UInt nb_facet = facet_to_element.size();
UInt nb_quad_per_facet = fe_engine_facet.getNbIntegrationPoints(type_facet);
// iterator to modify sigma_c for all the quadrature points of a facet
auto sigma_c_iterator =
sigma_c(type_facet).begin_reinterpret(nb_quad_per_facet, nb_facet);
for (UInt f = 0; f < nb_facet; ++f, ++sigma_c_iterator) {
const std::vector<Element> & element_list = facet_to_element(f);
// compute bounding volume
Real volume = 0;
auto elem = element_list.begin();
auto elem_end = element_list.end();
for (; elem != elem_end; ++elem) {
- if (*elem == ElementNull)
+ if (*elem == ElementNull) {
continue;
+ }
// unit vector for integration in order to obtain the volume
UInt nb_quadrature_points =
fe_engine.getNbIntegrationPoints(elem->type);
Vector<Real> unit_vector(nb_quadrature_points, 1);
volume += fe_engine.integrate(unit_vector, elem->type, elem->element,
elem->ghost_type);
}
// scale sigma_c
*sigma_c_iterator -= base_sigma_c;
*sigma_c_iterator *= std::pow(volume_s / volume, 1. / m_s);
*sigma_c_iterator += base_sigma_c;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::checkInsertion(
bool check_only) {
AKANTU_DEBUG_IN();
const Mesh & mesh_facets = model->getMeshFacets();
CohesiveElementInserter & inserter = model->getElementInserter();
for (auto && type_facet : mesh_facets.elementTypes(spatial_dimension - 1)) {
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
const auto & facets_check = inserter.getCheckFacets(type_facet);
auto & f_insertion = inserter.getInsertionFacets(type_facet);
auto & f_filter = facet_filter(type_facet);
auto & sig_c_eff = sigma_c_eff(type_cohesive);
auto & del_c = delta_c_eff(type_cohesive);
auto & ins_stress = insertion_stress(type_cohesive);
auto & trac_old = tractions.previous(type_cohesive);
const auto & f_stress = model->getStressOnFacets(type_facet);
const auto & sigma_lim = sigma_c(type_facet);
UInt nb_quad_facet =
model->getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
#ifndef AKANTU_NDEBUG
UInt nb_quad_cohesive = model->getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(type_cohesive);
AKANTU_DEBUG_ASSERT(nb_quad_cohesive == nb_quad_facet,
"The cohesive element and the corresponding facet do "
"not have the same numbers of integration points");
#endif
UInt nb_facet = f_filter.size();
// if (nb_facet == 0) continue;
auto sigma_lim_it = sigma_lim.begin();
Matrix<Real> stress_tmp(spatial_dimension, spatial_dimension);
Matrix<Real> normal_traction(spatial_dimension, nb_quad_facet);
Vector<Real> stress_check(nb_quad_facet);
UInt sp2 = spatial_dimension * spatial_dimension;
const auto & tangents = model->getTangents(type_facet);
const auto & normals = model->getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(type_facet);
auto normal_begin = normals.begin(spatial_dimension);
auto tangent_begin = tangents.begin(tangents.getNbComponent());
auto facet_stress_begin =
f_stress.begin(spatial_dimension, spatial_dimension * 2);
std::vector<Real> new_sigmas;
std::vector<Vector<Real>> new_normal_traction;
std::vector<Real> new_delta_c;
// loop over each facet belonging to this material
for (UInt f = 0; f < nb_facet; ++f, ++sigma_lim_it) {
UInt facet = f_filter(f);
// skip facets where check shouldn't be realized
- if (!facets_check(facet))
+ if (!facets_check(facet)) {
continue;
+ }
// compute the effective norm on each quadrature point of the facet
for (UInt q = 0; q < nb_quad_facet; ++q) {
UInt current_quad = facet * nb_quad_facet + q;
const Vector<Real> & normal = normal_begin[current_quad];
const Vector<Real> & tangent = tangent_begin[current_quad];
const Matrix<Real> & facet_stress_it = facet_stress_begin[current_quad];
// compute average stress on the current quadrature point
Matrix<Real> stress_1(facet_stress_it.storage(), spatial_dimension,
spatial_dimension);
Matrix<Real> stress_2(facet_stress_it.storage() + sp2,
spatial_dimension, spatial_dimension);
stress_tmp.copy(stress_1);
stress_tmp += stress_2;
stress_tmp /= 2.;
Vector<Real> normal_traction_vec(normal_traction(q));
// compute normal and effective stress
stress_check(q) = computeEffectiveNorm(stress_tmp, normal, tangent,
normal_traction_vec);
}
// verify if the effective stress overcomes the threshold
Real final_stress = stress_check.mean();
- if (max_quad_stress_insertion)
+ if (max_quad_stress_insertion) {
final_stress = *std::max_element(
stress_check.storage(), stress_check.storage() + nb_quad_facet);
+ }
if (final_stress > *sigma_lim_it) {
f_insertion(facet) = true;
- if (check_only)
+ if (check_only) {
continue;
+ }
// store the new cohesive material parameters for each quadrature
// point
for (UInt q = 0; q < nb_quad_facet; ++q) {
Real new_sigma = stress_check(q);
Vector<Real> normal_traction_vec(normal_traction(q));
- if (spatial_dimension != 3)
+ if (spatial_dimension != 3) {
normal_traction_vec *= -1.;
+ }
new_sigmas.push_back(new_sigma);
new_normal_traction.push_back(normal_traction_vec);
Real new_delta;
// set delta_c in function of G_c or a given delta_c value
- if (Math::are_float_equal(delta_c, 0.))
+ if (Math::are_float_equal(delta_c, 0.)) {
new_delta = 2 * G_c / new_sigma;
- else
+ } else {
new_delta = (*sigma_lim_it) / new_sigma * delta_c;
+ }
new_delta_c.push_back(new_delta);
}
}
}
// update material data for the new elements
UInt old_nb_quad_points = sig_c_eff.size();
UInt new_nb_quad_points = new_sigmas.size();
sig_c_eff.resize(old_nb_quad_points + new_nb_quad_points);
ins_stress.resize(old_nb_quad_points + new_nb_quad_points);
trac_old.resize(old_nb_quad_points + new_nb_quad_points);
del_c.resize(old_nb_quad_points + new_nb_quad_points);
for (UInt q = 0; q < new_nb_quad_points; ++q) {
sig_c_eff(old_nb_quad_points + q) = new_sigmas[q];
del_c(old_nb_quad_points + q) = new_delta_c[q];
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
ins_stress(old_nb_quad_points + q, dim) = new_normal_traction[q](dim);
trac_old(old_nb_quad_points + q, dim) = new_normal_traction[q](dim);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto traction_it = tractions(el_type, ghost_type).begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto traction_end = tractions(el_type, ghost_type).end(spatial_dimension);
auto sigma_c_it = sigma_c_eff(el_type, ghost_type).begin();
auto delta_max_it = delta_max(el_type, ghost_type).begin();
auto delta_c_it = delta_c_eff(el_type, ghost_type).begin();
auto damage_it = damage(el_type, ghost_type).begin();
auto insertion_stress_it =
insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++normal_it, ++sigma_c_it, ++delta_max_it,
++delta_c_it, ++damage_it, ++contact_traction_it, ++insertion_stress_it,
++contact_opening_it) {
-
- Real normal_opening_norm, tangential_opening_norm;
- bool penetration;
+ Real normal_opening_norm{0};
+ Real tangential_opening_norm{0};
+ bool penetration{false};
this->computeTractionOnQuad(
*traction_it, *opening_it, *normal_it, *delta_max_it, *delta_c_it,
*insertion_stress_it, *sigma_c_it, normal_opening, tangential_opening,
normal_opening_norm, tangential_opening_norm, *damage_it, penetration,
*contact_traction_it, *contact_opening_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::computeTangentTraction(
- const ElementType & el_type, Array<Real> & tangent_matrix,
+ ElementType el_type, Array<Real> & tangent_matrix,
const Array<Real> & normal, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
/// NB: delta_max_it points on delta_max_previous, i.e. the
/// delta_max related to the solution of the previous incremental
/// step
auto delta_max_it = delta_max.previous(el_type, ghost_type).begin();
auto sigma_c_it = sigma_c_eff(el_type, ghost_type).begin();
auto delta_c_it = delta_c_eff(el_type, ghost_type).begin();
auto damage_it = damage(el_type, ghost_type).begin();
auto contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end; ++tangent_it, ++normal_it, ++opening_it,
++delta_max_it, ++sigma_c_it, ++delta_c_it,
++damage_it, ++contact_opening_it) {
-
- Real normal_opening_norm, tangential_opening_norm;
- bool penetration;
+ Real normal_opening_norm{0};
+ Real tangential_opening_norm{0};
+ bool penetration{false};
this->computeTangentTractionOnQuad(
*tangent_it, *delta_max_it, *delta_c_it, *sigma_c_it, *opening_it,
*normal_it, normal_opening, tangential_opening, normal_opening_norm,
tangential_opening_norm, *damage_it, penetration, *contact_opening_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear, MaterialCohesiveLinear);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
index 2d2e77a09..686b164ea 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
@@ -1,187 +1,187 @@
/**
* @file material_cohesive_linear.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__
-#define __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__
+#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_HH_
+#define AKANTU_MATERIAL_COHESIVE_LINEAR_HH_
namespace akantu {
/**
* Cohesive material linear damage for extrinsic case
*
* parameters in the material files :
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default:
* 0)
* - G_cI : fracture energy for mode I (default: 0)
* - G_cII : fracture energy for mode II (default: 0)
* - penalty : stiffness in compression to prevent penetration
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinear : public MaterialCohesive {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveLinear(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
void updateInternalParameters() override;
/// check stress for cohesive elements' insertion
void checkInsertion(bool check_only = false) override;
/// compute effective stress norm for insertion check
Real computeEffectiveNorm(const Matrix<Real> & stress,
const Vector<Real> & normal,
const Vector<Real> & tangent,
- Vector<Real> & normal_stress) const;
+ Vector<Real> & normal_traction) const;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute tangent stiffness matrix
- void computeTangentTraction(const ElementType & el_type,
+ void computeTangentTraction(ElementType el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) override;
/**
* Scale insertion traction sigma_c according to the volume of the
* two elements surrounding a facet
*
* see the article: F. Zhou and J. F. Molinari "Dynamic crack
* propagation with cohesive elements: a methodology to address mesh
* dependency" International Journal for Numerical Methods in
* Engineering (2004)
*/
void scaleInsertionTraction();
/// compute the traction for a given quadrature point
inline void computeTractionOnQuad(
Vector<Real> & traction, Vector<Real> & opening,
const Vector<Real> & normal, Real & delta_max, const Real & delta_c,
const Vector<Real> & insertion_stress, const Real & sigma_c,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_traction,
Vector<Real> & contact_opening);
inline void computeTangentTractionOnQuad(
Matrix<Real> & tangent, Real & delta_max, const Real & delta_c,
const Real & sigma_c, Vector<Real> & opening, const Vector<Real> & normal,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_opening);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get sigma_c_eff
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(InsertionTraction, sigma_c_eff, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// beta parameter
Real beta;
/// beta square inverse to compute effective norm
Real beta2_inv;
/// mode I fracture energy
Real G_c;
/// kappa parameter
Real kappa;
/// constitutive law scalar to compute delta
Real beta2_kappa2;
/// constitutive law scalar to compute traction
Real beta2_kappa;
/// penalty coefficient
Real penalty;
/// reference volume used to scale sigma_c
Real volume_s;
/// weibull exponent used to scale sigma_c
Real m_s;
/// variable defining if we are recomputing the last loading step
/// after load_reduction
bool recompute;
/// critical effective stress
RandomInternalField<Real, CohesiveInternalField> sigma_c_eff;
/// effective critical displacement (each element can have a
/// different value)
CohesiveInternalField<Real> delta_c_eff;
/// stress at insertion
CohesiveInternalField<Real> insertion_stress;
/// variable saying if there should be penalty contact also after
/// breaking the cohesive elements
bool contact_after_breaking;
/// insertion of cohesive element when stress is high enough just on
/// one quadrature point
bool max_quad_stress_insertion;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "material_cohesive_linear_inline_impl.hh"
-#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__ */
+#endif /* AKANTU_MATERIAL_COHESIVE_LINEAR_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
index bce58696b..60831c62c 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
@@ -1,297 +1,304 @@
/**
* @file material_cohesive_linear_fatigue.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 20 2015
* @date last modification: Tue Feb 20 2018
*
* @brief See material_cohesive_linear_fatigue.hh for information
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_fatigue.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearFatigue<spatial_dimension>::MaterialCohesiveLinearFatigue(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesiveLinear<spatial_dimension>(model, id),
delta_prec("delta_prec", *this), K_plus("K_plus", *this),
K_minus("K_minus", *this), T_1d("T_1d", *this),
switches("switches", *this), delta_dot_prec("delta_dot_prec", *this),
normal_regime("normal_regime", *this) {
this->registerParam("delta_f", delta_f, Real(-1.),
_pat_parsable | _pat_readable, "delta_f");
this->registerParam("progressive_delta_f", progressive_delta_f, false,
_pat_parsable | _pat_readable,
"Whether or not delta_f is equal to delta_max");
this->registerParam("count_switches", count_switches, false,
_pat_parsable | _pat_readable,
"Count the opening/closing switches per element");
this->registerParam(
"fatigue_ratio", fatigue_ratio, Real(1.), _pat_parsable | _pat_readable,
"What portion of the cohesive law is subjected to fatigue");
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFatigue<spatial_dimension>::initMaterial() {
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
// check that delta_f has a proper value or assign a defaul value
- if (delta_f < 0)
+ if (delta_f < 0) {
delta_f = this->delta_c_eff;
- else if (delta_f < this->delta_c_eff)
+ } else if (delta_f < this->delta_c_eff) {
AKANTU_ERROR("Delta_f must be greater or equal to delta_c");
+ }
delta_prec.initialize(1);
K_plus.initialize(1);
K_minus.initialize(1);
T_1d.initialize(1);
normal_regime.initialize(1);
if (count_switches) {
switches.initialize(1);
delta_dot_prec.initialize(1);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFatigue<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
const Array<Real> & sigma_c_array = this->sigma_c_eff(el_type, ghost_type);
Array<Real> & delta_max_array = this->delta_max(el_type, ghost_type);
const Array<Real> & delta_c_array = this->delta_c_eff(el_type, ghost_type);
Array<Real> & damage_array = this->damage(el_type, ghost_type);
auto insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Array<Real> & delta_prec_array = delta_prec(el_type, ghost_type);
Array<Real> & K_plus_array = K_plus(el_type, ghost_type);
Array<Real> & K_minus_array = K_minus(el_type, ghost_type);
Array<Real> & T_1d_array = T_1d(el_type, ghost_type);
Array<bool> & normal_regime_array = normal_regime(el_type, ghost_type);
Array<UInt> * switches_array = nullptr;
Array<Real> * delta_dot_prec_array = nullptr;
if (count_switches) {
switches_array = &switches(el_type, ghost_type);
delta_dot_prec_array = &delta_dot_prec(el_type, ghost_type);
}
auto * memory_space = new Real[2 * spatial_dimension];
Vector<Real> normal_opening(memory_space, spatial_dimension);
Vector<Real> tangential_opening(memory_space + spatial_dimension,
spatial_dimension);
Real tolerance = Math::getTolerance();
/// loop on each quadrature point
for (UInt q = 0; traction_it != traction_end; ++traction_it, ++opening_it,
++normal_it, ++contact_traction_it, ++insertion_stress_it,
++contact_opening_it, ++q) {
/// compute normal and tangential opening vectors
Real normal_opening_norm = opening_it->dot(*normal_it);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \frac{\beta^2}{\kappa^2} \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
bool penetration = normal_opening_norm < -tolerance;
- if (this->contact_after_breaking == false &&
- Math::are_float_equal(damage_array(q), 1.))
+ if (not this->contact_after_breaking and
+ Math::are_float_equal(damage_array(q), 1.)) {
penetration = false;
+ }
if (penetration) {
/// use penalty coefficient in case of penetration
*contact_traction_it = normal_opening;
*contact_traction_it *= this->penalty;
*contact_opening_it = normal_opening;
/// don't consider penetration contribution for delta
*opening_it = tangential_opening;
- normal_opening.clear();
+ normal_opening.zero();
} else {
delta += normal_opening_norm * normal_opening_norm;
- contact_traction_it->clear();
- contact_opening_it->clear();
+ contact_traction_it->zero();
+ contact_opening_it->zero();
}
delta = std::sqrt(delta);
/**
* Compute traction @f$ \mathbf{T} = \left(
* \frac{\beta^2}{\kappa} \Delta_t \mathbf{t} + \Delta_n
* \mathbf{n} \right) \frac{\sigma_c}{\delta} \left( 1-
* \frac{\delta}{\delta_c} \right)@f$
*/
// update maximum displacement and damage
delta_max_array(q) = std::max(delta, delta_max_array(q));
damage_array(q) = std::min(delta_max_array(q) / delta_c_array(q), Real(1.));
Real delta_dot = delta - delta_prec_array(q);
// count switches if asked
if (count_switches) {
if ((delta_dot > 0. && (*delta_dot_prec_array)(q) <= 0.) ||
- (delta_dot < 0. && (*delta_dot_prec_array)(q) >= 0.))
+ (delta_dot < 0. && (*delta_dot_prec_array)(q) >= 0.)) {
++((*switches_array)(q));
+ }
(*delta_dot_prec_array)(q) = delta_dot;
}
// set delta_f equal to delta_max if desired
- if (progressive_delta_f)
+ if (progressive_delta_f) {
delta_f = delta_max_array(q);
+ }
// broken element case
- if (Math::are_float_equal(damage_array(q), 1.))
- traction_it->clear();
- // just inserted element case
- else if (Math::are_float_equal(damage_array(q), 0.)) {
- if (penetration)
- traction_it->clear();
- else
+ if (Math::are_float_equal(damage_array(q), 1.)) {
+ traction_it->zero();
+ // just inserted element case
+ } else if (Math::are_float_equal(damage_array(q), 0.)) {
+ if (penetration) {
+ traction_it->zero();
+ } else {
*traction_it = *insertion_stress_it;
+ }
// initialize the 1d traction to sigma_c
T_1d_array(q) = sigma_c_array(q);
}
// normal case
else {
// if element is closed then there are zero tractions
- if (delta <= tolerance)
- traction_it->clear();
- // otherwise compute new tractions if the new delta is different
- // than the previous one
- else if (std::abs(delta_dot) > tolerance) {
+ if (delta <= tolerance) {
+ traction_it->zero();
+ // otherwise compute new tractions if the new delta is different
+ // than the previous one
+ } else if (std::abs(delta_dot) > tolerance) {
// loading case
if (delta_dot > 0.) {
if (!normal_regime_array(q)) {
// equation (4) of the article
K_plus_array(q) *= 1. - delta_dot / delta_f;
// equivalent to equation (2) of the article
T_1d_array(q) += K_plus_array(q) * delta_dot;
// in case of reloading, traction must not exceed that of the
// envelop of the cohesive law
Real max_traction =
sigma_c_array(q) * (1 - delta / delta_c_array(q));
bool max_traction_exceeded = T_1d_array(q) > max_traction;
- if (max_traction_exceeded)
+ if (max_traction_exceeded) {
T_1d_array(q) = max_traction;
+ }
// switch to standard linear cohesive law
if (delta_max_array(q) > fatigue_ratio * delta_c_array(q)) {
// reset delta_max to avoid big jumps in the traction
delta_max_array(q) =
sigma_c_array(q) /
(T_1d_array(q) / delta + sigma_c_array(q) / delta_c_array(q));
damage_array(q) =
std::min(delta_max_array(q) / delta_c_array(q), Real(1.));
K_minus_array(q) = sigma_c_array(q) / delta_max_array(q) *
(1. - damage_array(q));
normal_regime_array(q) = true;
} else {
// equation (3) of the article
K_minus_array(q) = T_1d_array(q) / delta;
// if the traction is following the cohesive envelop, then
// K_plus has to be reset
- if (max_traction_exceeded)
+ if (max_traction_exceeded) {
K_plus_array(q) = K_minus_array(q);
+ }
}
} else {
// compute stiffness according to the standard law
K_minus_array(q) =
sigma_c_array(q) / delta_max_array(q) * (1. - damage_array(q));
}
}
// unloading case
else if (!normal_regime_array(q)) {
// equation (4) of the article
K_plus_array(q) +=
(K_plus_array(q) - K_minus_array(q)) * delta_dot / delta_f;
// equivalent to equation (2) of the article
T_1d_array(q) = K_minus_array(q) * delta;
}
// applying the actual stiffness
*traction_it = tangential_opening;
*traction_it *= this->beta2_kappa;
*traction_it += normal_opening;
*traction_it *= K_minus_array(q);
}
}
// update precendent delta
delta_prec_array(q) = delta;
}
delete[] memory_space;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear_fatigue, MaterialCohesiveLinearFatigue);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
index acec3010d..07044e052 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
@@ -1,131 +1,131 @@
/**
* @file material_cohesive_linear_fatigue.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Linear irreversible cohesive law with dissipative
* unloading-reloading cycles
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH__
-#define __AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH__
+#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH_
+#define AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Linear irreversible cohesive law with dissipative
* unloading-reloading cycles
*
* This law uses two different stiffnesses during unloading and
* reloading. The implementation is based on the article entitled "A
* cohesive model for fatigue crack growth" by Nguyen, Repetto, Ortiz
* and Radovitzky (2001). This law is identical to the
* MaterialCohesiveLinear one except for the unloading-reloading
* phase.
*
* input parameter:
*
* - delta_f : it must be greater than delta_c and it is inversely
* proportional to the dissipation in the unloading-reloading
* cycles (default: delta_c)
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearFatigue
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveLinearFatigue(SolidMechanicsModel & model,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the switches
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Switches, switches, UInt);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// delta_f parameter
Real delta_f;
/// variable saying if delta_f is equal to delta_max for each
/// element when the traction is computed
bool progressive_delta_f;
/// count the opening/closing switches per element
bool count_switches;
/// delta of the previous step
CohesiveInternalField<Real> delta_prec;
/// stiffness for reloading
CohesiveInternalField<Real> K_plus;
/// stiffness for unloading
CohesiveInternalField<Real> K_minus;
/// 1D traction in the cohesive law
CohesiveInternalField<Real> T_1d;
/// Number of opening/closing switches
CohesiveInternalField<UInt> switches;
/// delta increment of the previous time step
CohesiveInternalField<Real> delta_dot_prec;
/// has the element passed to normal regime (not in fatigue anymore)
CohesiveInternalField<bool> normal_regime;
/// ratio indicating until what point fatigue is applied in the cohesive law
Real fatigue_ratio;
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH__ */
+#endif /* AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
index 31de793e0..839eaaddd 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
@@ -1,276 +1,280 @@
/**
* @file material_cohesive_linear_friction.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Tue Jan 12 2016
* @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_friction.hh"
#include "solid_mechanics_model_cohesive.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearFriction<spatial_dimension>::
MaterialCohesiveLinearFriction(SolidMechanicsModel & model, const ID & id)
: MaterialParent(model, id), residual_sliding("residual_sliding", *this),
friction_force("friction_force", *this) {
AKANTU_DEBUG_IN();
this->registerParam("mu", mu_max, Real(0.), _pat_parsable | _pat_readable,
"Maximum value of the friction coefficient");
this->registerParam("penalty_for_friction", friction_penalty, Real(0.),
_pat_parsable | _pat_readable,
"Penalty parameter for the friction behavior");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialParent::initMaterial();
friction_force.initialize(spatial_dimension);
residual_sliding.initialize(1);
residual_sliding.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::computeTraction(
__attribute__((unused)) const Array<Real> & normal, ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
residual_sliding.resize();
friction_force.resize();
/// define iterators
auto traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
auto traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto previous_opening_it =
this->opening.previous(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_max_it = this->delta_max(el_type, ghost_type).begin();
auto delta_max_prev_it =
this->delta_max.previous(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_it = this->damage(el_type, ghost_type).begin();
auto insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
auto res_sliding_it = this->residual_sliding(el_type, ghost_type).begin();
auto res_sliding_prev_it =
this->residual_sliding.previous(el_type, ghost_type).begin();
auto friction_force_it =
this->friction_force(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
- if (not this->model->isDefaultSolverExplicit())
+ if (not this->model->isDefaultSolverExplicit()) {
this->delta_max(el_type, ghost_type)
.copy(this->delta_max.previous(el_type, ghost_type));
+ }
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++normal_it, ++sigma_c_it, ++delta_max_it,
++delta_c_it, ++damage_it, ++contact_traction_it, ++insertion_stress_it,
++contact_opening_it, ++delta_max_prev_it, ++res_sliding_it,
++res_sliding_prev_it, ++friction_force_it, ++previous_opening_it) {
- Real normal_opening_norm, tangential_opening_norm;
+ Real normal_opening_norm;
+ Real tangential_opening_norm;
bool penetration;
this->computeTractionOnQuad(
*traction_it, *opening_it, *normal_it, *delta_max_it, *delta_c_it,
*insertion_stress_it, *sigma_c_it, normal_opening, tangential_opening,
normal_opening_norm, tangential_opening_norm, *damage_it, penetration,
*contact_traction_it, *contact_opening_it);
if (penetration) {
/// the friction coefficient mu increases with the damage. It
/// equals the maximum value when damage = 1.
// Real damage = std::min(*delta_max_prev_it / *delta_c_it,
// Real(1.));
Real mu = mu_max; // * damage;
/// the definition of tau_max refers to the opening
/// (penetration) of the previous incremental step
Real normal_opening_prev_norm =
std::min(previous_opening_it->dot(*normal_it), Real(0.));
// Vector<Real> normal_opening_prev = (*normal_it);
// normal_opening_prev *= normal_opening_prev_norm;
Real tau_max = mu * this->penalty * (std::abs(normal_opening_prev_norm));
Real delta_sliding_norm =
std::abs(tangential_opening_norm - *res_sliding_prev_it);
/// tau is the norm of the friction force, acting tangentially to the
/// surface
Real tau = std::min(friction_penalty * delta_sliding_norm, tau_max);
- if ((tangential_opening_norm - *res_sliding_prev_it) < 0.0)
+ if ((tangential_opening_norm - *res_sliding_prev_it) < 0.0) {
tau = -tau;
+ }
/// from tau get the x and y components of friction, to be added in the
/// force vector
Vector<Real> tangent_unit_vector(spatial_dimension);
tangent_unit_vector = tangential_opening / tangential_opening_norm;
*friction_force_it = tau * tangent_unit_vector;
/// update residual_sliding
*res_sliding_it =
tangential_opening_norm - (std::abs(tau) / friction_penalty);
} else {
- friction_force_it->clear();
+ friction_force_it->zero();
}
*traction_it += *friction_force_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::computeTangentTraction(
- const ElementType & el_type, Array<Real> & tangent_matrix,
+ ElementType el_type, Array<Real> & tangent_matrix,
__attribute__((unused)) const Array<Real> & normal, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto previous_opening_it =
this->opening.previous(el_type, ghost_type).begin(spatial_dimension);
/**
* NB: delta_max_it points on delta_max_previous, i.e. the
* delta_max related to the solution of the previous incremental
* step
*/
auto delta_max_it = this->delta_max.previous(el_type, ghost_type).begin();
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_it = this->damage(el_type, ghost_type).begin();
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto res_sliding_prev_it =
this->residual_sliding.previous(el_type, ghost_type).begin();
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end;
++tangent_it, ++normal_it, ++opening_it, ++previous_opening_it,
++delta_max_it, ++sigma_c_it, ++delta_c_it, ++damage_it,
++contact_opening_it, ++res_sliding_prev_it) {
- Real normal_opening_norm, tangential_opening_norm;
+ Real normal_opening_norm;
+ Real tangential_opening_norm;
bool penetration;
this->computeTangentTractionOnQuad(
*tangent_it, *delta_max_it, *delta_c_it, *sigma_c_it, *opening_it,
*normal_it, normal_opening, tangential_opening, normal_opening_norm,
tangential_opening_norm, *damage_it, penetration, *contact_opening_it);
if (penetration) {
// Real damage = std::min(*delta_max_it / *delta_c_it, Real(1.));
Real mu = mu_max; // * damage;
Real normal_opening_prev_norm =
std::min(previous_opening_it->dot(*normal_it), Real(0.));
// Vector<Real> normal_opening_prev = (*normal_it);
// normal_opening_prev *= normal_opening_prev_norm;
Real tau_max = mu * this->penalty * (std::abs(normal_opening_prev_norm));
Real delta_sliding_norm =
std::abs(tangential_opening_norm - *res_sliding_prev_it);
// tau is the norm of the friction force, acting tangentially to the
// surface
Real tau = std::min(friction_penalty * delta_sliding_norm, tau_max);
if (tau < tau_max && tau_max > Math::getTolerance()) {
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye(1.);
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(*normal_it, *normal_it);
Matrix<Real> nn(n_outer_n);
I -= nn;
*tangent_it += I * friction_penalty;
}
}
// check if the tangential stiffness matrix is symmetric
// for (UInt h = 0; h < spatial_dimension; ++h){
// for (UInt l = h; l < spatial_dimension; ++l){
// if (l > h){
// Real k_ls = (*tangent_it)[spatial_dimension*h+l];
// Real k_us = (*tangent_it)[spatial_dimension*l+h];
// // std::cout << "k_ls = " << k_ls << std::endl;
// // std::cout << "k_us = " << k_us << std::endl;
// if (std::abs(k_ls) > 1e-13 && std::abs(k_us) > 1e-13){
// Real error = std::abs((k_ls - k_us) / k_us);
// if (error > 1e-10){
// std::cout << "non symmetric cohesive matrix" << std::endl;
// // std::cout << "error " << error << std::endl;
// }
// }
// }
// }
// }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear_friction, MaterialCohesiveLinearFriction);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
index 93c254e55..55c463118 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
@@ -1,104 +1,104 @@
/**
* @file material_cohesive_linear_friction.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH__
-#define __AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH__
+#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH_
+#define AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material linear with friction force
*
* parameters in the material files :
* - mu : friction coefficient
* - penalty_for_friction : Penalty parameter for the friction behavior
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearFriction
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
using MaterialParent = MaterialCohesiveLinear<spatial_dimension>;
public:
MaterialCohesiveLinearFriction(SolidMechanicsModel & model,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute tangent stiffness matrix
- void computeTangentTraction(const ElementType & el_type,
+ void computeTangentTraction(ElementType el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// maximum value of the friction coefficient
Real mu_max;
/// penalty parameter for the friction law
Real friction_penalty;
/// history parameter for the friction law
CohesiveInternalField<Real> residual_sliding;
/// friction force
CohesiveInternalField<Real> friction_force;
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH__ */
+#endif /* AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.hh
index 23960075a..9d9ac04bc 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.hh
@@ -1,265 +1,269 @@
/**
* @file material_cohesive_linear_inline_impl.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 22 2015
* @date last modification: Wed Feb 21 2018
*
* @brief Inline functions of the MaterialCohesiveLinear
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_HH__
-#define __AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_HH__
+#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_HH_
+#define AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline Real MaterialCohesiveLinear<dim>::computeEffectiveNorm(
const Matrix<Real> & stress, const Vector<Real> & normal,
const Vector<Real> & tangent, Vector<Real> & normal_traction) const {
normal_traction.mul<false>(stress, normal);
Real normal_contrib = normal_traction.dot(normal);
/// in 3D tangential components must be summed
Real tangent_contrib = 0;
if (dim == 2) {
Real tangent_contrib_tmp = normal_traction.dot(tangent);
tangent_contrib += tangent_contrib_tmp * tangent_contrib_tmp;
} else if (dim == 3) {
for (UInt s = 0; s < dim - 1; ++s) {
const Vector<Real> tangent_v(tangent.storage() + s * dim, dim);
Real tangent_contrib_tmp = normal_traction.dot(tangent_v);
tangent_contrib += tangent_contrib_tmp * tangent_contrib_tmp;
}
}
tangent_contrib = std::sqrt(tangent_contrib);
normal_contrib = std::max(Real(0.), normal_contrib);
return std::sqrt(normal_contrib * normal_contrib +
tangent_contrib * tangent_contrib * beta2_inv);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialCohesiveLinear<dim>::computeTractionOnQuad(
Vector<Real> & traction, Vector<Real> & opening,
const Vector<Real> & normal, Real & delta_max, const Real & delta_c,
const Vector<Real> & insertion_stress, const Real & sigma_c,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_traction,
Vector<Real> & contact_opening) {
/// compute normal and tangential opening vectors
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
tangential_opening = opening;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \frac{\beta^2}{\kappa^2} \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm / delta_c < -Math::getTolerance();
// penetration = normal_opening_norm < 0.;
- if (this->contact_after_breaking == false &&
- Math::are_float_equal(damage, 1.))
+ if (not this->contact_after_breaking and
+ Math::are_float_equal(damage, 1.)) {
penetration = false;
+ }
if (penetration) {
/// use penalty coefficient in case of penetration
contact_traction = normal_opening;
contact_traction *= this->penalty;
contact_opening = normal_opening;
/// don't consider penetration contribution for delta
opening = tangential_opening;
- normal_opening.clear();
+ normal_opening.zero();
} else {
delta += normal_opening_norm * normal_opening_norm;
- contact_traction.clear();
- contact_opening.clear();
+ contact_traction.zero();
+ contact_opening.zero();
}
delta = std::sqrt(delta);
/// update maximum displacement and damage
delta_max = std::max(delta_max, delta);
damage = std::min(delta_max / delta_c, Real(1.));
/**
* Compute traction @f$ \mathbf{T} = \left(
* \frac{\beta^2}{\kappa} \Delta_t \mathbf{t} + \Delta_n
* \mathbf{n} \right) \frac{\sigma_c}{\delta} \left( 1-
* \frac{\delta}{\delta_c} \right)@f$
*/
- if (Math::are_float_equal(damage, 1.))
- traction.clear();
- else if (Math::are_float_equal(damage, 0.)) {
- if (penetration)
- traction.clear();
- else
+ if (Math::are_float_equal(damage, 1.)) {
+ traction.zero();
+ } else if (Math::are_float_equal(damage, 0.)) {
+ if (penetration) {
+ traction.zero();
+ } else {
traction = insertion_stress;
+ }
} else {
traction = tangential_opening;
traction *= this->beta2_kappa;
traction += normal_opening;
AKANTU_DEBUG_ASSERT(delta_max != 0.,
"Division by zero, tolerance might be too low");
traction *= sigma_c / delta_max * (1. - damage);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialCohesiveLinear<dim>::computeTangentTractionOnQuad(
Matrix<Real> & tangent, Real & delta_max, const Real & delta_c,
const Real & sigma_c, Vector<Real> & opening, const Vector<Real> & normal,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_opening) {
/**
* During the update of the residual the interpenetrations are
* stored in the array "contact_opening", therefore, in the case
* of penetration, in the array "opening" there are only the
* tangential components.
*/
opening += contact_opening;
/// compute normal and tangential opening vectors
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
tangential_opening = opening;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
Real delta =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
- if (this->contact_after_breaking == false &&
- Math::are_float_equal(damage, 1.))
+ if (not this->contact_after_breaking and
+ Math::are_float_equal(damage, 1.)) {
penetration = false;
+ }
Real derivative = 0; // derivative = d(t/delta)/ddelta
Real t = 0;
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(normal, normal);
if (penetration) {
/// stiffness in compression given by the penalty parameter
tangent += n_outer_n;
tangent *= penalty;
opening = tangential_opening;
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
} else {
delta += normal_opening_norm * normal_opening_norm;
}
delta = std::sqrt(delta);
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
- if (delta < Math::getTolerance())
+ if (delta < Math::getTolerance()) {
delta = delta_c / 1000.;
+ }
if (delta >= delta_max) {
if (delta <= delta_c) {
derivative = -sigma_c / (delta * delta);
t = sigma_c * (1 - delta / delta_c);
} else {
derivative = 0.;
t = 0.;
}
} else if (delta < delta_max) {
Real tmax = sigma_c * (1 - delta_max / delta_c);
t = tmax / delta_max * delta;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye(this->beta2_kappa);
Matrix<Real> nn(n_outer_n);
nn *= (1. - this->beta2_kappa);
nn += I;
nn *= t / delta;
Vector<Real> t_tilde(normal_opening);
t_tilde *= (1. - this->beta2_kappa2);
Vector<Real> mm(opening);
mm *= this->beta2_kappa2;
t_tilde += mm;
Vector<Real> t_hat(normal_opening);
t_hat += this->beta2_kappa * tangential_opening;
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(t_hat, t_tilde);
prov *= derivative / delta;
prov += nn;
Matrix<Real> prov_t = prov.transpose();
tangent += prov_t;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
/* -------------------------------------------------------------------------- */
-#endif //__AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_HH__
+#endif //AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_HH_
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
index e1f789372..0da10cc32 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
@@ -1,412 +1,418 @@
/**
* @file material_cohesive_linear_uncoupled.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Mon Jul 25 2016
* @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <numeric>
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_uncoupled.hh"
#include "solid_mechanics_model_cohesive.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearUncoupled<spatial_dimension>::
MaterialCohesiveLinearUncoupled(SolidMechanicsModel & model, const ID & id)
: MaterialCohesiveLinear<spatial_dimension>(model, id),
delta_n_max("delta_n_max", *this), delta_t_max("delta_t_max", *this),
damage_n("damage_n", *this), damage_t("damage_t", *this) {
AKANTU_DEBUG_IN();
this->registerParam(
"roughness", R, Real(1.), _pat_parsable | _pat_readable,
"Roughness to define coupling between mode II and mode I");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
delta_n_max.initialize(1);
delta_t_max.initialize(1);
damage_n.initialize(1);
damage_t.initialize(1);
delta_n_max.initializeHistory();
delta_t_max.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::computeTraction(
- const Array<Real> &, ElementType el_type, GhostType ghost_type) {
+ const Array<Real> & /*unused*/, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
delta_n_max.resize();
delta_t_max.resize();
damage_n.resize();
damage_t.resize();
/// define iterators
auto traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
auto traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_n_max_it = delta_n_max(el_type, ghost_type).begin();
auto delta_t_max_it = delta_t_max(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_n_it = damage_n(el_type, ghost_type).begin();
auto damage_t_it = damage_t(el_type, ghost_type).begin();
auto insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++contact_traction_it, ++contact_opening_it,
++normal_it, ++sigma_c_it, ++delta_n_max_it, ++delta_t_max_it,
++delta_c_it, ++damage_n_it, ++damage_t_it, ++insertion_stress_it) {
- Real normal_opening_norm, tangential_opening_norm;
+ Real normal_opening_norm;
+ Real tangential_opening_norm;
bool penetration;
Real delta_c2_R2 = *delta_c_it * (*delta_c_it) / R / R;
/// compute normal and tangential opening vectors
normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening = *normal_it;
normal_opening *= normal_opening_norm;
// std::cout<< "normal_opening_norm = " << normal_opening_norm
// <<std::endl;
Vector<Real> tangential_opening = *opening_it;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
/// compute effective opening displacement
Real delta_n =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
Real delta_t =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
- if (this->contact_after_breaking == false &&
- Math::are_float_equal(*damage_n_it, 1.))
+ if (not this->contact_after_breaking and
+ Math::are_float_equal(*damage_n_it, 1.)) {
penetration = false;
+ }
if (penetration) {
/// use penalty coefficient in case of penetration
*contact_traction_it = normal_opening;
*contact_traction_it *= this->penalty;
*contact_opening_it = normal_opening;
/// don't consider penetration contribution for delta
//*opening_it = tangential_opening;
- normal_opening.clear();
+ normal_opening.zero();
} else {
delta_n += normal_opening_norm * normal_opening_norm;
delta_t += normal_opening_norm * normal_opening_norm * delta_c2_R2;
- contact_traction_it->clear();
- contact_opening_it->clear();
+ contact_traction_it->zero();
+ contact_opening_it->zero();
}
delta_n = std::sqrt(delta_n);
delta_t = std::sqrt(delta_t);
/// update maximum displacement and damage
*delta_n_max_it = std::max(*delta_n_max_it, delta_n);
*damage_n_it = std::min(*delta_n_max_it / *delta_c_it, Real(1.));
*delta_t_max_it = std::max(*delta_t_max_it, delta_t);
*damage_t_it = std::min(*delta_t_max_it / *delta_c_it, Real(1.));
Vector<Real> normal_traction(spatial_dimension);
Vector<Real> shear_traction(spatial_dimension);
/// NORMAL TRACTIONS
- if (Math::are_float_equal(*damage_n_it, 1.))
- normal_traction.clear();
- else if (Math::are_float_equal(*damage_n_it, 0.)) {
- if (penetration)
- normal_traction.clear();
- else
+ if (Math::are_float_equal(*damage_n_it, 1.)) {
+ normal_traction.zero();
+ } else if (Math::are_float_equal(*damage_n_it, 0.)) {
+ if (penetration) {
+ normal_traction.zero();
+ } else {
normal_traction = *insertion_stress_it;
+ }
} else {
// the following formulation holds both in loading and in
// unloading-reloading
normal_traction = normal_opening;
AKANTU_DEBUG_ASSERT(*delta_n_max_it != 0.,
"Division by zero, tolerance might be too low");
normal_traction *= *sigma_c_it / (*delta_n_max_it) * (1. - *damage_n_it);
}
/// SHEAR TRACTIONS
- if (Math::are_float_equal(*damage_t_it, 1.))
- shear_traction.clear();
- else if (Math::are_float_equal(*damage_t_it, 0.)) {
- shear_traction.clear();
+ if (Math::are_float_equal(*damage_t_it, 1.) or
+ Math::are_float_equal(*damage_t_it, 0.)) {
+ shear_traction.zero();
} else {
shear_traction = tangential_opening;
AKANTU_DEBUG_ASSERT(*delta_t_max_it != 0.,
"Division by zero, tolerance might be too low");
shear_traction *= this->beta2_kappa;
shear_traction *= *sigma_c_it / (*delta_t_max_it) * (1. - *damage_t_it);
}
*traction_it = normal_traction;
*traction_it += shear_traction;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::computeTangentTraction(
- const ElementType & el_type, Array<Real> & tangent_matrix,
- const Array<Real> &, GhostType ghost_type) {
+ ElementType el_type, Array<Real> & tangent_matrix,
+ const Array<Real> & /*unused*/, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
/// NB: delta_max_it points on delta_max_previous, i.e. the
/// delta_max related to the solution of the previous incremental
/// step
auto delta_n_max_it = delta_n_max.previous(el_type, ghost_type).begin();
auto delta_t_max_it = delta_t_max.previous(el_type, ghost_type).begin();
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_n_it = damage_n(el_type, ghost_type).begin();
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end; ++tangent_it, ++normal_it, ++opening_it,
++sigma_c_it, ++delta_c_it,
++delta_n_max_it, ++delta_t_max_it,
++damage_n_it, ++contact_opening_it) {
- Real normal_opening_norm, tangential_opening_norm;
+ Real normal_opening_norm;
+ Real tangential_opening_norm;
bool penetration;
Real delta_c2_R2 = *delta_c_it * (*delta_c_it) / R / R;
/**
* During the update of the residual the interpenetrations are
* stored in the array "contact_opening", therefore, in the case
* of penetration, in the array "opening" there are only the
* tangential components.
*/
*opening_it += *contact_opening_it;
/// compute normal and tangential opening vectors
normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening = *normal_it;
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening = *opening_it;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
Real delta_n =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
Real delta_t =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
- if (this->contact_after_breaking == false &&
- Math::are_float_equal(*damage_n_it, 1.))
+ if (not this->contact_after_breaking and
+ Math::are_float_equal(*damage_n_it, 1.)) {
penetration = false;
+ }
Real derivative = 0; // derivative = d(t/delta)/ddelta
Real T = 0;
/// TANGENT STIFFNESS FOR NORMAL TRACTIONS
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(*normal_it, *normal_it);
if (penetration) {
/// stiffness in compression given by the penalty parameter
*tangent_it = n_outer_n;
*tangent_it *= this->penalty;
//*opening_it = tangential_opening;
- normal_opening.clear();
+ normal_opening.zero();
} else {
delta_n += normal_opening_norm * normal_opening_norm;
delta_n = std::sqrt(delta_n);
delta_t += normal_opening_norm * normal_opening_norm * delta_c2_R2;
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
- if (delta_n < Math::getTolerance())
+ if (delta_n < Math::getTolerance()) {
delta_n = *delta_c_it / 1000.;
+ }
// loading
if (delta_n >= *delta_n_max_it) {
if (delta_n <= *delta_c_it) {
derivative = -(*sigma_c_it) / (delta_n * delta_n);
T = *sigma_c_it * (1 - delta_n / *delta_c_it);
} else {
derivative = 0.;
T = 0.;
}
// unloading-reloading
} else if (delta_n < *delta_n_max_it) {
Real T_max = *sigma_c_it * (1 - *delta_n_max_it / *delta_c_it);
derivative = 0.;
T = T_max / *delta_n_max_it * delta_n;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> nn(n_outer_n);
nn *= T / delta_n;
Vector<Real> Delta_tilde(normal_opening);
Delta_tilde *= (1. - this->beta2_kappa2);
Vector<Real> mm(*opening_it);
mm *= this->beta2_kappa2;
Delta_tilde += mm;
const Vector<Real> & Delta_hat(normal_opening);
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(Delta_hat, Delta_tilde);
prov *= derivative / delta_n;
prov += nn;
Matrix<Real> prov_t = prov.transpose();
*tangent_it = prov_t;
}
derivative = 0.;
T = 0.;
/// TANGENT STIFFNESS FOR SHEAR TRACTIONS
delta_t = std::sqrt(delta_t);
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
- if (delta_t < Math::getTolerance())
+ if (delta_t < Math::getTolerance()) {
delta_t = *delta_c_it / 1000.;
+ }
// loading
if (delta_t >= *delta_t_max_it) {
if (delta_t <= *delta_c_it) {
derivative = -(*sigma_c_it) / (delta_t * delta_t);
T = *sigma_c_it * (1 - delta_t / *delta_c_it);
} else {
derivative = 0.;
T = 0.;
}
// unloading-reloading
} else if (delta_t < *delta_t_max_it) {
Real T_max = *sigma_c_it * (1 - *delta_t_max_it / *delta_c_it);
derivative = 0.;
T = T_max / *delta_t_max_it * delta_t;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye();
Matrix<Real> nn(n_outer_n);
I -= nn;
I *= T / delta_t;
Vector<Real> Delta_tilde(normal_opening);
Delta_tilde *= (delta_c2_R2 - this->beta2_kappa2);
Vector<Real> mm(*opening_it);
mm *= this->beta2_kappa2;
Delta_tilde += mm;
Vector<Real> Delta_hat(tangential_opening);
Delta_hat *= this->beta2_kappa;
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(Delta_hat, Delta_tilde);
prov *= derivative / delta_t;
prov += I;
Matrix<Real> prov_t = prov.transpose();
*tangent_it += prov_t;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear_uncoupled,
MaterialCohesiveLinearUncoupled);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
index a247b2031..a931b7feb 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
@@ -1,101 +1,101 @@
/**
* @file material_cohesive_linear_uncoupled.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH__
-#define __AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH__
+#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH_
+#define AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material linear with two different laws for mode I and
* mode II, for extrinsic case
*
* parameters in the material files :
* - roughness : define the interaction between mode I and mode II (default: 0)
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearUncoupled
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
// typedef MaterialCohesiveLinear<spatial_dimension> MaterialParent;
public:
MaterialCohesiveLinearUncoupled(SolidMechanicsModel & model,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute tangent stiffness matrix
- void computeTangentTraction(const ElementType & el_type,
+ void computeTangentTraction(ElementType el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// parameter to tune the interaction between mode II and mode I
Real R;
/// maximum normal displacement
CohesiveInternalField<Real> delta_n_max;
/// maximum tangential displacement
CohesiveInternalField<Real> delta_t_max;
/// damage associated to normal tractions
CohesiveInternalField<Real> damage_n;
/// damage associated to shear tractions
CohesiveInternalField<Real> damage_t;
};
} // namespace akantu
-#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH__ */
+#endif /* AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
index a03a52dc9..ca05da5d8 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
@@ -1,557 +1,568 @@
/**
* @file material_cohesive.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
* @date last modification: Mon Feb 19 2018
*
* @brief Specialization of the material class for cohesive elements
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
#include "aka_random_generator.hh"
#include "dof_synchronizer.hh"
#include "fe_engine_template.hh"
#include "integrator_gauss.hh"
#include "shape_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MaterialCohesive::MaterialCohesive(SolidMechanicsModel & model, const ID & id)
: Material(model, id),
facet_filter("facet_filter", id, this->getMemoryID()),
fem_cohesive(
model.getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine")),
reversible_energy("reversible_energy", *this),
total_energy("total_energy", *this), opening("opening", *this),
tractions("tractions", *this),
contact_tractions("contact_tractions", *this),
contact_opening("contact_opening", *this), delta_max("delta max", *this),
use_previous_delta_max(false), use_previous_opening(false),
damage("damage", *this), sigma_c("sigma_c", *this),
normal(0, spatial_dimension, "normal") {
AKANTU_DEBUG_IN();
this->model = dynamic_cast<SolidMechanicsModelCohesive *>(&model);
this->registerParam("sigma_c", sigma_c, _pat_parsable | _pat_readable,
"Critical stress");
this->registerParam("delta_c", delta_c, Real(0.),
_pat_parsable | _pat_readable, "Critical displacement");
this->element_filter.initialize(this->model->getMesh(),
_spatial_dimension = spatial_dimension,
_element_kind = _ek_cohesive);
// this->model->getMesh().initElementTypeMapArray(
// this->element_filter, 1, spatial_dimension, false, _ek_cohesive);
- if (this->model->getIsExtrinsic())
+ if (this->model->getIsExtrinsic()) {
this->facet_filter.initialize(this->model->getMeshFacets(),
_spatial_dimension = spatial_dimension - 1,
_element_kind = _ek_regular);
+ }
// this->model->getMeshFacets().initElementTypeMapArray(facet_filter, 1,
// spatial_dimension -
// 1);
this->reversible_energy.initialize(1);
this->total_energy.initialize(1);
this->tractions.initialize(spatial_dimension);
this->tractions.initializeHistory();
this->contact_tractions.initialize(spatial_dimension);
this->contact_opening.initialize(spatial_dimension);
this->opening.initialize(spatial_dimension);
this->opening.initializeHistory();
this->delta_max.initialize(1);
this->damage.initialize(1);
- if (this->model->getIsExtrinsic())
+ if (this->model->getIsExtrinsic()) {
this->sigma_c.initialize(1);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MaterialCohesive::~MaterialCohesive() = default;
/* -------------------------------------------------------------------------- */
void MaterialCohesive::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
- if (this->use_previous_delta_max)
+ if (this->use_previous_delta_max) {
this->delta_max.initializeHistory();
- if (this->use_previous_opening)
+ }
+ if (this->use_previous_opening) {
this->opening.initializeHistory();
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_material_cohesive,
"Cohesive Tractions", tractions);
#endif
auto & internal_force = const_cast<Array<Real> &>(model->getInternalForce());
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type,
_ek_cohesive)) {
auto & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
- if (nb_element == 0)
+ if (nb_element == 0) {
continue;
+ }
const auto & shapes = fem_cohesive.getShapes(type, ghost_type);
auto & traction = tractions(type, ghost_type);
auto & contact_traction = contact_tractions(type, ghost_type);
UInt size_of_shapes = shapes.getNbComponent();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points =
fem_cohesive.getNbIntegrationPoints(type, ghost_type);
/// compute @f$t_i N_a@f$
- Array<Real> * traction_cpy = new Array<Real>(
- nb_element * nb_quadrature_points, spatial_dimension * size_of_shapes);
+ auto * traction_cpy = new Array<Real>(nb_element * nb_quadrature_points,
+ spatial_dimension * size_of_shapes);
auto traction_it = traction.begin(spatial_dimension, 1);
auto contact_traction_it = contact_traction.begin(spatial_dimension, 1);
auto shapes_filtered_begin = shapes.begin(1, size_of_shapes);
auto traction_cpy_it =
traction_cpy->begin(spatial_dimension, size_of_shapes);
Matrix<Real> traction_tmp(spatial_dimension, 1);
for (UInt el = 0; el < nb_element; ++el) {
UInt current_quad = elem_filter(el) * nb_quadrature_points;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++traction_it,
++contact_traction_it, ++current_quad, ++traction_cpy_it) {
const Matrix<Real> & shapes_filtered =
shapes_filtered_begin[current_quad];
traction_tmp.copy(*traction_it);
traction_tmp += *contact_traction_it;
traction_cpy_it->mul<false, false>(traction_tmp, shapes_filtered);
}
}
/**
* compute @f$\int t \cdot N\, dS@f$ by @f$ \sum_q \mathbf{N}^t
* \mathbf{t}_q \overline w_q J_q@f$
*/
- Array<Real> * partial_int_t_N = new Array<Real>(
+ auto * partial_int_t_N = new Array<Real>(
nb_element, spatial_dimension * size_of_shapes, "int_t_N");
fem_cohesive.integrate(*traction_cpy, *partial_int_t_N,
spatial_dimension * size_of_shapes, type, ghost_type,
elem_filter);
delete traction_cpy;
- Array<Real> * int_t_N = new Array<Real>(
+ auto * int_t_N = new Array<Real>(
nb_element, 2 * spatial_dimension * size_of_shapes, "int_t_N");
Real * int_t_N_val = int_t_N->storage();
Real * partial_int_t_N_val = partial_int_t_N->storage();
for (UInt el = 0; el < nb_element; ++el) {
std::copy_n(partial_int_t_N_val, size_of_shapes * spatial_dimension,
int_t_N_val);
std::copy_n(partial_int_t_N_val, size_of_shapes * spatial_dimension,
int_t_N_val + size_of_shapes * spatial_dimension);
- for (UInt n = 0; n < size_of_shapes * spatial_dimension; ++n)
+ for (UInt n = 0; n < size_of_shapes * spatial_dimension; ++n) {
int_t_N_val[n] *= -1.;
+ }
int_t_N_val += nb_nodes_per_element * spatial_dimension;
partial_int_t_N_val += size_of_shapes * spatial_dimension;
}
delete partial_int_t_N;
/// assemble
model->getDOFManager().assembleElementalArrayLocalArray(
*int_t_N, internal_force, type, ghost_type, 1, elem_filter);
delete int_t_N;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type,
_ek_cohesive)) {
UInt nb_quadrature_points =
fem_cohesive.getNbIntegrationPoints(type, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<Real> & shapes = fem_cohesive.getShapes(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
- if (!nb_element)
+ if (nb_element == 0U) {
continue;
+ }
UInt size_of_shapes = shapes.getNbComponent();
- Array<Real> * shapes_filtered = new Array<Real>(
- nb_element * nb_quadrature_points, size_of_shapes, "filtered shapes");
+ auto * shapes_filtered = new Array<Real>(nb_element * nb_quadrature_points,
+ size_of_shapes, "filtered shapes");
Real * shapes_filtered_val = shapes_filtered->storage();
UInt * elem_filter_val = elem_filter.storage();
for (UInt el = 0; el < nb_element; ++el) {
- auto shapes_val = shapes.storage() + elem_filter_val[el] *
- size_of_shapes *
- nb_quadrature_points;
+ auto * shapes_val = shapes.storage() + elem_filter_val[el] *
+ size_of_shapes *
+ nb_quadrature_points;
memcpy(shapes_filtered_val, shapes_val,
size_of_shapes * nb_quadrature_points * sizeof(Real));
shapes_filtered_val += size_of_shapes * nb_quadrature_points;
}
Matrix<Real> A(spatial_dimension * size_of_shapes,
spatial_dimension * nb_nodes_per_element);
for (UInt i = 0; i < spatial_dimension * size_of_shapes; ++i) {
A(i, i) = 1;
A(i, i + spatial_dimension * size_of_shapes) = -1;
}
/// get the tangent matrix @f$\frac{\partial{(t/\delta)}}{\partial{\delta}}
/// @f$
- Array<Real> * tangent_stiffness_matrix = new Array<Real>(
+ auto * tangent_stiffness_matrix = new Array<Real>(
nb_element * nb_quadrature_points,
spatial_dimension * spatial_dimension, "tangent_stiffness_matrix");
// Array<Real> * normal = new Array<Real>(nb_element *
// nb_quadrature_points, spatial_dimension, "normal");
normal.resize(nb_quadrature_points);
computeNormal(model->getCurrentPosition(), normal, type, ghost_type);
/// compute openings @f$\mathbf{\delta}@f$
// computeOpening(model->getDisplacement(), opening(type, ghost_type), type,
// ghost_type);
- tangent_stiffness_matrix->clear();
+ tangent_stiffness_matrix->zero();
computeTangentTraction(type, *tangent_stiffness_matrix, normal, ghost_type);
// delete normal;
UInt size_at_nt_d_n_a = spatial_dimension * nb_nodes_per_element *
spatial_dimension * nb_nodes_per_element;
- Array<Real> * at_nt_d_n_a = new Array<Real>(
- nb_element * nb_quadrature_points, size_at_nt_d_n_a, "A^t*N^t*D*N*A");
+ auto * at_nt_d_n_a = new Array<Real>(nb_element * nb_quadrature_points,
+ size_at_nt_d_n_a, "A^t*N^t*D*N*A");
Array<Real>::iterator<Vector<Real>> shapes_filt_it =
shapes_filtered->begin(size_of_shapes);
Array<Real>::matrix_iterator D_it =
tangent_stiffness_matrix->begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator At_Nt_D_N_A_it =
at_nt_d_n_a->begin(spatial_dimension * nb_nodes_per_element,
spatial_dimension * nb_nodes_per_element);
Array<Real>::matrix_iterator At_Nt_D_N_A_end =
at_nt_d_n_a->end(spatial_dimension * nb_nodes_per_element,
spatial_dimension * nb_nodes_per_element);
Matrix<Real> N(spatial_dimension, spatial_dimension * size_of_shapes);
Matrix<Real> N_A(spatial_dimension,
spatial_dimension * nb_nodes_per_element);
Matrix<Real> D_N_A(spatial_dimension,
spatial_dimension * nb_nodes_per_element);
for (; At_Nt_D_N_A_it != At_Nt_D_N_A_end;
++At_Nt_D_N_A_it, ++D_it, ++shapes_filt_it) {
- N.clear();
+ N.zero();
/**
* store the shapes in voigt notations matrix @f$\mathbf{N} =
* \begin{array}{cccccc} N_0(\xi) & 0 & N_1(\xi) &0 & N_2(\xi) & 0 \\
* 0 & * N_0(\xi)& 0 &N_1(\xi)& 0 & N_2(\xi) \end{array} @f$
**/
- for (UInt i = 0; i < spatial_dimension; ++i)
- for (UInt n = 0; n < size_of_shapes; ++n)
+ for (UInt i = 0; i < spatial_dimension; ++i) {
+ for (UInt n = 0; n < size_of_shapes; ++n) {
N(i, i + spatial_dimension * n) = (*shapes_filt_it)(n);
+ }
+ }
/**
* compute stiffness matrix @f$ \mathbf{K} = \delta \mathbf{U}^T
* \int_{\Gamma_c} {\mathbf{P}^t \frac{\partial{\mathbf{t}}}
*{\partial{\delta}}
* \mathbf{P} d\Gamma \Delta \mathbf{U}} @f$
**/
N_A.mul<false, false>(N, A);
D_N_A.mul<false, false>(*D_it, N_A);
(*At_Nt_D_N_A_it).mul<true, false>(D_N_A, N_A);
}
delete tangent_stiffness_matrix;
delete shapes_filtered;
- Array<Real> * K_e = new Array<Real>(nb_element, size_at_nt_d_n_a, "K_e");
+ auto * K_e = new Array<Real>(nb_element, size_at_nt_d_n_a, "K_e");
fem_cohesive.integrate(*at_nt_d_n_a, *K_e, size_at_nt_d_n_a, type,
ghost_type, elem_filter);
delete at_nt_d_n_a;
model->getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _unsymmetric, elem_filter);
delete K_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- *
* Compute traction from displacements
*
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void MaterialCohesive::computeTraction(GhostType ghost_type) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_material_cohesive,
"Cohesive Openings", opening);
#endif
- for (auto & type : element_filter.elementTypes(spatial_dimension, ghost_type,
- _ek_cohesive)) {
+ for (const auto & type : element_filter.elementTypes(
+ spatial_dimension, ghost_type, _ek_cohesive)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
- if (nb_element == 0)
+ if (nb_element == 0) {
continue;
+ }
UInt nb_quadrature_points =
nb_element * fem_cohesive.getNbIntegrationPoints(type, ghost_type);
normal.resize(nb_quadrature_points);
/// compute normals @f$\mathbf{n}@f$
computeNormal(model->getCurrentPosition(), normal, type, ghost_type);
/// compute openings @f$\mathbf{\delta}@f$
computeOpening(model->getDisplacement(), opening(type, ghost_type), type,
ghost_type);
/// compute traction @f$\mathbf{t}@f$
computeTraction(normal, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::computeNormal(const Array<Real> & position,
Array<Real> & normal, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem_cohesive =
this->model->getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine");
- normal.clear();
+ normal.zero();
#define COMPUTE_NORMAL(type) \
fem_cohesive.getShapeFunctions() \
.computeNormalsOnIntegrationPoints<type, CohesiveReduceFunctionMean>( \
position, normal, ghost_type, element_filter(type, ghost_type));
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(COMPUTE_NORMAL);
#undef COMPUTE_NORMAL
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::computeOpening(const Array<Real> & displacement,
Array<Real> & opening, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem_cohesive =
this->model->getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine");
#define COMPUTE_OPENING(type) \
fem_cohesive.getShapeFunctions() \
.interpolateOnIntegrationPoints<type, CohesiveReduceFunctionOpening>( \
displacement, opening, spatial_dimension, ghost_type, \
element_filter(type, ghost_type));
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(COMPUTE_OPENING);
#undef COMPUTE_OPENING
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::updateEnergies(ElementType type) {
AKANTU_DEBUG_IN();
- if (Mesh::getKind(type) != _ek_cohesive)
+ if (Mesh::getKind(type) != _ek_cohesive) {
return;
+ }
Vector<Real> b(spatial_dimension);
Vector<Real> h(spatial_dimension);
auto erev = reversible_energy(type).begin();
auto etot = total_energy(type).begin();
auto traction_it = tractions(type).begin(spatial_dimension);
auto traction_old_it = tractions.previous(type).begin(spatial_dimension);
auto opening_it = opening(type).begin(spatial_dimension);
auto opening_old_it = opening.previous(type).begin(spatial_dimension);
auto traction_end = tractions(type).end(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end; ++traction_it, ++traction_old_it,
++opening_it, ++opening_old_it, ++erev,
++etot) {
/// trapezoidal integration
b = *opening_it;
b -= *opening_old_it;
h = *traction_old_it;
h += *traction_it;
*etot += .5 * b.dot(h);
*erev = .5 * traction_it->dot(*opening_it);
}
/// update old values
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getReversibleEnergy() {
AKANTU_DEBUG_IN();
Real erev = 0.;
/// integrate reversible energy for each type of elements
- for (auto & type : element_filter.elementTypes(spatial_dimension, _not_ghost,
- _ek_cohesive)) {
+ for (const auto & type : element_filter.elementTypes(
+ spatial_dimension, _not_ghost, _ek_cohesive)) {
erev +=
fem_cohesive.integrate(reversible_energy(type, _not_ghost), type,
_not_ghost, element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return erev;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getDissipatedEnergy() {
AKANTU_DEBUG_IN();
Real edis = 0.;
/// integrate dissipated energy for each type of elements
- for (auto & type : element_filter.elementTypes(spatial_dimension, _not_ghost,
- _ek_cohesive)) {
+ for (const auto & type : element_filter.elementTypes(
+ spatial_dimension, _not_ghost, _ek_cohesive)) {
Array<Real> dissipated_energy(total_energy(type, _not_ghost));
dissipated_energy -= reversible_energy(type, _not_ghost);
edis += fem_cohesive.integrate(dissipated_energy, type, _not_ghost,
element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return edis;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getContactEnergy() {
AKANTU_DEBUG_IN();
Real econ = 0.;
/// integrate contact energy for each type of elements
- for (auto & type : element_filter.elementTypes(spatial_dimension, _not_ghost,
- _ek_cohesive)) {
+ for (const auto & type : element_filter.elementTypes(
+ spatial_dimension, _not_ghost, _ek_cohesive)) {
auto & el_filter = element_filter(type, _not_ghost);
UInt nb_quad_per_el = fem_cohesive.getNbIntegrationPoints(type, _not_ghost);
UInt nb_quad_points = el_filter.size() * nb_quad_per_el;
Array<Real> contact_energy(nb_quad_points);
auto contact_traction_it =
contact_tractions(type, _not_ghost).begin(spatial_dimension);
auto contact_opening_it =
contact_opening(type, _not_ghost).begin(spatial_dimension);
/// loop on each quadrature point
for (UInt q = 0; q < nb_quad_points;
++contact_traction_it, ++contact_opening_it, ++q) {
contact_energy(q) = .5 * contact_traction_it->dot(*contact_opening_it);
}
econ += fem_cohesive.integrate(contact_energy, type, _not_ghost, el_filter);
}
AKANTU_DEBUG_OUT();
return econ;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getEnergy(const std::string & type) {
- AKANTU_DEBUG_IN();
-
- if (type == "reversible")
+ if (type == "reversible") {
return getReversibleEnergy();
- else if (type == "dissipated")
+ }
+ if (type == "dissipated") {
return getDissipatedEnergy();
- else if (type == "cohesive contact")
+ }
+ if (type == "cohesive contact") {
return getContactEnergy();
+ }
- AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
index a7b1a28ce..9bc05fb2e 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
@@ -1,234 +1,234 @@
/**
* @file material_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Feb 21 2018
*
* @brief Specialization of the material class for cohesive elements
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#include "cohesive_internal_field.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MATERIAL_COHESIVE_HH__
-#define __AKANTU_MATERIAL_COHESIVE_HH__
+#ifndef AKANTU_MATERIAL_COHESIVE_HH_
+#define AKANTU_MATERIAL_COHESIVE_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
class MaterialCohesive : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MyFEEngineCohesiveType =
FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive>;
public:
MaterialCohesive(SolidMechanicsModel & model, const ID & id = "");
~MaterialCohesive() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// compute tractions (including normals and openings)
void computeTraction(GhostType ghost_type = _not_ghost);
/// assemble residual
void assembleInternalForces(GhostType ghost_type = _not_ghost) override;
/// check stress for cohesive elements' insertion, by default it
/// also updates the cohesive elements' data
virtual void checkInsertion(bool /*check_only*/ = false) {
AKANTU_TO_IMPLEMENT();
}
/// interpolate stress on given positions for each element (empty
/// implemantation to avoid the generic call to be done on cohesive elements)
virtual void interpolateStress(const ElementType /*type*/,
Array<Real> & /*result*/) {}
/// compute the stresses
void computeAllStresses(GhostType /*ghost_type*/ = _not_ghost) override{};
// add the facet to be handled by the material
UInt addFacet(const Element & element);
protected:
- virtual void computeTangentTraction(const ElementType & /*el_type*/,
+ virtual void computeTangentTraction(ElementType /*el_type*/,
Array<Real> & /*tangent_matrix*/,
const Array<Real> & /*normal*/,
GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// compute the normal
void computeNormal(const Array<Real> & position, Array<Real> & normal,
ElementType type, GhostType ghost_type);
/// compute the opening
void computeOpening(const Array<Real> & displacement, Array<Real> & opening,
ElementType type, GhostType ghost_type);
template <ElementType type>
void computeNormal(const Array<Real> & position, Array<Real> & normal,
GhostType ghost_type);
/// assemble stiffness
void assembleStiffnessMatrix(GhostType ghost_type) override;
/// constitutive law
virtual void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) = 0;
/// parallelism functions
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
protected:
void updateEnergies(ElementType el_type) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the opening
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Opening, opening, Real);
/// get the traction
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Traction, tractions, Real);
/// get damage
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
/// get facet filter
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(FacetFilter, facet_filter, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(FacetFilter, facet_filter, UInt);
AKANTU_GET_MACRO(FacetFilter, facet_filter,
const ElementTypeMapArray<UInt> &);
// AKANTU_GET_MACRO(ElementFilter, element_filter, const
// ElementTypeMapArray<UInt> &);
/// compute reversible energy
Real getReversibleEnergy();
/// compute dissipated energy
Real getDissipatedEnergy();
/// compute contact energy
Real getContactEnergy();
/// get energy
Real getEnergy(const std::string & type) override;
/// return the energy (identified by id) for the provided element
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override {
return Material::getEnergy(energy_id, type, index);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// list of facets assigned to this material
ElementTypeMapArray<UInt> facet_filter;
/// Link to the cohesive fem object in the model
FEEngine & fem_cohesive;
private:
/// reversible energy by quadrature point
CohesiveInternalField<Real> reversible_energy;
/// total energy by quadrature point
CohesiveInternalField<Real> total_energy;
protected:
/// opening in all elements and quadrature points
CohesiveInternalField<Real> opening;
/// traction in all elements and quadrature points
CohesiveInternalField<Real> tractions;
/// traction due to contact
CohesiveInternalField<Real> contact_tractions;
/// normal openings for contact tractions
CohesiveInternalField<Real> contact_opening;
/// maximum displacement
CohesiveInternalField<Real> delta_max;
/// tell if the previous delta_max state is needed (in iterative schemes)
bool use_previous_delta_max;
/// tell if the previous opening state is needed (in iterative schemes)
bool use_previous_opening;
/// damage
CohesiveInternalField<Real> damage;
/// pointer to the solid mechanics model for cohesive elements
SolidMechanicsModelCohesive * model;
/// critical stress
RandomInternalField<Real, FacetInternalField> sigma_c;
/// critical displacement
Real delta_c;
/// array to temporarily store the normals
Array<Real> normal;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_cohesive_inline_impl.hh"
#include "cohesive_internal_field_tmpl.hh"
-#endif /* __AKANTU_MATERIAL_COHESIVE_HH__ */
+#endif /* AKANTU_MATERIAL_COHESIVE_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
index 31d7c83cf..e1338e6e0 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
@@ -1,707 +1,725 @@
/**
* @file solid_mechanics_model_cohesive.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Wed Feb 21 2018
*
* @brief Solid mechanics model for cohesive elements
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
#include "aka_iterators.hh"
#include "cohesive_element_inserter.hh"
#include "element_synchronizer.hh"
#include "facet_synchronizer.hh"
#include "fe_engine_template.hh"
#include "global_ids_updater.hh"
#include "integrator_gauss.hh"
#include "material_cohesive.hh"
#include "mesh_accessor.hh"
#include "mesh_global_data_updater.hh"
#include "parser.hh"
#include "shape_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
class CohesiveMeshGlobalDataUpdater : public MeshGlobalDataUpdater {
public:
CohesiveMeshGlobalDataUpdater(SolidMechanicsModelCohesive & model)
: model(model), mesh(model.getMesh()),
global_ids_updater(model.getMesh(), *model.cohesive_synchronizer) {}
/* ------------------------------------------------------------------------ */
std::tuple<UInt, UInt>
updateData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event) override {
- auto cohesive_nodes_event =
+ auto *cohesive_nodes_event =
dynamic_cast<CohesiveNewNodesEvent *>(&nodes_event);
- if (not cohesive_nodes_event)
+ if (cohesive_nodes_event == nullptr) {
return std::make_tuple(nodes_event.getList().size(),
elements_event.getList().size());
+ }
/// update nodes type
auto & new_nodes = cohesive_nodes_event->getList();
auto & old_nodes = cohesive_nodes_event->getOldNodesList();
auto local_nb_new_nodes = new_nodes.size();
auto nb_new_nodes = local_nb_new_nodes;
if (mesh.isDistributed()) {
MeshAccessor mesh_accessor(mesh);
auto & nodes_flags = mesh_accessor.getNodesFlags();
auto nb_old_nodes = nodes_flags.size();
nodes_flags.resize(nb_old_nodes + local_nb_new_nodes);
for (auto && data : zip(old_nodes, new_nodes)) {
- UInt old_node, new_node;
+ UInt old_node;
+ UInt new_node;
std::tie(old_node, new_node) = data;
nodes_flags(new_node) = nodes_flags(old_node);
}
model.updateCohesiveSynchronizers();
nb_new_nodes = global_ids_updater.updateGlobalIDs(new_nodes.size());
}
Vector<UInt> nb_new_stuff = {nb_new_nodes, elements_event.getList().size()};
const auto & comm = mesh.getCommunicator();
comm.allReduce(nb_new_stuff, SynchronizerOperation::_sum);
if (nb_new_stuff(1) > 0) {
mesh.sendEvent(elements_event);
MeshUtils::resetFacetToDouble(mesh.getMeshFacets());
}
if (nb_new_stuff(0) > 0) {
mesh.sendEvent(nodes_event);
// mesh.sendEvent(global_ids_updater.getChangedNodeEvent());
}
return std::make_tuple(nb_new_stuff(0), nb_new_stuff(1));
}
private:
SolidMechanicsModelCohesive & model;
Mesh & mesh;
GlobalIdsUpdater global_ids_updater;
};
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::SolidMechanicsModelCohesive(
Mesh & mesh, UInt dim, const ID & id, const MemoryID & memory_id)
: SolidMechanicsModel(mesh, dim, id, memory_id,
ModelType::_solid_mechanics_model_cohesive),
tangents("tangents", id), facet_stress("facet_stress", id),
facet_material("facet_material", id) {
AKANTU_DEBUG_IN();
registerFEEngineObject<MyFEEngineCohesiveType>("CohesiveFEEngine", mesh,
Model::spatial_dimension);
auto && tmp_material_selector =
std::make_shared<DefaultMaterialCohesiveSelector>(*this);
tmp_material_selector->setFallback(this->material_selector);
this->material_selector = tmp_material_selector;
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("cohesive elements", id);
this->mesh.addDumpMeshToDumper("cohesive elements", mesh,
Model::spatial_dimension, _not_ghost,
_ek_cohesive);
#endif
if (this->mesh.isDistributed()) {
/// create the distributed synchronizer for cohesive elements
this->cohesive_synchronizer = std::make_unique<ElementSynchronizer>(
mesh, "cohesive_distributed_synchronizer");
auto & synchronizer = mesh.getElementSynchronizer();
this->cohesive_synchronizer->split(synchronizer, [](auto && el) {
return Mesh::getKind(el.type) == _ek_cohesive;
});
this->registerSynchronizer(*cohesive_synchronizer,
SynchronizationTag::_material_id);
this->registerSynchronizer(*cohesive_synchronizer,
SynchronizationTag::_smm_stress);
this->registerSynchronizer(*cohesive_synchronizer,
SynchronizationTag::_smm_boundary);
}
this->inserter = std::make_unique<CohesiveElementInserter>(
this->mesh, id + ":cohesive_element_inserter");
registerFEEngineObject<MyFEEngineFacetType>(
"FacetsFEEngine", mesh.getMeshFacets(), Model::spatial_dimension - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::~SolidMechanicsModelCohesive() = default;
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::setTimeStep(Real time_step,
const ID & solver_id) {
SolidMechanicsModel::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper("cohesive elements").setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initFullImpl(const ModelOptions & options) {
AKANTU_DEBUG_IN();
const auto & smmc_options =
aka::as_type<SolidMechanicsModelCohesiveOptions>(options);
this->is_extrinsic = smmc_options.is_extrinsic;
inserter->setIsExtrinsic(is_extrinsic);
if (mesh.isDistributed()) {
auto & mesh_facets = inserter->getMeshFacets();
auto & synchronizer =
aka::as_type<FacetSynchronizer>(mesh_facets.getElementSynchronizer());
// synchronizeGhostFacetsConnectivity();
/// create the facet synchronizer for extrinsic simulations
if (is_extrinsic) {
facet_stress_synchronizer = std::make_unique<ElementSynchronizer>(
synchronizer, id + ":facet_stress_synchronizer");
facet_stress_synchronizer->swapSendRecv();
this->registerSynchronizer(*facet_stress_synchronizer,
SynchronizationTag::_smmc_facets_stress);
}
}
MeshAccessor mesh_accessor(mesh);
mesh_accessor.registerGlobalDataUpdater(
std::make_unique<CohesiveMeshGlobalDataUpdater>(*this));
ParserSection section;
bool is_empty;
std::tie(section, is_empty) = this->getParserSection();
if (not is_empty) {
auto inserter_section =
section.getSubSections(ParserType::_cohesive_inserter);
if (inserter_section.begin() != inserter_section.end()) {
inserter->parseSection(*inserter_section.begin());
}
}
SolidMechanicsModel::initFullImpl(options);
AKANTU_DEBUG_OUT();
} // namespace akantu
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initMaterials() {
AKANTU_DEBUG_IN();
// make sure the material are instantiated
- if (not are_materials_instantiated)
+ if (not are_materials_instantiated) {
instantiateMaterials();
+ }
/// find the first cohesive material
UInt cohesive_index = UInt(-1);
for (auto && material : enumerate(materials)) {
- if (dynamic_cast<MaterialCohesive *>(std::get<1>(material).get())) {
+ if (dynamic_cast<MaterialCohesive *>(std::get<1>(material).get()) !=
+ nullptr) {
cohesive_index = std::get<0>(material);
break;
}
}
- if (cohesive_index == UInt(-1))
+ if (cohesive_index == UInt(-1)) {
AKANTU_EXCEPTION("No cohesive materials in the material input file");
+ }
material_selector->setFallback(cohesive_index);
// set the facet information in the material in case of dynamic insertion
// to know what material to call for stress checks
const Mesh & mesh_facets = inserter->getMeshFacets();
facet_material.initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_element = true,
_default_value = material_selector->getFallbackValue());
for_each_element(
mesh_facets,
[&](auto && element) {
auto mat_index = (*material_selector)(element);
auto & mat = aka::as_type<MaterialCohesive>(*materials[mat_index]);
facet_material(element) = mat_index;
if (is_extrinsic) {
mat.addFacet(element);
}
},
_spatial_dimension = spatial_dimension - 1, _ghost_type = _not_ghost);
SolidMechanicsModel::initMaterials();
if (is_extrinsic) {
this->initAutomaticInsertion();
} else {
this->insertIntrinsicElements();
}
AKANTU_DEBUG_OUT();
} // namespace akantu
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*/
void SolidMechanicsModelCohesive::initModel() {
AKANTU_DEBUG_IN();
SolidMechanicsModel::initModel();
/// add cohesive type connectivity
ElementType type = _not_defined;
for (auto && type_ghost : ghost_types) {
for (const auto & tmp_type :
mesh.elementTypes(spatial_dimension, type_ghost)) {
const auto & connectivity = mesh.getConnectivity(tmp_type, type_ghost);
- if (connectivity.size() == 0)
+ if (connectivity.empty()) {
continue;
+ }
type = tmp_type;
auto type_facet = Mesh::getFacetType(type);
auto type_cohesive = FEEngine::getCohesiveElementType(type_facet);
mesh.addConnectivityType(type_cohesive, type_ghost);
}
}
AKANTU_DEBUG_ASSERT(type != _not_defined, "No elements in the mesh");
getFEEngine("CohesiveFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("CohesiveFEEngine").initShapeFunctions(_ghost);
if (is_extrinsic) {
getFEEngine("FacetsFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("FacetsFEEngine").initShapeFunctions(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::insertIntrinsicElements() {
AKANTU_DEBUG_IN();
inserter->insertIntrinsicElements();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initAutomaticInsertion() {
AKANTU_DEBUG_IN();
this->inserter->limitCheckFacets();
this->updateFacetStressSynchronizer();
this->resizeFacetStress();
/// compute normals on facets
this->computeNormals();
this->initStressInterpolation();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateAutomaticInsertion() {
AKANTU_DEBUG_IN();
this->inserter->limitCheckFacets();
this->updateFacetStressSynchronizer();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initStressInterpolation() {
Mesh & mesh_facets = inserter->getMeshFacets();
/// compute quadrature points coordinates on facets
Array<Real> & position = mesh.getNodes();
ElementTypeMapArray<Real> quad_facets("quad_facets", id);
quad_facets.initialize(mesh_facets, _nb_component = Model::spatial_dimension,
_spatial_dimension = Model::spatial_dimension - 1);
// mesh_facets.initElementTypeMapArray(quad_facets, Model::spatial_dimension,
// Model::spatial_dimension - 1);
getFEEngine("FacetsFEEngine")
.interpolateOnIntegrationPoints(position, quad_facets);
/// compute elements quadrature point positions and build
/// element-facet quadrature points data structure
ElementTypeMapArray<Real> elements_quad_facets("elements_quad_facets", id);
elements_quad_facets.initialize(
mesh, _nb_component = Model::spatial_dimension,
_spatial_dimension = Model::spatial_dimension);
// mesh.initElementTypeMapArray(elements_quad_facets,
// Model::spatial_dimension,
// Model::spatial_dimension);
for (auto elem_gt : ghost_types) {
- for (auto & type : mesh.elementTypes(Model::spatial_dimension, elem_gt)) {
+ for (const auto & type : mesh.elementTypes(Model::spatial_dimension, elem_gt)) {
UInt nb_element = mesh.getNbElement(type, elem_gt);
- if (nb_element == 0)
+ if (nb_element == 0) {
continue;
+ }
/// compute elements' quadrature points and list of facet
/// quadrature points positions by element
const auto & facet_to_element =
mesh_facets.getSubelementToElement(type, elem_gt);
auto & el_q_facet = elements_quad_facets(type, elem_gt);
auto facet_type = Mesh::getFacetType(type);
auto nb_quad_per_facet =
getFEEngine("FacetsFEEngine").getNbIntegrationPoints(facet_type);
auto nb_facet_per_elem = facet_to_element.getNbComponent();
// small hack in the loop to skip boundary elements, they are silently
// initialized to NaN to see if this causes problems
el_q_facet.resize(nb_element * nb_facet_per_elem * nb_quad_per_facet,
std::numeric_limits<Real>::quiet_NaN());
for (auto && data :
zip(make_view(facet_to_element),
make_view(el_q_facet, spatial_dimension, nb_quad_per_facet))) {
const auto & global_facet = std::get<0>(data);
auto & el_q = std::get<1>(data);
- if (global_facet == ElementNull)
+ if (global_facet == ElementNull) {
continue;
+ }
Matrix<Real> quad_f =
make_view(quad_facets(global_facet.type, global_facet.ghost_type),
spatial_dimension, nb_quad_per_facet)
.begin()[global_facet.element];
el_q = quad_f;
// for (UInt q = 0; q < nb_quad_per_facet; ++q) {
// for (UInt s = 0; s < Model::spatial_dimension; ++s) {
// el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
// f * nb_quad_per_facet + q,
// s) = quad_f(global_facet * nb_quad_per_facet + q,
// s);
// }
// }
//}
}
}
}
/// loop over non cohesive materials
for (auto && material : materials) {
- if (dynamic_cast<MaterialCohesive *>(material.get()))
+ if (aka::is_of_type<MaterialCohesive>(material)) {
continue;
+ }
/// initialize the interpolation function
material->initElementalFieldInterpolation(elements_quad_facets);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::assembleInternalForces() {
AKANTU_DEBUG_IN();
// f_int += f_int_cohe
for (auto & material : this->materials) {
try {
auto & mat = aka::as_type<MaterialCohesive>(*material);
mat.computeTraction(_not_ghost);
} catch (std::bad_cast & bce) {
}
}
SolidMechanicsModel::assembleInternalForces();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::computeNormals() {
AKANTU_DEBUG_IN();
Mesh & mesh_facets = this->inserter->getMeshFacets();
this->getFEEngine("FacetsFEEngine")
.computeNormalsOnIntegrationPoints(_not_ghost);
/**
* @todo store tangents while computing normals instead of
* recomputing them as follows:
*/
/* ------------------------------------------------------------------------ */
UInt tangent_components =
Model::spatial_dimension * (Model::spatial_dimension - 1);
tangents.initialize(mesh_facets, _nb_component = tangent_components,
_spatial_dimension = Model::spatial_dimension - 1);
// mesh_facets.initElementTypeMapArray(tangents, tangent_components,
// Model::spatial_dimension - 1);
for (auto facet_type :
mesh_facets.elementTypes(Model::spatial_dimension - 1)) {
const Array<Real> & normals =
this->getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(facet_type);
Array<Real> & tangents = this->tangents(facet_type);
Math::compute_tangents(normals, tangents);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::interpolateStress() {
ElementTypeMapArray<Real> by_elem_result("temporary_stress_by_facets", id);
for (auto & material : materials) {
- auto * mat = dynamic_cast<MaterialCohesive *>(material.get());
- if (mat == nullptr)
+ if (not aka::is_of_type<MaterialCohesive>(material)) {
/// interpolate stress on facet quadrature points positions
material->interpolateStressOnFacets(facet_stress, by_elem_result);
+ }
}
this->synchronize(SynchronizationTag::_smmc_facets_stress);
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::checkCohesiveStress() {
AKANTU_DEBUG_IN();
if (not is_extrinsic) {
AKANTU_EXCEPTION(
"This function can only be used for extrinsic cohesive elements");
}
interpolateStress();
for (auto & mat : materials) {
- auto * mat_cohesive = dynamic_cast<MaterialCohesive *>(mat.get());
- if (mat_cohesive) {
+ if (aka::is_of_type<MaterialCohesive>(mat)) {
/// check which not ghost cohesive elements are to be created
+ auto * mat_cohesive = aka::as_type<MaterialCohesive>(mat.get());
mat_cohesive->checkInsertion();
}
}
/// communicate data among processors
// this->synchronize(SynchronizationTag::_smmc_facets);
/// insert cohesive elements
UInt nb_new_elements = inserter->insertElements();
// if (nb_new_elements > 0) {
// this->reinitializeSolver();
// }
AKANTU_DEBUG_OUT();
return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onElementsAdded(
const Array<Element> & element_list, const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
SolidMechanicsModel::onElementsAdded(element_list, event);
- if (is_extrinsic)
+ if (is_extrinsic) {
resizeFacetStress();
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onNodesAdded(const Array<UInt> & new_nodes,
const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
SolidMechanicsModel::onNodesAdded(new_nodes, event);
const CohesiveNewNodesEvent * cohesive_event;
if ((cohesive_event = dynamic_cast<const CohesiveNewNodesEvent *>(&event)) ==
- nullptr)
+ nullptr) {
return;
+ }
const auto & old_nodes = cohesive_event->getOldNodesList();
auto copy = [this, &new_nodes, &old_nodes](auto & arr) {
- UInt new_node, old_node;
+ UInt new_node;
+ UInt old_node;
auto view = make_view(arr, spatial_dimension);
auto begin = view.begin();
for (auto && pair : zip(new_nodes, old_nodes)) {
std::tie(new_node, old_node) = pair;
auto old_ = begin + old_node;
auto new_ = begin + new_node;
*new_ = *old_;
}
};
copy(*displacement);
copy(*blocked_dofs);
- if (velocity)
+ if (velocity) {
copy(*velocity);
+ }
- if (acceleration)
+ if (acceleration) {
copy(*acceleration);
+ }
- if (current_position)
+ if (current_position) {
copy(*current_position);
+ }
- if (previous_displacement)
+ if (previous_displacement) {
copy(*previous_displacement);
+ }
// if (external_force)
// copy(*external_force);
// if (internal_force)
// copy(*internal_force);
- if (displacement_increment)
+ if (displacement_increment) {
copy(*displacement_increment);
+ }
copy(getDOFManager().getSolution("displacement"));
// this->assembleMassLumped();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::afterSolveStep(bool converged) {
AKANTU_DEBUG_IN();
/*
* This is required because the Cauchy stress is the stress measure that
* is used to check the insertion of cohesive elements
*/
if (converged) {
for (auto & mat : materials) {
- if (mat->isFiniteDeformation())
+ if (mat->isFiniteDeformation()) {
mat->computeAllCauchyStresses(_not_ghost);
+ }
}
}
SolidMechanicsModel::afterSolveStep(converged);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::printself(std::ostream & stream,
int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "SolidMechanicsModelCohesive ["
<< "\n";
SolidMechanicsModel::printself(stream, indent + 2);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::resizeFacetStress() {
AKANTU_DEBUG_IN();
this->facet_stress.initialize(getFEEngine("FacetsFEEngine"),
_nb_component =
2 * spatial_dimension * spatial_dimension,
_spatial_dimension = spatial_dimension - 1);
// for (auto && ghost_type : ghost_types) {
- // for (const auto & type :
+ // for (const const auto & type :
// mesh_facets.elementTypes(spatial_dimension - 1, ghost_type)) {
// UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);
// UInt nb_quadrature_points = getFEEngine("FacetsFEEngine")
// .getNbIntegrationPoints(type,
// ghost_type);
// UInt new_size = nb_facet * nb_quadrature_points;
// facet_stress(type, ghost_type).resize(new_size);
// }
// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::addDumpGroupFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
- const std::string & group_name, const ElementKind & element_kind,
+ const std::string & group_name, ElementKind element_kind,
bool padding_flag) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = Model::spatial_dimension;
ElementKind _element_kind = element_kind;
if (dumper_name == "cohesive elements") {
_element_kind = _ek_cohesive;
} else if (dumper_name == "facets") {
spatial_dimension = Model::spatial_dimension - 1;
}
SolidMechanicsModel::addDumpGroupFieldToDumper(dumper_name, field_id,
group_name, spatial_dimension,
_element_kind, padding_flag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onDump() {
this->flattenAllRegisteredInternals(_ek_cohesive);
SolidMechanicsModel::onDump();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
index 4fba0cb27..f7fffe588 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
@@ -1,309 +1,308 @@
/**
* @file solid_mechanics_model_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Mon Feb 05 2018
*
* @brief Solid mechanics model for cohesive elements
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
#include "material_selector_cohesive.hh"
#include "random_internal_field.hh" // included to have the specialization of
// ParameterTyped::operator Real()
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__
-#define __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__
+#ifndef AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH_
+#define AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class FacetSynchronizer;
class FacetStressSynchronizer;
class ElementSynchronizer;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
struct FacetsCohesiveIntegrationOrderFunctor {
template <ElementType type, ElementType cohesive_type =
CohesiveFacetProperty<type>::cohesive_type>
struct _helper {
static constexpr int get() {
return ElementClassProperty<cohesive_type>::polynomial_degree;
}
};
template <ElementType type> struct _helper<type, _not_defined> {
static constexpr int get() {
return ElementClassProperty<type>::polynomial_degree;
}
};
template <ElementType type> static inline constexpr int getOrder() {
return _helper<type>::get();
}
};
/* -------------------------------------------------------------------------- */
/* Solid Mechanics Model for Cohesive elements */
/* -------------------------------------------------------------------------- */
class SolidMechanicsModelCohesive : public SolidMechanicsModel,
public SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
class NewCohesiveNodesEvent : public NewNodesEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(OldNodesList, old_nodes, Array<UInt> &);
AKANTU_GET_MACRO(OldNodesList, old_nodes, const Array<UInt> &);
protected:
Array<UInt> old_nodes;
};
using MyFEEngineCohesiveType =
FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive>;
using MyFEEngineFacetType =
FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular,
FacetsCohesiveIntegrationOrderFunctor>;
- SolidMechanicsModelCohesive(Mesh & mesh,
- UInt spatial_dimension = _all_dimensions,
+ SolidMechanicsModelCohesive(Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "solid_mechanics_model_cohesive",
const MemoryID & memory_id = 0);
~SolidMechanicsModelCohesive() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize the cohesive model
void initFullImpl(const ModelOptions & options) override;
public:
/// set the value of the time step
void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// assemble the residual for the explicit scheme
void assembleInternalForces() override;
/// function to perform a stress check on each facet and insert
/// cohesive elements if needed (returns the number of new cohesive
/// elements)
UInt checkCohesiveStress();
/// interpolate stress on facets
void interpolateStress();
/// update automatic insertion after a change in the element inserter
void updateAutomaticInsertion();
/// insert intrinsic cohesive elements
void insertIntrinsicElements();
// template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria
// criteria> bool solveStepCohesive(Real tolerance, Real & error, UInt
// max_iteration = 100,
// bool load_reduction = false,
// Real tol_increase_factor = 1.0,
// bool do_not_factorize = false);
protected:
/// initialize stress interpolation
void initStressInterpolation();
/// initialize the model
void initModel() override;
/// initialize cohesive material
void initMaterials() override;
/// init facet filters for cohesive materials
void initFacetFilter();
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
private:
/// insert cohesive elements along a given physical surface of the mesh
void insertElementsFromMeshData(const std::string & physical_name);
/// initialize completely the model for extrinsic elements
void initAutomaticInsertion();
/// compute facets' normals
void computeNormals();
/// resize facet stress
void resizeFacetStress();
/// init facets_check array
void initFacetsCheck();
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
- void onNodesAdded(const Array<UInt> & nodes_list,
+ void onNodesAdded(const Array<UInt> & new_nodes,
const NewNodesEvent & event) override;
- void onElementsAdded(const Array<Element> & nodes_list,
+ void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
void afterSolveStep(bool converged = true) override;
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
void onDump() override;
void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
- const ElementKind & element_kind,
+ ElementKind element_kind,
bool padding_flag) override;
public:
/// register the tags associated with the parallel synchronizer for
/// cohesive elements
// void initParallel(MeshPartition * partition,
// DataAccessor * data_accessor = NULL,
// bool extrinsic = false);
protected:
//void synchronizeGhostFacetsConnectivity();
void updateCohesiveSynchronizers();
void updateFacetStressSynchronizer();
friend class CohesiveElementInserter;
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override;
protected:
UInt getNbQuadsForFacetCheck(const Array<Element> & elements) const;
template <typename T>
void packFacetStressDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements) const;
template <typename T>
void unpackFacetStressDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements) const;
template <typename T, bool pack_helper>
void packUnpackFacetStressDataHelper(ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & element) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get facet mesh
AKANTU_GET_MACRO(MeshFacets, mesh.getMeshFacets(), const Mesh &);
/// get stress on facets vector
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(StressOnFacets, facet_stress, Real);
/// get facet material
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(FacetMaterial, facet_material, UInt);
/// get facet material
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(FacetMaterial, facet_material, UInt);
/// get facet material
AKANTU_GET_MACRO(FacetMaterial, facet_material,
const ElementTypeMapArray<UInt> &);
/// @todo THIS HAS TO BE CHANGED
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Tangents, tangents, Real);
/// get element inserter
AKANTU_GET_MACRO_NOT_CONST(ElementInserter, *inserter,
CohesiveElementInserter &);
/// get is_extrinsic boolean
AKANTU_GET_MACRO(IsExtrinsic, is_extrinsic, bool);
/// get cohesive elements synchronizer
AKANTU_GET_MACRO_NOT_CONST(CohesiveSynchronizer, *cohesive_synchronizer,
ElementSynchronizer &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
friend class CohesiveMeshGlobalDataUpdater;
/// @todo store tangents when normals are computed:
ElementTypeMapArray<Real> tangents;
/// stress on facets on the two sides by quadrature point
ElementTypeMapArray<Real> facet_stress;
/// material to use if a cohesive element is created on a facet
ElementTypeMapArray<UInt> facet_material;
bool is_extrinsic{false};
/// cohesive element inserter
std::unique_ptr<CohesiveElementInserter> inserter;
/// facet stress synchronizer
std::unique_ptr<ElementSynchronizer> facet_stress_synchronizer;
/// cohesive elements synchronizer
std::unique_ptr<ElementSynchronizer> cohesive_synchronizer;
};
} // namespace akantu
#include "solid_mechanics_model_cohesive_inline_impl.hh"
-#endif /* __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__ */
+#endif /* AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.hh
index 6dff21676..ada180a26 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.hh
@@ -1,305 +1,305 @@
/**
* @file solid_mechanics_model_cohesive_inline_impl.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jan 18 2013
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of inline functions for the Cohesive element model
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_HH__
-#define __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_HH__
+#ifndef AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_HH_
+#define AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
// template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
// bool SolidMechanicsModelCohesive::solveStepCohesive(
// Real tolerance, Real & error, UInt max_iteration, bool load_reduction,
// Real tol_increase_factor, bool do_not_factorize) {
// // EventManager::sendEvent(
// // SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
// // this->implicitPred();
// // bool insertion_new_element = true;
// // bool converged = false;
// // Array<Real> * displacement_tmp = NULL;
// // Array<Real> * velocity_tmp = NULL;
// // Array<Real> * acceleration_tmp = NULL;
// // StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
// // Int prank = comm.whoAmI();
// // /// Loop for the insertion of new cohesive elements
// // while (insertion_new_element) {
// // if (is_extrinsic) {
// // /**
// // * If in extrinsic the solution of the previous incremental step
// // * is saved in temporary arrays created for displacements,
// // * velocities and accelerations. Such arrays are used to find
// // * the solution with the Newton-Raphson scheme (this is done by
// // * pointing the pointer "displacement" to displacement_tmp). In
// // * this way, inside the array "displacement" is kept the
// // * solution of the previous incremental step, and in
// // * "displacement_tmp" is saved the current solution.
// // */
// // if (!displacement_tmp)
// // displacement_tmp = new Array<Real>(0, spatial_dimension);
// // displacement_tmp->copy(*(this->displacement));
// // if (!velocity_tmp)
// // velocity_tmp = new Array<Real>(0, spatial_dimension);
// // velocity_tmp->copy(*(this->velocity));
// // if (!acceleration_tmp) {
// // acceleration_tmp = new Array<Real>(0, spatial_dimension);
// // }
// // acceleration_tmp->copy(*(this->acceleration));
// // std::swap(displacement, displacement_tmp);
// // std::swap(velocity, velocity_tmp);
// // std::swap(acceleration, acceleration_tmp);
// // }
// // this->updateResidual();
// // AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
// // "You should first initialize the implicit solver and
// "
// // "assemble the stiffness matrix");
// // bool need_factorize = !do_not_factorize;
// // if (method == _implicit_dynamic) {
// // AKANTU_DEBUG_ASSERT(mass_matrix != NULL, "You should first initialize
// "
// // "the implicit solver and "
// // "assemble the mass matrix");
// // }
// // switch (cmethod) {
// // case _scm_newton_raphson_tangent:
// // case _scm_newton_raphson_tangent_not_computed:
// // break;
// // case _scm_newton_raphson_tangent_modified:
// // this->assembleStiffnessMatrix();
// // break;
// // default:
// // AKANTU_ERROR("The resolution method "
// // << cmethod << " has not been implemented!");
// // }
// // UInt iter = 0;
// // converged = false;
// // error = 0.;
// // if (criteria == SolveConvergenceCriteria::_residual) {
// // converged = this->testConvergence<criteria>(tolerance, error);
// // if (converged)
// // return converged;
// // }
// // /// Loop to solve the nonlinear system
// // do {
// // if (cmethod == _scm_newton_raphson_tangent)
// // this->assembleStiffnessMatrix();
// // solve<NewmarkBeta::_displacement_corrector>(*increment, 1.,
// // need_factorize);
// // this->implicitCorr();
// // this->updateResidual();
// // converged = this->testConvergence<criteria>(tolerance, error);
// // iter++;
// // AKANTU_DEBUG_INFO("[" << criteria << "] Convergence iteration "
// // << std::setw(std::log10(max_iteration)) << iter
// // << ": error " << error
// // << (converged ? " < " : " > ") << tolerance);
// // switch (cmethod) {
// // case _scm_newton_raphson_tangent:
// // need_factorize = true;
// // break;
// // case _scm_newton_raphson_tangent_not_computed:
// // case _scm_newton_raphson_tangent_modified:
// // need_factorize = false;
// // break;
// // default:
// // AKANTU_ERROR("The resolution method "
// // << cmethod << " has not been implemented!");
// // }
// // } while (!converged && iter < max_iteration);
// // /**
// // * This is to save the obtained result and proceed with the
// // * simulation even if the error is higher than the pre-fixed
// // * tolerance. This is done only after loading reduction
// // * (load_reduction = true).
// // */
// // // if (load_reduction && (error < tolerance * tol_increase_factor))
// // // converged = true;
// // if ((error < tolerance * tol_increase_factor))
// // converged = true;
// // if (converged) {
// // } else if (iter == max_iteration) {
// // if (prank == 0) {
// // AKANTU_DEBUG_WARNING(
// // "[" << criteria << "] Convergence not reached after "
// // << std::setw(std::log10(max_iteration)) << iter << "
// iteration"
// // << (iter == 1 ? "" : "s") << "!" << std::endl);
// // }
// // }
// // if (is_extrinsic) {
// // /**
// // * If is extrinsic the pointer "displacement" is moved back to
// // * the array displacement. In this way, the array displacement is
// // * correctly resized during the checkCohesiveStress function (in
// // * case new cohesive elements are added). This is possible
// // * because the procedure called by checkCohesiveStress does not
// // * use the displacement field (the correct one is now stored in
// // * displacement_tmp), but directly the stress field that is
// // * already computed.
// // */
// // Array<Real> * tmp_swap;
// // tmp_swap = displacement_tmp;
// // displacement_tmp = this->displacement;
// // this->displacement = tmp_swap;
// // tmp_swap = velocity_tmp;
// // velocity_tmp = this->velocity;
// // this->velocity = tmp_swap;
// // tmp_swap = acceleration_tmp;
// // acceleration_tmp = this->acceleration;
// // this->acceleration = tmp_swap;
// // /// If convergence is reached, call checkCohesiveStress in order
// // /// to check if cohesive elements have to be introduced
// // if (converged) {
// // UInt new_cohesive_elements = checkCohesiveStress();
// // if (new_cohesive_elements == 0) {
// // insertion_new_element = false;
// // } else {
// // insertion_new_element = true;
// // }
// // }
// // }
// // if (!converged && load_reduction)
// // insertion_new_element = false;
// // /**
// // * If convergence is not reached, there is the possibility to
// // * return back to the main file and reduce the load. Before doing
// // * this, a pre-fixed value as to be defined for the parameter
// // * delta_max of the cohesive elements introduced in the current
// // * incremental step. This is done by calling the function
// // * checkDeltaMax.
// // */
// // if (!converged) {
// // insertion_new_element = false;
// // for (UInt m = 0; m < materials.size(); ++m) {
// // try {
// // MaterialCohesive & mat =
// // aka::as_type<MaterialCohesive>(*materials[m]);
// // mat.checkDeltaMax(_not_ghost);
// // } catch (std::bad_cast &) {
// // }
// // }
// // }
// // } // end loop for the insertion of new cohesive elements
// // /**
// // * When the solution to the current incremental step is computed (no
// // * more cohesive elements have to be introduced), call the function
// // * to compute the energies.
// // */
// // if ((is_extrinsic && converged)) {
// // for (UInt m = 0; m < materials.size(); ++m) {
// // try {
// // MaterialCohesive & mat =
// // aka::as_type<MaterialCohesive>(*materials[m]);
// // mat.computeEnergies();
// // } catch (std::bad_cast & bce) {
// // }
// // }
// // EventManager::sendEvent(
// // SolidMechanicsModelEvent::AfterSolveStepEvent(method));
// // /**
// // * The function resetVariables is necessary to correctly set a
// // * variable that permit to decrease locally the penalty parameter
// // * for compression.
// // */
// // for (UInt m = 0; m < materials.size(); ++m) {
// // try {
// // MaterialCohesive & mat =
// // aka::as_type<MaterialCohesive>(*materials[m]);
// // mat.resetVariables(_not_ghost);
// // } catch (std::bad_cast &) {
// // }
// // }
// // /// The correct solution is saved
// // this->displacement->copy(*displacement_tmp);
// // this->velocity->copy(*velocity_tmp);
// // this->acceleration->copy(*acceleration_tmp);
// // }
// // delete displacement_tmp;
// // delete velocity_tmp;
// // delete acceleration_tmp;
// // return insertion_new_element;
//}
} // namespace akantu
-#endif /* __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
index 51d48c77f..4e6559c5e 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
@@ -1,488 +1,514 @@
/**
* @file solid_mechanics_model_cohesive_parallel.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 05 2014
* @date last modification: Tue Feb 20 2018
*
* @brief Functions for parallel cohesive elements
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "solid_mechanics_model_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModelCohesive::synchronizeGhostFacetsConnectivity() {
// AKANTU_DEBUG_IN();
// const Communicator & comm = mesh.getCommunicator();
// Int psize = comm.getNbProc();
// if (psize == 1) {
// AKANTU_DEBUG_OUT();
// return;
// }
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateCohesiveSynchronizers() {
/// update synchronizers if needed
- if (not mesh.isDistributed())
+ if (not mesh.isDistributed()) {
return;
+ }
auto & mesh_facets = inserter->getMeshFacets();
auto & facet_synchronizer = mesh_facets.getElementSynchronizer();
const auto & cfacet_synchronizer = facet_synchronizer;
// update the cohesive element synchronizer
cohesive_synchronizer->updateSchemes([&](auto && scheme, auto && proc,
auto && direction) {
auto & facet_scheme =
cfacet_synchronizer.getCommunications().getScheme(proc, direction);
for (auto && facet : facet_scheme) {
const auto & cohesive_element = const_cast<const Mesh &>(mesh_facets)
.getElementToSubelement(facet)[1];
if (cohesive_element == ElementNull or
- cohesive_element.kind() != _ek_cohesive)
+ cohesive_element.kind() != _ek_cohesive) {
continue;
+ }
auto && cohesive_type = FEEngine::getCohesiveElementType(facet.type);
auto old_nb_cohesive_elements =
mesh.getNbElement(cohesive_type, facet.ghost_type);
old_nb_cohesive_elements -=
mesh_facets
.getData<UInt>("facet_to_double", facet.type, facet.ghost_type)
.size();
if (cohesive_element.element >= old_nb_cohesive_elements) {
scheme.push_back(cohesive_element);
}
}
});
- if (not facet_stress_synchronizer)
+ if (not facet_stress_synchronizer) {
return;
+ }
const auto & element_synchronizer = mesh.getElementSynchronizer();
const auto & comm = mesh.getCommunicator();
auto && my_rank = comm.whoAmI();
// update the facet stress synchronizer
facet_stress_synchronizer->updateSchemes([&](auto && scheme, auto && proc,
auto && /*direction*/) {
auto it_element = scheme.begin();
for (auto && element : scheme) {
auto && facet_check = inserter->getCheckFacets(
element.type, element.ghost_type)(element.element); // slow access
// here
if (facet_check) {
auto && connected_elements = mesh_facets.getElementToSubelement(
element.type, element.ghost_type)(element.element); // slow access
// here
auto && rank_left = element_synchronizer.getRank(connected_elements[0]);
auto && rank_right =
element_synchronizer.getRank(connected_elements[1]);
// keep element if the element is still a boundary element between two
// processors
if ((rank_left == Int(proc) and rank_right == my_rank) or
(rank_left == my_rank and rank_right == Int(proc))) {
*it_element = element;
++it_element;
}
}
}
scheme.resize(it_element - scheme.begin());
});
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateFacetStressSynchronizer() {
if (facet_stress_synchronizer != nullptr) {
const auto & rank_to_element =
mesh.getElementSynchronizer().getElementToRank();
const auto & facet_checks = inserter->getCheckFacets();
const auto & mesh_facets = inserter->getMeshFacets();
const auto & element_to_facet = mesh_facets.getElementToSubelement();
UInt rank = mesh.getCommunicator().whoAmI();
facet_stress_synchronizer->updateSchemes(
[&](auto & scheme, auto & proc, auto & /*direction*/) {
UInt el = 0;
for (auto && element : scheme) {
- if (not facet_checks(element))
+ if (not facet_checks(element)) {
continue;
+ }
const auto & next_el = element_to_facet(element);
UInt rank_left = rank_to_element(next_el[0]);
UInt rank_right = rank_to_element(next_el[1]);
if ((rank_left == rank and rank_right == proc) or
(rank_left == proc and rank_right == rank)) {
scheme[el] = element;
++el;
}
}
scheme.resize(el);
});
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SolidMechanicsModelCohesive::packFacetStressDataHelper(
const ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
packUnpackFacetStressDataHelper<T, true>(
const_cast<ElementTypeMapArray<T> &>(data_to_pack), buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SolidMechanicsModelCohesive::unpackFacetStressDataHelper(
ElementTypeMapArray<T> & data_to_unpack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
packUnpackFacetStressDataHelper<T, false>(data_to_unpack, buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void SolidMechanicsModelCohesive::packUnpackFacetStressDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt nb_quad_per_elem = 0;
UInt sp2 = spatial_dimension * spatial_dimension;
UInt nb_component = sp2 * 2;
bool element_rank = false;
Mesh & mesh_facets = inserter->getMeshFacets();
Array<T> * vect = nullptr;
Array<std::vector<Element>> * element_to_facet = nullptr;
auto & fe_engine = this->getFEEngine("FacetsFEEngine");
for (auto && el : elements) {
- if (el.type == _not_defined)
+ if (el.type == _not_defined) {
AKANTU_EXCEPTION(
"packUnpackFacetStressDataHelper called with wrong inputs");
+ }
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect = &data_to_pack(el.type, el.ghost_type);
element_to_facet =
&(mesh_facets.getElementToSubelement(el.type, el.ghost_type));
nb_quad_per_elem =
fe_engine.getNbIntegrationPoints(el.type, el.ghost_type);
}
- if (pack_helper)
+ if (pack_helper) {
element_rank =
(*element_to_facet)(el.element)[0].ghost_type != _not_ghost;
- else
+ } else {
element_rank =
(*element_to_facet)(el.element)[0].ghost_type == _not_ghost;
+ }
for (UInt q = 0; q < nb_quad_per_elem; ++q) {
Vector<T> data(vect->storage() +
(el.element * nb_quad_per_elem + q) * nb_component +
element_rank * sp2,
sp2);
- if (pack_helper)
+ if (pack_helper) {
buffer << data;
- else
+ } else {
buffer >> data;
+ }
}
}
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::getNbQuadsForFacetCheck(
const Array<Element> & elements) const {
UInt nb_quads = 0;
UInt nb_quad_per_facet = 0;
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
auto & fe_engine = this->getFEEngine("FacetsFEEngine");
- for (auto & el : elements) {
+ for (const auto & el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
nb_quad_per_facet =
fe_engine.getNbIntegrationPoints(el.type, el.ghost_type);
}
nb_quads += nb_quad_per_facet;
}
return nb_quads;
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
- if (elements.size() == 0)
+ if (elements.empty()) {
return 0;
+ }
/// regular element case
if (elements(0).kind() == _ek_regular) {
switch (tag) {
// case SynchronizationTag::_smmc_facets: {
// size += elements.size() * sizeof(bool);
// break;
// }
case SynchronizationTag::_smmc_facets_stress: {
UInt nb_quads = getNbQuadsForFacetCheck(elements);
size += nb_quads * spatial_dimension * spatial_dimension * sizeof(Real);
break;
}
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
- if (Mesh::getSpatialDimension(element.type) == (spatial_dimension - 1))
+ if (Mesh::getSpatialDimension(element.type) ==
+ (spatial_dimension - 1)) {
size += sizeof(UInt);
+ }
}
size += SolidMechanicsModel::getNbData(elements, tag);
break;
}
- default: { size += SolidMechanicsModel::getNbData(elements, tag); }
+ default: {
+ size += SolidMechanicsModel::getNbData(elements, tag);
+ }
}
}
/// cohesive element case
else if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case SynchronizationTag::_material_id: {
size += elements.size() * sizeof(UInt);
break;
}
case SynchronizationTag::_smm_boundary: {
UInt nb_nodes_per_element = 0;
for (auto && el : elements) {
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
// force, displacement, boundary
size += nb_nodes_per_element * spatial_dimension *
(2 * sizeof(Real) + sizeof(bool));
break;
}
default:
break;
}
if (tag != SynchronizationTag::_material_id &&
tag != SynchronizationTag::_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
size += mat.getNbData(elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
- if (elements.size() == 0)
+ if (elements.empty()) {
return;
+ }
if (elements(0).kind() == _ek_regular) {
switch (tag) {
// case SynchronizationTag::_smmc_facets: {
// packElementalDataHelper(inserter->getInsertionFacetsByElement(),
// buffer,
// elements, false, getFEEngine());
// break;
// }
case SynchronizationTag::_smmc_facets_stress: {
packFacetStressDataHelper(facet_stress, buffer, elements);
break;
}
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
- if (Mesh::getSpatialDimension(element.type) != (spatial_dimension - 1))
+ if (Mesh::getSpatialDimension(element.type) !=
+ (spatial_dimension - 1)) {
continue;
+ }
buffer << material_index(element);
}
SolidMechanicsModel::packData(buffer, elements, tag);
break;
}
- default: { SolidMechanicsModel::packData(buffer, elements, tag); }
+ default: {
+ SolidMechanicsModel::packData(buffer, elements, tag);
+ }
}
AKANTU_DEBUG_OUT();
return;
}
if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case SynchronizationTag::_material_id: {
packElementalDataHelper(material_index, buffer, elements, false,
getFEEngine("CohesiveFEEngine"));
break;
}
case SynchronizationTag::_smm_boundary: {
packNodalDataHelper(*internal_force, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
- default: {}
+ default: {
+ }
}
if (tag != SynchronizationTag::_material_id &&
tag != SynchronizationTag::_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.packData(buffer, elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
- if (elements.size() == 0)
+ if (elements.empty()) {
return;
+ }
if (elements(0).kind() == _ek_regular) {
switch (tag) {
// case SynchronizationTag::_smmc_facets: {
// unpackElementalDataHelper(inserter->getInsertionFacetsByElement(),
// buffer,
// elements, false, getFEEngine());
// break;
// }
case SynchronizationTag::_smmc_facets_stress: {
unpackFacetStressDataHelper(facet_stress, buffer, elements);
break;
}
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
- if (Mesh::getSpatialDimension(element.type) != (spatial_dimension - 1))
+ if (Mesh::getSpatialDimension(element.type) !=
+ (spatial_dimension - 1)) {
continue;
+ }
UInt recv_mat_index;
buffer >> recv_mat_index;
UInt & mat_index = material_index(element);
- if (mat_index != UInt(-1))
+ if (mat_index != UInt(-1)) {
continue;
+ }
// add ghosts element to the correct material
mat_index = recv_mat_index;
auto & mat = aka::as_type<MaterialCohesive>(*materials[mat_index]);
if (is_extrinsic) {
mat.addFacet(element);
}
facet_material(element) = recv_mat_index;
}
SolidMechanicsModel::unpackData(buffer, elements, tag);
break;
}
- default: { SolidMechanicsModel::unpackData(buffer, elements, tag); }
+ default: {
+ SolidMechanicsModel::unpackData(buffer, elements, tag);
+ }
}
AKANTU_DEBUG_OUT();
return;
}
if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
UInt recv_mat_index;
buffer >> recv_mat_index;
UInt & mat_index = material_index(element);
- if (mat_index != UInt(-1))
+ if (mat_index != UInt(-1)) {
continue;
+ }
// add ghosts element to the correct material
mat_index = recv_mat_index;
UInt index = materials[mat_index]->addElement(element);
material_local_numbering(element) = index;
}
break;
}
case SynchronizationTag::_smm_boundary: {
unpackNodalDataHelper(*internal_force, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
- default: {}
+ default: {
+ }
}
if (tag != SynchronizationTag::_material_id &&
tag != SynchronizationTag::_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.unpackData(buffer, elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
index a490c68c5..a10b96a4b 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
@@ -1,173 +1,170 @@
/**
* @file embedded_interface_intersector.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri May 01 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Class that loads the interface from mesh and computes intersections
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "embedded_interface_intersector.hh"
#include "mesh_segment_intersector.hh"
/// Helper macro for types in the mesh. Creates an intersector and computes
/// intersection queries
#define INTERFACE_INTERSECTOR_CASE(dim, type) \
do { \
MeshSegmentIntersector<dim, type> intersector(this->mesh, interface_mesh); \
name_to_primitives_it = name_to_primitives_map.begin(); \
for (; name_to_primitives_it != name_to_primitives_end; \
++name_to_primitives_it) { \
intersector.setPhysicalName(name_to_primitives_it->first); \
intersector.buildResultFromQueryList(name_to_primitives_it->second); \
} \
} while (0)
#define INTERFACE_INTERSECTOR_CASE_2D(type) INTERFACE_INTERSECTOR_CASE(2, type)
#define INTERFACE_INTERSECTOR_CASE_3D(type) INTERFACE_INTERSECTOR_CASE(3, type)
namespace akantu {
EmbeddedInterfaceIntersector::EmbeddedInterfaceIntersector(
Mesh & mesh, const Mesh & primitive_mesh)
: MeshGeomAbstract(mesh),
interface_mesh(mesh.getSpatialDimension(), "interface_mesh"),
primitive_mesh(primitive_mesh) {
// Initiating mesh connectivity and data
interface_mesh.addConnectivityType(_segment_2, _not_ghost);
interface_mesh.addConnectivityType(_segment_2, _ghost);
interface_mesh.getElementalData<Element>("associated_element")
.alloc(0, 1, _segment_2);
interface_mesh.getElementalData<std::string>("physical_names")
.alloc(0, 1, _segment_2);
}
-EmbeddedInterfaceIntersector::~EmbeddedInterfaceIntersector() {}
-
void EmbeddedInterfaceIntersector::constructData(GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
const UInt dim = this->mesh.getSpatialDimension();
- if (dim == 1)
+ if (dim == 1) {
AKANTU_ERROR(
"No embedded model in 1D. Deactivate intersection initialization");
+ }
- Array<std::string> * physical_names = NULL;
+ Array<std::string> * physical_names = nullptr;
try {
physical_names = &const_cast<Array<std::string> &>(
this->primitive_mesh.getData<std::string>("physical_names",
_segment_2));
} catch (debug::Exception & e) {
AKANTU_ERROR("You must define physical names to reinforcements in "
"order to use the embedded model");
throw e;
}
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_segment_2);
- Array<UInt>::const_vector_iterator connectivity =
+ auto connectivity =
primitive_mesh.getConnectivity(_segment_2).begin(nb_nodes_per_element);
- Array<std::string>::scalar_iterator names_it = physical_names->begin(),
- names_end = physical_names->end();
+ auto names_it = physical_names->begin();
+ auto names_end = physical_names->end();
std::map<std::string, std::list<K::Segment_3>> name_to_primitives_map;
// Loop over the physical names and register segment lists in
// name_to_primitives_map
for (; names_it != names_end; ++names_it) {
UInt element_id = names_it - physical_names->begin();
const Vector<UInt> el_connectivity = connectivity[element_id];
K::Segment_3 segment = this->createSegment(el_connectivity);
name_to_primitives_map[*names_it].push_back(segment);
}
// Loop over the background types of the mesh
- std::map<std::string, std::list<K::Segment_3>>::iterator
- name_to_primitives_it,
- name_to_primitives_end = name_to_primitives_map.end();
+ auto name_to_primitives_end = name_to_primitives_map.end();
+ decltype(name_to_primitives_end) name_to_primitives_it;
for (auto type : this->mesh.elementTypes(dim, _not_ghost)) {
// Used in AKANTU_BOOST_ELEMENT_SWITCH
AKANTU_DEBUG_INFO("Computing intersections with background element type "
<< type);
switch (dim) {
case 1:
break;
case 2:
// Compute intersections for supported 2D elements
AKANTU_BOOST_ELEMENT_SWITCH(INTERFACE_INTERSECTOR_CASE_2D,
(_triangle_3)(_triangle_6));
break;
case 3:
// Compute intersections for supported 3D elements
AKANTU_BOOST_ELEMENT_SWITCH(INTERFACE_INTERSECTOR_CASE_3D,
(_tetrahedron_4));
break;
}
}
AKANTU_DEBUG_OUT();
}
K::Segment_3
EmbeddedInterfaceIntersector::createSegment(const Vector<UInt> & connectivity) {
AKANTU_DEBUG_IN();
- K::Point_3 *source = NULL, *target = NULL;
+ std::unique_ptr<K::Point_3> source;
+ std::unique_ptr<K::Point_3> target;
const Array<Real> & nodes = this->primitive_mesh.getNodes();
if (this->mesh.getSpatialDimension() == 2) {
- source = new K::Point_3(nodes(connectivity(0), 0),
- nodes(connectivity(0), 1), 0.);
- target = new K::Point_3(nodes(connectivity(1), 0),
- nodes(connectivity(1), 1), 0.);
+ source = std::make_unique<K::Point_3>(nodes(connectivity(0), 0),
+ nodes(connectivity(0), 1), 0.);
+ target = std::make_unique<K::Point_3>(nodes(connectivity(1), 0),
+ nodes(connectivity(1), 1), 0.);
} else if (this->mesh.getSpatialDimension() == 3) {
- source =
- new K::Point_3(nodes(connectivity(0), 0), nodes(connectivity(0), 1),
- nodes(connectivity(0), 2));
- target =
- new K::Point_3(nodes(connectivity(1), 0), nodes(connectivity(1), 1),
- nodes(connectivity(1), 2));
+ source = std::make_unique<K::Point_3>(nodes(connectivity(0), 0),
+ nodes(connectivity(0), 1),
+ nodes(connectivity(0), 2));
+ target = std::make_unique<K::Point_3>(nodes(connectivity(1), 0),
+ nodes(connectivity(1), 1),
+ nodes(connectivity(1), 2));
}
K::Segment_3 segment(*source, *target);
- delete source;
- delete target;
AKANTU_DEBUG_OUT();
return segment;
}
} // namespace akantu
#undef INTERFACE_INTERSECTOR_CASE
#undef INTERFACE_INTERSECTOR_CASE_2D
#undef INTERFACE_INTERSECTOR_CASE_3D
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
index fa4b38733..54520ec8a 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
@@ -1,97 +1,97 @@
/**
* @file embedded_interface_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri May 01 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Class that loads the interface from mesh and computes intersections
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
-#define __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
+#ifndef AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH_
+#define AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_geom_abstract.hh"
#include "mesh_geom_common.hh"
#include "mesh_segment_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace {
using K = cgal::Cartesian;
}
/**
* @brief Computes the intersections of the reinforcements defined in the
* primitive mesh
*
* The purpose of this class is to look for reinforcements in the primitive
* mesh, which
* should be defined by physical groups with the same names as the reinforcement
* materials
* in the model.
*
* It then constructs the CGAL primitives from the elements of those
* reinforcements
* and computes the intersections with the background mesh, to create an
* `interface_mesh`,
* which is in turn used by the EmbeddedInterfaceModel.
*
* @see MeshSegmentIntersector, MeshGeomAbstract
* @see EmbeddedInterfaceModel
*/
class EmbeddedInterfaceIntersector : public MeshGeomAbstract {
public:
/// Construct from mesh and a reinforcement mesh
explicit EmbeddedInterfaceIntersector(Mesh & mesh,
const Mesh & primitive_mesh);
/// Destructor
- virtual ~EmbeddedInterfaceIntersector();
+ ~EmbeddedInterfaceIntersector() override = default;
public:
/// Generate the interface mesh
- virtual void constructData(GhostType ghost_type = _not_ghost);
+ void constructData(GhostType ghost_type = _not_ghost) override;
/// Create a segment with an element connectivity
K::Segment_3 createSegment(const Vector<UInt> & connectivity);
/// Getter for interface mesh
AKANTU_GET_MACRO_NOT_CONST(InterfaceMesh, interface_mesh, Mesh &);
protected:
/// Resulting mesh of intersection
Mesh interface_mesh;
/// Mesh used for primitive construction
const Mesh & primitive_mesh;
};
} // namespace akantu
-#endif // __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
+#endif // AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH_
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
index e17a9b330..b71f9e3cc 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
@@ -1,172 +1,173 @@
/**
* @file embedded_interface_model.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Wed Feb 14 2018
*
* @brief Model of Solid Mechanics with embedded interfaces
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "embedded_interface_model.hh"
#include "integrator_gauss.hh"
#include "material_elastic.hh"
#include "material_reinforcement.hh"
#include "mesh_iterators.hh"
#include "shape_lagrange.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumpable_inline_impl.hh"
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
EmbeddedInterfaceModel::EmbeddedInterfaceModel(Mesh & mesh,
Mesh & primitive_mesh,
UInt spatial_dimension,
const ID & id,
const MemoryID & memory_id)
: SolidMechanicsModel(mesh, spatial_dimension, id, memory_id),
intersector(mesh, primitive_mesh), interface_mesh(nullptr),
primitive_mesh(primitive_mesh), interface_material_selector(nullptr) {
this->model_type = ModelType::_embedded_model;
// This pointer should be deleted by ~SolidMechanicsModel()
auto mat_sel_pointer =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
*this);
this->setMaterialSelector(mat_sel_pointer);
interface_mesh = &(intersector.getInterfaceMesh());
// Create 1D FEEngine on the interface mesh
registerFEEngineObject<MyFEEngineType>("EmbeddedInterfaceFEEngine",
*interface_mesh, 1);
// Registering allocator for material reinforcement
MaterialFactory::getInstance().registerAllocator(
"reinforcement",
- [&](UInt dim, const ID & constitutive, SolidMechanicsModel &,
+ [&](UInt dim, const ID & constitutive, SolidMechanicsModel & /*unused*/,
const ID & id) -> std::unique_ptr<Material> {
if (constitutive == "elastic") {
using mat = MaterialElastic<1>;
switch (dim) {
case 2:
return std::make_unique<MaterialReinforcement<mat, 2>>(*this, id);
case 3:
return std::make_unique<MaterialReinforcement<mat, 3>>(*this, id);
default:
AKANTU_EXCEPTION("Dimension 1 is invalid for reinforcements");
}
} else {
AKANTU_EXCEPTION("Reinforcement type" << constitutive
<< " is not recognized");
}
});
}
/* -------------------------------------------------------------------------- */
EmbeddedInterfaceModel::~EmbeddedInterfaceModel() {
delete interface_material_selector;
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::initFullImpl(const ModelOptions & options) {
const auto & eim_options =
aka::as_type<EmbeddedInterfaceModelOptions>(options);
// Do no initialize interface_mesh if told so
- if (eim_options.has_intersections)
+ if (eim_options.has_intersections) {
intersector.constructData();
+ }
SolidMechanicsModel::initFullImpl(options);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("reinforcement", id);
this->mesh.addDumpMeshToDumper("reinforcement", *interface_mesh, 1,
_not_ghost, _ek_regular);
#endif
}
void EmbeddedInterfaceModel::initModel() {
// Initialize interface FEEngine
SolidMechanicsModel::initModel();
FEEngine & engine = getFEEngine("EmbeddedInterfaceFEEngine");
engine.initShapeFunctions(_not_ghost);
engine.initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::assignMaterialToElements(
const ElementTypeMapArray<UInt> * filter) {
delete interface_material_selector;
interface_material_selector =
new InterfaceMeshDataMaterialSelector<std::string>("physical_names",
*this);
for_each_element(getInterfaceMesh(),
[&](auto && element) {
auto mat_index = (*interface_material_selector)(element);
// material_index(element) = mat_index;
materials[mat_index]->addElement(element);
// this->material_local_numbering(element) = index;
},
_element_filter = filter, _spatial_dimension = 1);
SolidMechanicsModel::assignMaterialToElements(filter);
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::addDumpGroupFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
- const std::string & group_name, const ElementKind & element_kind,
+ const std::string & group_name, ElementKind element_kind,
bool padding_flag) {
#ifdef AKANTU_USE_IOHELPER
std::shared_ptr<dumpers::Field> field;
// If dumper is reinforcement, create a 1D elemental field
- if (dumper_name == "reinforcement")
+ if (dumper_name == "reinforcement") {
field = this->createElementalField(field_id, group_name, padding_flag, 1,
element_kind);
- else {
+ } else {
try {
SolidMechanicsModel::addDumpGroupFieldToDumper(
dumper_name, field_id, group_name, element_kind, padding_flag);
} catch (...) {
}
}
if (field) {
DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name, group_name);
Model::addDumpGroupFieldToDumper(field_id, field, dumper);
}
#endif
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
index 4d3902974..452ca95c5 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
@@ -1,155 +1,155 @@
/**
* @file embedded_interface_model.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Model of Solid Mechanics with embedded interfaces
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
-#define __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
+#ifndef AKANTU_EMBEDDED_INTERFACE_MODEL_HH_
+#define AKANTU_EMBEDDED_INTERFACE_MODEL_HH_
#include "aka_common.hh"
#include "mesh.hh"
#include "solid_mechanics_model.hh"
#include "embedded_interface_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Solid mechanics model using the embedded model.
*
* This SolidMechanicsModel subclass implements the embedded model,
* a method used to represent 1D elements in a finite elements model
* (eg. reinforcements in concrete).
*
* In addition to the SolidMechanicsModel properties, this model has
* a mesh of the 1D elements embedded in the model, and an instance of the
* EmbeddedInterfaceIntersector class for the computation of the intersections
* of the
* 1D elements with the background (bulk) mesh.
*
* @see MaterialReinforcement
*/
class EmbeddedInterfaceModel : public SolidMechanicsModel {
using MyFEEngineType = SolidMechanicsModel::MyFEEngineType;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief Constructor
*
* @param mesh main mesh (concrete)
* @param primitive_mesh mesh of the embedded reinforcement
* @param spatial_dimension the spatial dimension to be considered by this model
* @param id the id of the model
* @param memory_id the id of the memory manager to use
*/
EmbeddedInterfaceModel(Mesh & mesh, Mesh & primitive_mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "embedded_interface_model",
const MemoryID & memory_id = 0);
/// Destructor
~EmbeddedInterfaceModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Initialise the model
void initFullImpl(
const ModelOptions & options = EmbeddedInterfaceModelOptions()) override;
/// Initialise the materials
void
assignMaterialToElements(const ElementTypeMapArray<UInt> * filter) override;
/// Initialize the embedded shape functions
void initModel() override;
/// Allows filtering of dump fields which need to be dumpes on interface mesh
void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
- const ElementKind & element_kind,
+ ElementKind element_kind,
bool padding_flag) override;
// virtual ElementTypeMap<UInt> getInternalDataPerElem(const std::string &
// field_name,
- // const ElementKind &
+ // ElementKind
// kind);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get interface mesh
AKANTU_GET_MACRO(InterfaceMesh, *interface_mesh, Mesh &);
/// Get associated elements
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(
InterfaceAssociatedElements,
interface_mesh->getData<Element>("associated_element"), Element);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Intersector object to build the interface mesh
EmbeddedInterfaceIntersector intersector;
/// Interface mesh (weak reference)
Mesh * interface_mesh;
/// Mesh used to create the CGAL primitives for intersections
Mesh & primitive_mesh;
/// Material selector for interface
MaterialSelector * interface_material_selector;
};
/// Material selector based on mesh data for interface elements
template <typename T>
class InterfaceMeshDataMaterialSelector
: public ElementDataMaterialSelector<T> {
public:
InterfaceMeshDataMaterialSelector(const std::string & name,
const EmbeddedInterfaceModel & model,
UInt first_index = 1)
: ElementDataMaterialSelector<T>(
model.getInterfaceMesh().getData<T>(name), model, first_index) {}
};
} // namespace akantu
-#endif // __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
+#endif // AKANTU_EMBEDDED_INTERFACE_MODEL_HH_
diff --git a/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh b/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
index 7a2d16469..986b46735 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
@@ -1,125 +1,125 @@
/**
* @file solid_mechanics_model_event_handler.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief EventHandler implementation for SolidMechanicsEvents
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH__
-#define __AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH__
+#ifndef AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH_
+#define AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH_
namespace akantu {
/// akantu::SolidMechanicsModelEvent is the base event for model
namespace SolidMechanicsModelEvent {
struct BeforeSolveStepEvent {
BeforeSolveStepEvent(AnalysisMethod & method) : method(method) {}
AnalysisMethod method;
};
struct AfterSolveStepEvent {
AfterSolveStepEvent(AnalysisMethod & method) : method(method) {}
AnalysisMethod method;
};
struct BeforeDumpEvent {
BeforeDumpEvent() = default;
};
struct BeginningOfDamageIterationEvent {
BeginningOfDamageIterationEvent() = default;
};
struct AfterDamageEvent {
AfterDamageEvent() = default;
};
} // namespace SolidMechanicsModelEvent
/// akantu::SolidMechanicsModelEvent
class SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
virtual ~SolidMechanicsModelEventHandler() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// Send what is before the solve step to the beginning of solve step through
/// EventManager
inline void
sendEvent(const SolidMechanicsModelEvent::BeforeSolveStepEvent & event) {
onBeginningSolveStep(event.method);
}
/// Send what is after the solve step to the end of solve step through
/// EventManager
inline void
sendEvent(const SolidMechanicsModelEvent::AfterSolveStepEvent & event) {
onEndSolveStep(event.method);
}
/// Send what is before dump to current dump through EventManager
inline void
sendEvent(__attribute__((unused))
const SolidMechanicsModelEvent::BeforeDumpEvent & event) {
onDump();
}
/// Send what is at the beginning of damage iteration to Damage iteration
/// through EventManager
inline void sendEvent(
__attribute__((unused))
const SolidMechanicsModelEvent::BeginningOfDamageIterationEvent & event) {
onDamageIteration();
}
/// Send what is after damage for the damage update through EventManager
inline void
sendEvent(__attribute__((unused))
const SolidMechanicsModelEvent::AfterDamageEvent & event) {
onDamageUpdate();
}
template <class EventHandler> friend class EventHandlerManager;
/* ------------------------------------------------------------------------ */
/* Interface */
/* ------------------------------------------------------------------------ */
public:
/// function to implement to react on akantu::BeforeSolveStepEvent
virtual void onBeginningSolveStep(__attribute__((unused))
const AnalysisMethod & method) {}
/// function to implement to react on akantu::AfterSolveStepEvent
virtual void onEndSolveStep(__attribute__((unused))
const AnalysisMethod & method) {}
/// function to implement to react on akantu::BeforeDumpEvent
virtual void onDump() {}
/// function to implement to react on akantu::BeginningOfDamageIterationEvent
virtual void onDamageIteration() {}
/// function to implement to react on akantu::AfterDamageEvent
virtual void onDamageUpdate() {}
};
} // namespace akantu
-#endif /* __AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH__ */
+#endif /* AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_inline_impl.hh b/src/model/solid_mechanics/solid_mechanics_model_inline_impl.hh
index 38d702369..b51c65190 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_inline_impl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_inline_impl.hh
@@ -1,101 +1,101 @@
/**
* @file solid_mechanics_model_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Tue Dec 05 2017
*
* @brief Implementation of the inline functions of the SolidMechanicsModel
* class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "material_selector.hh"
#include "material_selector_tmpl.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_HH__
-#define __AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_HH__
+#ifndef AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_HH_
+#define AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline decltype(auto) SolidMechanicsModel::getMaterials() {
return make_dereference_adaptor(materials);
}
/* -------------------------------------------------------------------------- */
inline decltype(auto) SolidMechanicsModel::getMaterials() const {
return make_dereference_adaptor(materials);
}
/* -------------------------------------------------------------------------- */
inline Material & SolidMechanicsModel::getMaterial(UInt mat_index) {
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The model " << id << " has no material no "
<< mat_index);
return *materials[mat_index];
}
/* -------------------------------------------------------------------------- */
inline const Material & SolidMechanicsModel::getMaterial(UInt mat_index) const {
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The model " << id << " has no material no "
<< mat_index);
return *materials[mat_index];
}
/* -------------------------------------------------------------------------- */
inline Material & SolidMechanicsModel::getMaterial(const std::string & name) {
std::map<std::string, UInt>::const_iterator it =
materials_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
"The model " << id << " has no material named " << name);
return *materials[it->second];
}
/* -------------------------------------------------------------------------- */
inline UInt
SolidMechanicsModel::getMaterialIndex(const std::string & name) const {
auto it = materials_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
"The model " << id << " has no material named " << name);
return it->second;
}
/* -------------------------------------------------------------------------- */
inline const Material &
SolidMechanicsModel::getMaterial(const std::string & name) const {
auto it = materials_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
"The model " << id << " has no material named " << name);
return *materials[it->second];
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_io.cc b/src/model/solid_mechanics/solid_mechanics_model_io.cc
index 8977f977d..b7603d9cb 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_io.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_io.cc
@@ -1,334 +1,341 @@
/**
* @file solid_mechanics_model_io.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Jul 09 2017
* @date last modification: Sun Dec 03 2017
*
* @brief Dumpable part of the SolidMechnicsModel
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "group_manager_inline_impl.hh"
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_element_partition.hh"
#include "dumper_elemental_field.hh"
#include "dumper_field.hh"
#include "dumper_homogenizing_field.hh"
#include "dumper_internal_material_field.hh"
#include "dumper_iohelper.hh"
#include "dumper_material_padders.hh"
#include "dumper_paraview.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::isInternal(const std::string & field_name,
- const ElementKind & element_kind) {
+ ElementKind element_kind) {
/// check if at least one material contains field_id as an internal
for (auto & material : materials) {
bool is_internal = material->isInternal<Real>(field_name, element_kind);
- if (is_internal)
+ if (is_internal) {
return true;
+ }
}
return false;
}
/* -------------------------------------------------------------------------- */
ElementTypeMap<UInt>
SolidMechanicsModel::getInternalDataPerElem(const std::string & field_name,
- const ElementKind & element_kind) {
+ ElementKind element_kind) {
- if (!(this->isInternal(field_name, element_kind)))
+ if (!(this->isInternal(field_name, element_kind))) {
AKANTU_EXCEPTION("unknown internal " << field_name);
+ }
for (auto & material : materials) {
- if (material->isInternal<Real>(field_name, element_kind))
+ if (material->isInternal<Real>(field_name, element_kind)) {
return material->getInternalDataPerElem<Real>(field_name, element_kind);
+ }
}
return ElementTypeMap<UInt>();
}
/* -------------------------------------------------------------------------- */
ElementTypeMapArray<Real> &
SolidMechanicsModel::flattenInternal(const std::string & field_name,
- const ElementKind & kind,
+ ElementKind kind,
const GhostType ghost_type) {
auto key = std::make_pair(field_name, kind);
ElementTypeMapArray<Real> * internal_flat;
auto it = this->registered_internals.find(key);
if (it == this->registered_internals.end()) {
auto internal = std::make_unique<ElementTypeMapArray<Real>>(
field_name, this->id, this->memory_id);
internal_flat = internal.get();
this->registered_internals[key] = std::move(internal);
} else {
internal_flat = it->second.get();
}
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, kind)) {
if (internal_flat->exists(type, ghost_type)) {
auto & internal = (*internal_flat)(type, ghost_type);
internal.resize(0);
}
}
for (auto & material : materials) {
- if (material->isInternal<Real>(field_name, kind))
+ if (material->isInternal<Real>(field_name, kind)) {
material->flattenInternal(field_name, *internal_flat, ghost_type, kind);
+ }
}
return *internal_flat;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::flattenAllRegisteredInternals(
- const ElementKind & kind) {
+ ElementKind kind) {
ElementKind _kind;
ID _id;
for (auto & internal : this->registered_internals) {
std::tie(_id, _kind) = internal.first;
- if (kind == _kind)
+ if (kind == _kind) {
this->flattenInternal(_id, kind);
+ }
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onDump() {
this->flattenAllRegisteredInternals(_ek_regular);
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
std::shared_ptr<dumpers::Field> SolidMechanicsModel::createElementalField(
const std::string & field_name, const std::string & group_name,
- bool padding_flag, const UInt & spatial_dimension,
- const ElementKind & kind) {
+ bool padding_flag, UInt spatial_dimension,
+ ElementKind kind) {
std::shared_ptr<dumpers::Field> field;
- if (field_name == "partitions")
+ if (field_name == "partitions") {
field = mesh.createElementalField<UInt, dumpers::ElementPartitionField>(
mesh.getConnectivities(), group_name, spatial_dimension, kind);
- else if (field_name == "material_index")
+ } else if (field_name == "material_index") {
field = mesh.createElementalField<UInt, Vector, dumpers::ElementalField>(
material_index, group_name, spatial_dimension, kind);
- else {
+ } else {
// this copy of field_name is used to compute derivated data such as
// strain and von mises stress that are based on grad_u and stress
std::string field_name_copy(field_name);
if (field_name == "strain" || field_name == "Green strain" ||
field_name == "principal strain" ||
- field_name == "principal Green strain")
+ field_name == "principal Green strain") {
field_name_copy = "grad_u";
- else if (field_name == "Von Mises stress")
+ } else if (field_name == "Von Mises stress") {
field_name_copy = "stress";
+ }
bool is_internal = this->isInternal(field_name_copy, kind);
if (is_internal) {
auto nb_data_per_elem =
this->getInternalDataPerElem(field_name_copy, kind);
auto & internal_flat = this->flattenInternal(field_name_copy, kind);
field = mesh.createElementalField<Real, dumpers::InternalMaterialField>(
internal_flat, group_name, spatial_dimension, kind, nb_data_per_elem);
std::unique_ptr<dumpers::ComputeFunctorInterface> func;
if (field_name == "strain") {
func = std::make_unique<dumpers::ComputeStrain<false>>(*this);
} else if (field_name == "Von Mises stress") {
func = std::make_unique<dumpers::ComputeVonMisesStress>(*this);
} else if (field_name == "Green strain") {
func = std::make_unique<dumpers::ComputeStrain<true>>(*this);
} else if (field_name == "principal strain") {
func = std::make_unique<dumpers::ComputePrincipalStrain<false>>(*this);
} else if (field_name == "principal Green strain") {
func = std::make_unique<dumpers::ComputePrincipalStrain<true>>(*this);
}
if (func) {
field = dumpers::FieldComputeProxy::createFieldCompute(field,
std::move(func));
}
// treat the paddings
if (padding_flag) {
if (field_name == "stress") {
if (spatial_dimension == 2) {
auto foo = std::make_unique<dumpers::StressPadder<2>>(*this);
field = dumpers::FieldComputeProxy::createFieldCompute(
field, std::move(foo));
}
} else if (field_name == "strain" || field_name == "Green strain") {
if (spatial_dimension == 2) {
auto foo = std::make_unique<dumpers::StrainPadder<2>>(*this);
field = dumpers::FieldComputeProxy::createFieldCompute(
field, std::move(foo));
}
}
}
// homogenize the field
auto foo = dumpers::HomogenizerProxy::createHomogenizer(*field);
field =
dumpers::FieldComputeProxy::createFieldCompute(field, std::move(foo));
}
}
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
SolidMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["displacement"] = this->displacement.get();
real_nodal_fields["mass"] = this->mass.get();
real_nodal_fields["velocity"] = this->velocity.get();
real_nodal_fields["acceleration"] = this->acceleration.get();
real_nodal_fields["external_force"] = this->external_force.get();
real_nodal_fields["internal_force"] = this->internal_force.get();
real_nodal_fields["increment"] = this->displacement_increment.get();
if (field_name == "force") {
AKANTU_EXCEPTION("The 'force' field has been renamed in 'external_force'");
} else if (field_name == "residual") {
AKANTU_EXCEPTION(
"The 'residual' field has been replaced by 'internal_force'");
}
std::shared_ptr<dumpers::Field> field;
- if (padding_flag)
+ if (padding_flag) {
field = this->mesh.createNodalField(real_nodal_fields[field_name],
group_name, 3);
- else
+ } else {
field =
this->mesh.createNodalField(real_nodal_fields[field_name], group_name);
+ }
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> SolidMechanicsModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs.get();
std::shared_ptr<dumpers::Field> field;
field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
SolidMechanicsModel::createElementalField(const std::string &,
const std::string &, bool,
- const UInt &, const ElementKind &) {
+ const UInt &, ElementKind) {
return nullptr;
}
/* --------------------------------------------------------------------------
*/
std::shaed_ptr<dumpers::Field>
SolidMechanicsModel::createNodalFieldReal(const std::string &,
const std::string &, bool) {
return nullptr;
}
/* --------------------------------------------------------------------------
*/
std::shared_ptr<dumpers::Field>
SolidMechanicsModel::createNodalFieldBool(const std::string &,
const std::string &, bool) {
return nullptr;
}
#endif
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(const std::string & dumper_name) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name);
}
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(const std::string & dumper_name, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name, step);
}
/* -------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(const std::string & dumper_name, Real time,
UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name, time, step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump() {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(Real time, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(time, step);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_mass.cc b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
index c4c2f3608..89ab7708d 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_mass.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
@@ -1,151 +1,154 @@
/**
* @file solid_mechanics_model_mass.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 05 2010
* @date last modification: Wed Nov 08 2017
*
* @brief function handling mass computation
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "material.hh"
#include "model_solver.hh"
#include "shape_lagrange.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ComputeRhoFunctor {
public:
explicit ComputeRhoFunctor(const SolidMechanicsModel & model)
: model(model){};
void operator()(Matrix<Real> & rho, const Element & element) {
const Array<UInt> & mat_indexes =
model.getMaterialByElement(element.type, element.ghost_type);
Real mat_rho =
model.getMaterial(mat_indexes(element.element)).getParam("rho");
rho.set(mat_rho);
}
private:
const SolidMechanicsModel & model;
};
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped() {
AKANTU_DEBUG_IN();
- if (not need_to_reassemble_lumped_mass)
+ if (not need_to_reassemble_lumped_mass) {
return;
+ }
this->allocNodalField(this->mass, spatial_dimension, "mass");
- mass->clear();
+ mass->zero();
if (!this->getDOFManager().hasLumpedMatrix("M")) {
this->getDOFManager().getNewLumpedMatrix("M");
}
- this->getDOFManager().clearLumpedMatrix("M");
+ this->getDOFManager().zeroLumpedMatrix("M");
assembleMassLumped(_not_ghost);
assembleMassLumped(_ghost);
this->getDOFManager().getLumpedMatrixPerDOFs("displacement", "M",
*(this->mass));
/// for not connected nodes put mass to one in order to avoid
#if !defined(AKANTU_NDEBUG)
bool has_unconnected_nodes = false;
auto mass_it = mass->begin_reinterpret(mass->size() * mass->getNbComponent());
auto mass_end = mass->end_reinterpret(mass->size() * mass->getNbComponent());
for (; mass_it != mass_end; ++mass_it) {
if (std::abs(*mass_it) < std::numeric_limits<Real>::epsilon() ||
Math::isnan(*mass_it)) {
has_unconnected_nodes = true;
break;
}
}
- if (has_unconnected_nodes)
+ if (has_unconnected_nodes) {
AKANTU_DEBUG_WARNING("There are nodes that seem to not be connected to any "
"elements, beware that they have lumped mass of 0.");
+ }
#endif
this->synchronize(SynchronizationTag::_smm_mass);
need_to_reassemble_lumped_mass = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMass() {
AKANTU_DEBUG_IN();
- if (not need_to_reassemble_mass)
+ if (not need_to_reassemble_mass) {
return;
+ }
- this->getDOFManager().clearMatrix("M");
+ this->getDOFManager().zeroMatrix("M");
assembleMass(_not_ghost);
need_to_reassemble_mass = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped(GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor compute_rho(*this);
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, _ek_regular)) {
fem.assembleFieldLumped(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMass(GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor compute_rho(*this);
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, _ek_regular)) {
fem.assembleFieldMatrix(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_material.cc b/src/model/solid_mechanics/solid_mechanics_model_material.cc
index eda89a444..7580b96a6 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_material.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_material.cc
@@ -1,254 +1,259 @@
/**
* @file solid_mechanics_model_material.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Nov 26 2010
* @date last modification: Tue Feb 20 2018
*
* @brief instatiation of materials
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "aka_math.hh"
#include "material_non_local.hh"
#include "mesh_iterators.hh"
#include "non_local_manager.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Material &
SolidMechanicsModel::registerNewMaterial(const ParserSection & section) {
std::string mat_name;
std::string mat_type = section.getName();
std::string opt_param = section.getOption();
try {
std::string tmp = section.getParameter("name");
mat_name = tmp; /** this can seam weird, but there is an ambiguous operator
* overload that i couldn't solve. @todo remove the
* weirdness of this code
*/
} catch (debug::Exception &) {
AKANTU_ERROR("A material of type \'"
<< mat_type
<< "\' in the input file has been defined without a name!");
}
Material & mat = this->registerNewMaterial(mat_name, mat_type, opt_param);
mat.parseSection(section);
return mat;
}
/* -------------------------------------------------------------------------- */
Material & SolidMechanicsModel::registerNewMaterial(const ID & mat_name,
const ID & mat_type,
const ID & opt_param) {
AKANTU_DEBUG_ASSERT(materials_names_to_id.find(mat_name) ==
materials_names_to_id.end(),
"A material with this name '"
<< mat_name << "' has already been registered. "
<< "Please use unique names for materials");
UInt mat_count = materials.size();
materials_names_to_id[mat_name] = mat_count;
std::stringstream sstr_mat;
sstr_mat << this->id << ":" << mat_count << ":" << mat_type;
ID mat_id = sstr_mat.str();
std::unique_ptr<Material> material = MaterialFactory::getInstance().allocate(
mat_type, spatial_dimension, opt_param, *this, mat_id);
materials.push_back(std::move(material));
return *(materials.back());
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::instantiateMaterials() {
ParserSection model_section;
bool is_empty;
std::tie(model_section, is_empty) = this->getParserSection();
if (not is_empty) {
auto model_materials = model_section.getSubSections(ParserType::_material);
for (const auto & section : model_materials) {
this->registerNewMaterial(section);
}
}
auto sub_sections = this->parser.getSubSections(ParserType::_material);
for (const auto & section : sub_sections) {
this->registerNewMaterial(section);
}
#ifdef AKANTU_DAMAGE_NON_LOCAL
for (auto & material : materials) {
- if (dynamic_cast<MaterialNonLocalInterface *>(material.get()) == nullptr)
+ if (dynamic_cast<MaterialNonLocalInterface *>(material.get()) == nullptr) {
continue;
+ }
this->non_local_manager = std::make_unique<NonLocalManager>(
*this, *this, id + ":non_local_manager", memory_id);
break;
}
#endif
- if (materials.empty())
+ if (materials.empty()) {
AKANTU_EXCEPTION("No materials where instantiated for the model"
<< getID());
+ }
are_materials_instantiated = true;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assignMaterialToElements(
const ElementTypeMapArray<UInt> * filter) {
for_each_element(
mesh,
[&](auto && element) {
UInt mat_index = (*material_selector)(element);
AKANTU_DEBUG_ASSERT(
mat_index < materials.size(),
"The material selector returned an index that does not exists");
material_index(element) = mat_index;
},
_element_filter = filter, _ghost_type = _not_ghost);
- if (non_local_manager)
+ if (non_local_manager) {
non_local_manager->synchronize(*this, SynchronizationTag::_material_id);
+ }
for_each_element(
mesh,
[&](auto && element) {
auto mat_index = material_index(element);
auto index = materials[mat_index]->addElement(element);
material_local_numbering(element) = index;
},
_element_filter = filter, _ghost_type = _not_ghost);
// synchronize the element material arrays
this->synchronize(SynchronizationTag::_material_id);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initMaterials() {
- AKANTU_DEBUG_ASSERT(materials.size() != 0, "No material to initialize !");
+ AKANTU_DEBUG_ASSERT(not materials.empty(), "No material to initialize !");
// if (!are_materials_instantiated)
// instantiateMaterials();
this->assignMaterialToElements();
for (auto & material : materials) {
/// init internals properties
material->initMaterial();
}
this->synchronize(SynchronizationTag::_smm_init_mat);
if (this->non_local_manager) {
this->non_local_manager->initialize();
}
}
/* -------------------------------------------------------------------------- */
Int SolidMechanicsModel::getInternalIndexFromID(const ID & id) const {
AKANTU_DEBUG_IN();
auto it = materials.begin();
auto end = materials.end();
- for (; it != end; ++it)
+ for (; it != end; ++it) {
if ((*it)->getID() == id) {
AKANTU_DEBUG_OUT();
return (it - materials.begin());
}
+ }
AKANTU_DEBUG_OUT();
return -1;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::reassignMaterial() {
AKANTU_DEBUG_IN();
std::vector<Array<Element>> element_to_add(materials.size());
std::vector<Array<Element>> element_to_remove(materials.size());
Element element;
for (auto ghost_type : ghost_types) {
element.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
element.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<UInt> & mat_indexes = material_index(type, ghost_type);
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
UInt old_material = mat_indexes(el);
UInt new_material = (*material_selector)(element);
if (old_material != new_material) {
element_to_add[new_material].push_back(element);
element_to_remove[old_material].push_back(element);
}
}
}
}
UInt mat_index = 0;
for (auto mat_it = materials.begin(); mat_it != materials.end();
++mat_it, ++mat_index) {
(*mat_it)->removeElements(element_to_remove[mat_index]);
(*mat_it)->addElements(element_to_add[mat_index]);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::applyEigenGradU(
const Matrix<Real> & prescribed_eigen_grad_u, const ID & material_name,
const GhostType ghost_type) {
AKANTU_DEBUG_ASSERT(prescribed_eigen_grad_u.size() ==
spatial_dimension * spatial_dimension,
"The prescribed grad_u is not of the good size");
for (auto & material : materials) {
- if (material->getName() == material_name)
+ if (material->getName() == material_name) {
material->applyEigenGradU(prescribed_eigen_grad_u, ghost_type);
+ }
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh b/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh
index 9ce4760df..b5294877c 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh
@@ -1,61 +1,61 @@
/**
* @file solid_mechanics_model_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Nov 07 2017
*
* @brief template part of solid mechanics model
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH__
-#define __AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH__
+#ifndef AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH_
+#define AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH_
namespace akantu {
#define FWD(...) ::std::forward<decltype(__VA_ARGS__)>(__VA_ARGS__)
/* -------------------------------------------------------------------------- */
template <typename Operation>
void SolidMechanicsModel::splitByMaterial(const Array<Element> & elements,
Operation && op) const {
std::vector<Array<Element>> elements_per_mat(materials.size());
this->splitElementByMaterial(elements, elements_per_mat);
for (auto && mat : zip(materials, elements_per_mat)) {
FWD(op)(FWD(*std::get<0>(mat)), FWD(std::get<1>(mat)));
}
}
#undef FWD
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH__ */
+#endif /* AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH_ */
diff --git a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
index 82504d3b5..990560be4 100644
--- a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
+++ b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
@@ -1,136 +1,135 @@
/**
* @file structural_element_bernoulli_beam_2.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 11 2017
* @date last modification: Wed Jan 10 2018
*
* @brief Specific functions for bernoulli beam 2d
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH__
-#define __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH__
+#ifndef AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH_
+#define AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline void StructuralMechanicsModel::assembleMass<_bernoulli_beam_2>() {
AKANTU_DEBUG_IN();
constexpr ElementType type = _bernoulli_beam_2;
auto & fem = getFEEngineClass<MyFEEngineType>();
auto nb_element = mesh.getNbElement(type);
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type);
auto nb_fields_to_interpolate = ElementClass<type>::getNbStressComponents();
auto nt_n_field_size = nb_degree_of_freedom * nb_nodes_per_element;
Array<Real> n(nb_element * nb_quadrature_points,
nb_fields_to_interpolate * nt_n_field_size, "N");
- Array<Real> * rho_field =
- new Array<Real>(nb_element * nb_quadrature_points, 1, "Rho");
- rho_field->clear();
+ auto * rho_field =
+ new Array<Real>(nb_element * nb_quadrature_points, 1, 0., "Rho");
computeRho(*rho_field, type, _not_ghost);
#if 0
bool sign = true;
for (auto && ghost_type : ghost_types) {
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
0, 0, 0, sign, ghost_type); // Ni ui -> u
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
1, 1, 1, sign, ghost_type); // Mi vi -> v
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
2, 2, 1, sign, ghost_type); // Li Theta_i -> v
fem.assembleFieldMatrix(*rho_field, nb_degree_of_freedom, *mass_matrix, n,
rotation_matrix, type, ghost_type);
}
#endif
delete rho_field;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeRotationMatrix<_bernoulli_beam_2>(
Array<Real> & rotations) {
auto type = _bernoulli_beam_2;
auto nodes_it = mesh.getNodes().begin(this->spatial_dimension);
for (auto && tuple :
zip(make_view(mesh.getConnectivity(type), 2),
make_view(rotations, nb_degree_of_freedom, nb_degree_of_freedom))) {
auto & connec = std::get<0>(tuple);
auto & R = std::get<1>(tuple);
Vector<Real> x2 = nodes_it[connec(1)]; // X2
Vector<Real> x1 = nodes_it[connec(0)]; // X1
auto le = x1.distance(x2);
auto c = (x2(0) - x1(0)) / le;
auto s = (x2(1) - x1(1)) / le;
/// Definition of the rotation matrix
R = {{c, s, 0.}, {-s, c, 0.}, {0., 0., 1.}};
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<_bernoulli_beam_2>(
Array<Real> & tangent_moduli) {
// auto nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_2);
auto nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_2);
auto tangent_size = 2;
- tangent_moduli.clear();
+ tangent_moduli.zero();
auto D_it = tangent_moduli.begin(tangent_size, tangent_size);
auto el_mat = element_material(_bernoulli_beam_2, _not_ghost).begin();
for (auto & mat : element_material(_bernoulli_beam_2, _not_ghost)) {
auto E = materials[mat].E;
auto A = materials[mat].A;
auto I = materials[mat].I;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it) {
auto & D = *D_it;
D(0, 0) = E * A;
D(1, 1) = E * I;
}
}
}
} // namespace akantu
-#endif /* __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH__ */
+#endif /* AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH_ */
diff --git a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
index 33099ae14..26e01970f 100644
--- a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
+++ b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
@@ -1,189 +1,189 @@
/**
* @file structural_element_bernoulli_beam_3.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Wed Oct 11 2017
* @date last modification: Tue Feb 20 2018
*
* @brief Specific functions for bernoulli beam 3d
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH__
-#define __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH__
+#ifndef AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH_
+#define AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH_
#include "structural_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline void StructuralMechanicsModel::assembleMass<_bernoulli_beam_3>() {
AKANTU_DEBUG_IN();
#if 0
GhostType ghost_type = _not_ghost;
ElementType type = _bernoulli_beam_3;
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
UInt nb_element = getFEEngine().getMesh().getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
UInt nb_fields_to_interpolate =
getTangentStiffnessVoigtSize<_bernoulli_beam_3>();
UInt nt_n_field_size = nb_degree_of_freedom * nb_nodes_per_element;
Array<Real> * n =
new Array<Real>(nb_element * nb_quadrature_points,
nb_fields_to_interpolate * nt_n_field_size, "N");
n->clear();
Array<Real> * rho_field =
new Array<Real>(nb_element * nb_quadrature_points, "Rho");
rho_field->clear();
computeRho(*rho_field, type, _not_ghost);
/* --------------------------------------------------------------------------
*/
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
0, 0, 0, true, ghost_type); // Ni ui -> u
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
1, 1, 1, true, ghost_type); // Mi vi -> v
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
2, 5, 1, true, ghost_type); // Li Theta_z_i -> v
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
1, 2, 2, true, ghost_type); // Mi wi -> w
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
2, 4, 2, false, ghost_type); // -Li Theta_y_i -> w
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
0, 3, 3, true, ghost_type); // Ni Theta_x_i->Theta_x
/* --------------------------------------------------------------------------
*/
fem.assembleFieldMatrix(*rho_field, nb_degree_of_freedom, *mass_matrix, n,
rotation_matrix, type, ghost_type);
delete n;
delete rho_field;
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeRotationMatrix<_bernoulli_beam_3>(
Array<Real> & rotations) {
ElementType type = _bernoulli_beam_3;
Mesh & mesh = getFEEngine().getMesh();
UInt nb_element = mesh.getNbElement(type);
auto n_it = mesh.getNormals(type).begin(spatial_dimension);
Array<UInt>::iterator<Vector<UInt>> connec_it =
mesh.getConnectivity(type).begin(2);
auto nodes_it = mesh.getNodes().begin(spatial_dimension);
Matrix<Real> Pe(spatial_dimension, spatial_dimension);
Matrix<Real> Pg(spatial_dimension, spatial_dimension);
Matrix<Real> inv_Pg(spatial_dimension, spatial_dimension);
Vector<Real> x_n(spatial_dimension); // x vect n
Array<Real>::matrix_iterator R_it =
rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
for (UInt e = 0; e < nb_element; ++e, ++n_it, ++connec_it, ++R_it) {
Vector<Real> & n = *n_it;
Matrix<Real> & R = *R_it;
Vector<UInt> & connec = *connec_it;
Vector<Real> x;
x = nodes_it[connec(1)]; // X2
Vector<Real> y;
y = nodes_it[connec(0)]; // X1
Real l = x.distance(y);
x -= y; // X2 - X1
x_n.crossProduct(x, n);
Pe.eye();
Pe(0, 0) *= l;
Pe(1, 1) *= -l;
Pg(0, 0) = x(0);
Pg(0, 1) = x_n(0);
Pg(0, 2) = n(0);
Pg(1, 0) = x(1);
Pg(1, 1) = x_n(1);
Pg(1, 2) = n(1);
Pg(2, 0) = x(2);
Pg(2, 1) = x_n(2);
Pg(2, 2) = n(2);
inv_Pg.inverse(Pg);
Pe *= inv_Pg;
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
R(i, j) = Pe(i, j);
R(i + spatial_dimension, j + spatial_dimension) = Pe(i, j);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<_bernoulli_beam_3>(
Array<Real> & tangent_moduli) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_3);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_3);
UInt tangent_size = 4;
- tangent_moduli.clear();
+ tangent_moduli.zero();
Array<Real>::matrix_iterator D_it =
tangent_moduli.begin(tangent_size, tangent_size);
for (UInt e = 0; e < nb_element; ++e) {
UInt mat = element_material(_bernoulli_beam_3, _not_ghost)(e);
Real E = materials[mat].E;
Real A = materials[mat].A;
Real Iz = materials[mat].Iz;
Real Iy = materials[mat].Iy;
Real GJ = materials[mat].GJ;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it) {
Matrix<Real> & D = *D_it;
D(0, 0) = E * A;
D(1, 1) = E * Iz;
D(2, 2) = E * Iy;
D(3, 3) = GJ;
}
}
}
} // namespace akantu
-#endif /* __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH__ */
+#endif /* AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH_ */
diff --git a/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh b/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
index 62e94e497..240715e4b 100644
--- a/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
+++ b/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
@@ -1,79 +1,79 @@
/**
* @file structural_element_kirchhoff_shell.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Wed Oct 11 2017
* @date last modification: Wed Feb 21 2018
*
* @brief Specific functions for bernoulli kirchhoff shell
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_KIRCHHOFF_SHELL_HH__
-#define __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_KIRCHHOFF_SHELL_HH__
+#ifndef AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_KIRCHHOFF_SHELL_HH_
+#define AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_KIRCHHOFF_SHELL_HH_
#include "structural_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline void
StructuralMechanicsModel::assembleMass<_discrete_kirchhoff_triangle_18>() {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<
_discrete_kirchhoff_triangle_18>(Array<Real> & tangent_moduli) {
auto tangent_size =
ElementClass<_discrete_kirchhoff_triangle_18>::getNbStressComponents();
auto nb_quad =
getFEEngine().getNbIntegrationPoints(_discrete_kirchhoff_triangle_18);
auto H_it = tangent_moduli.begin(tangent_size, tangent_size);
for (UInt mat :
element_material(_discrete_kirchhoff_triangle_18, _not_ghost)) {
auto & m = materials[mat];
for (UInt q = 0; q < nb_quad; ++q, ++H_it) {
auto & H = *H_it;
- H.clear();
+ H.zero();
Matrix<Real> D = {{1, m.nu, 0}, {m.nu, 1, 0}, {0, 0, (1 - m.nu) / 2}};
D *= m.E * m.t / (1 - m.nu * m.nu);
H.block(D, 0, 0); // in plane membrane behavior
H.block(D * Math::pow<3>(m.t) / 12., 3, 3); // bending behavior
}
}
}
} // namespace akantu
-#endif /* __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_DISCRETE_KIRCHHOFF_TRIANGLE_18_HH__ \
+#endif /* AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_DISCRETE_KIRCHHOFF_TRIANGLE_18_HH_ \
*/
diff --git a/src/model/structural_mechanics/structural_mechanics_model.cc b/src/model/structural_mechanics/structural_mechanics_model.cc
index 2ddd94392..4461283aa 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model.cc
@@ -1,455 +1,464 @@
/**
* @file structural_mechanics_model.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Wed Feb 21 2018
*
* @brief Model implementation for Structural Mechanics elements
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model.hh"
#include "dof_manager.hh"
#include "integrator_gauss.hh"
#include "mesh.hh"
#include "shape_structural.hh"
#include "sparse_matrix.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumpable_inline_impl.hh"
#include "dumper_elemental_field.hh"
#include "dumper_iohelper_paraview.hh"
#include "group_manager_inline_impl.hh"
#endif
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model_inline_impl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::StructuralMechanicsModel(Mesh & mesh, UInt dim,
const ID & id,
const MemoryID & memory_id)
: Model(mesh, ModelType::_structural_mechanics_model, dim, id, memory_id),
time_step(NAN), f_m2a(1.0), stress("stress", id, memory_id),
element_material("element_material", id, memory_id),
set_ID("beam sets", id, memory_id),
rotation_matrix("rotation_matices", id, memory_id) {
AKANTU_DEBUG_IN();
registerFEEngineObject<MyFEEngineType>("StructuralMechanicsFEEngine", mesh,
spatial_dimension);
- if (spatial_dimension == 2)
+ if (spatial_dimension == 2) {
nb_degree_of_freedom = 3;
- else if (spatial_dimension == 3)
+ } else if (spatial_dimension == 3) {
nb_degree_of_freedom = 6;
- else {
+ } else {
AKANTU_TO_IMPLEMENT();
}
#ifdef AKANTU_USE_IOHELPER
- this->mesh.registerDumper<DumperParaview>("structural_mechanics_model", id, true);
+ this->mesh.registerDumper<DumperParaview>("structural_mechanics_model", id,
+ true);
#endif
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_structural);
this->initDOFManager();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::~StructuralMechanicsModel() = default;
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initFullImpl(const ModelOptions & options) {
// <<<< This is the SolidMechanicsModel implementation for future ref >>>>
// material_index.initialize(mesh, _element_kind = _ek_not_defined,
// _default_value = UInt(-1), _with_nb_element =
// true);
// material_local_numbering.initialize(mesh, _element_kind = _ek_not_defined,
// _with_nb_element = true);
// Model::initFullImpl(options);
// // initialize pbc
// if (this->pbc_pair.size() != 0)
// this->initPBC();
// // initialize the materials
// if (this->parser.getLastParsedFile() != "") {
// this->instantiateMaterials();
// }
// this->initMaterials();
// this->initBC(*this, *displacement, *displacement_increment,
// *external_force);
// <<<< END >>>>
Model::initFullImpl(options);
// Initializing stresses
ElementTypeMap<UInt> stress_components;
/// TODO this is ugly af, maybe add a function to FEEngine
- for (auto & type : mesh.elementTypes(_spatial_dimension = _all_dimensions,
- _element_kind = _ek_structural)) {
+ for (auto && type : mesh.elementTypes(_spatial_dimension = _all_dimensions,
+ _element_kind = _ek_structural)) {
UInt nb_components = 0;
// Getting number of components for each element type
#define GET_(type) nb_components = ElementClass<type>::getNbStressComponents()
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(GET_);
#undef GET_
stress_components(nb_components, type);
}
stress.initialize(
getFEEngine(), _spatial_dimension = _all_dimensions,
_element_kind = _ek_structural, _all_ghost_types = true,
- _nb_component = [&stress_components](const ElementType & type,
- const GhostType &) -> UInt {
+ _nb_component = [&stress_components](ElementType type,
+ GhostType /*unused*/) -> UInt {
return stress_components(type);
});
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initFEEngineBoundary() {
/// TODO: this function should not be reimplemented
/// we're just avoiding a call to Model::initFEEngineBoundary()
}
/* -------------------------------------------------------------------------- */
// void StructuralMechanicsModel::setTimeStep(Real time_step) {
// this->time_step = time_step;
// #if defined(AKANTU_USE_IOHELPER)
// this->mesh.getDumper().setTimeStep(time_step);
// #endif
// }
/* -------------------------------------------------------------------------- */
/* Initialisation */
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initSolver(
- TimeStepSolverType time_step_solver_type, NonLinearSolverType) {
+ TimeStepSolverType time_step_solver_type, NonLinearSolverType /*unused*/) {
AKANTU_DEBUG_IN();
this->allocNodalField(displacement_rotation, nb_degree_of_freedom,
"displacement");
this->allocNodalField(external_force, nb_degree_of_freedom, "external_force");
this->allocNodalField(internal_force, nb_degree_of_freedom, "internal_force");
this->allocNodalField(blocked_dofs, nb_degree_of_freedom, "blocked_dofs");
auto & dof_manager = this->getDOFManager();
if (!dof_manager.hasDOFs("displacement")) {
dof_manager.registerDOFs("displacement", *displacement_rotation,
_dst_nodal);
dof_manager.registerBlockedDOFs("displacement", *this->blocked_dofs);
}
if (time_step_solver_type == TimeStepSolverType::_dynamic ||
time_step_solver_type == TimeStepSolverType::_dynamic_lumped) {
this->allocNodalField(velocity, spatial_dimension, "velocity");
this->allocNodalField(acceleration, spatial_dimension, "acceleration");
if (!dof_manager.hasDOFsDerivatives("displacement", 1)) {
dof_manager.registerDOFsDerivative("displacement", 1, *this->velocity);
dof_manager.registerDOFsDerivative("displacement", 2,
*this->acceleration);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initModel() {
for (auto && type : mesh.elementTypes(_element_kind = _ek_structural)) {
// computeRotationMatrix(type);
element_material.alloc(mesh.getNbElement(type), 1, type);
}
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
- getDOFManager().getMatrix("K").clear();
+ getDOFManager().getMatrix("K").zero();
- for (auto & type :
+ for (const auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_structural)) {
#define ASSEMBLE_STIFFNESS_MATRIX(type) assembleStiffnessMatrix<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(ASSEMBLE_STIFFNESS_MATRIX);
#undef ASSEMBLE_STIFFNESS_MATRIX
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeStresses() {
AKANTU_DEBUG_IN();
- for (auto & type :
+ for (const auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_structural)) {
#define COMPUTE_STRESS_ON_QUAD(type) computeStressOnQuad<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(COMPUTE_STRESS_ON_QUAD);
#undef COMPUTE_STRESS_ON_QUAD
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void StructuralMechanicsModel::computeRotationMatrix(const ElementType & type) {
+void StructuralMechanicsModel::computeRotationMatrix(ElementType type) {
Mesh & mesh = getFEEngine().getMesh();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type);
if (!rotation_matrix.exists(type)) {
rotation_matrix.alloc(nb_element,
nb_degree_of_freedom * nb_nodes_per_element *
nb_degree_of_freedom * nb_nodes_per_element,
type);
} else {
rotation_matrix(type).resize(nb_element);
}
- rotation_matrix(type).clear();
+ rotation_matrix(type).zero();
Array<Real> rotations(nb_element,
nb_degree_of_freedom * nb_degree_of_freedom);
- rotations.clear();
+ rotations.zero();
#define COMPUTE_ROTATION_MATRIX(type) computeRotationMatrix<type>(rotations);
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(COMPUTE_ROTATION_MATRIX);
#undef COMPUTE_ROTATION_MATRIX
auto R_it = rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
auto T_it =
rotation_matrix(type).begin(nb_degree_of_freedom * nb_nodes_per_element,
nb_degree_of_freedom * nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el, ++R_it, ++T_it) {
auto & T = *T_it;
auto & R = *R_it;
for (UInt k = 0; k < nb_nodes_per_element; ++k) {
- for (UInt i = 0; i < nb_degree_of_freedom; ++i)
- for (UInt j = 0; j < nb_degree_of_freedom; ++j)
+ for (UInt i = 0; i < nb_degree_of_freedom; ++i) {
+ for (UInt j = 0; j < nb_degree_of_freedom; ++j) {
T(k * nb_degree_of_freedom + i, k * nb_degree_of_freedom + j) =
R(i, j);
+ }
+ }
}
}
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> StructuralMechanicsModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs;
return mesh.createNodalField(uint_nodal_fields[field_name], group_name);
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
StructuralMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
UInt n;
if (spatial_dimension == 2) {
n = 2;
} else {
n = 3;
}
+ UInt padding_size = 0;
+ if (padding_flag) {
+ padding_size = 3;
+ }
+
if (field_name == "displacement") {
return mesh.createStridedNodalField(displacement_rotation, group_name, n, 0,
- padding_flag);
+ padding_size);
}
if (field_name == "rotation") {
return mesh.createStridedNodalField(displacement_rotation, group_name,
nb_degree_of_freedom - n, n,
- padding_flag);
+ padding_size);
}
if (field_name == "force") {
return mesh.createStridedNodalField(external_force, group_name, n, 0,
- padding_flag);
+ padding_size);
}
if (field_name == "momentum") {
return mesh.createStridedNodalField(
- external_force, group_name, nb_degree_of_freedom - n, n, padding_flag);
+ external_force, group_name, nb_degree_of_freedom - n, n, padding_size);
}
if (field_name == "internal_force") {
return mesh.createStridedNodalField(internal_force, group_name, n, 0,
- padding_flag);
+ padding_size);
}
if (field_name == "internal_momentum") {
return mesh.createStridedNodalField(
- internal_force, group_name, nb_degree_of_freedom - n, n, padding_flag);
+ internal_force, group_name, nb_degree_of_freedom - n, n, padding_size);
}
return nullptr;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> StructuralMechanicsModel::createElementalField(
- const std::string & field_name, const std::string & group_name, bool,
- const UInt & spatial_dimension, const ElementKind & kind) {
+ const std::string & field_name, const std::string & group_name, bool /*unused*/,
+ UInt spatial_dimension, ElementKind kind) {
std::shared_ptr<dumpers::Field> field;
- if (field_name == "element_index_by_material")
+ if (field_name == "element_index_by_material") {
field = mesh.createElementalField<UInt, Vector, dumpers::ElementalField>(
field_name, group_name, spatial_dimension, kind);
-
+ }
return field;
}
/* -------------------------------------------------------------------------- */
/* Virtual methods from SolverCallback */
/* -------------------------------------------------------------------------- */
/// get the type of matrix needed
MatrixType StructuralMechanicsModel::getMatrixType(const ID & /*id*/) {
return _symmetric;
}
/// callback to assemble a Matrix
void StructuralMechanicsModel::assembleMatrix(const ID & id) {
- if (id == "K")
+ if (id == "K") {
assembleStiffnessMatrix();
+ }
}
/// callback to assemble a lumped Matrix
void StructuralMechanicsModel::assembleLumpedMatrix(const ID & /*id*/) {}
/// callback to assemble the residual StructuralMechanicsModel::(rhs)
void StructuralMechanicsModel::assembleResidual() {
AKANTU_DEBUG_IN();
auto & dof_manager = getDOFManager();
- internal_force->clear();
+ internal_force->zero();
computeStresses();
assembleInternalForce();
dof_manager.assembleToResidual("displacement", *internal_force, -1);
dof_manager.assembleToResidual("displacement", *external_force, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Virtual methods from Model */
/* -------------------------------------------------------------------------- */
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
StructuralMechanicsModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _static: {
return std::make_tuple("static", TimeStepSolverType::_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
}
default:
return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
}
}
/* ------------------------------------------------------------------------ */
ModelSolverOptions StructuralMechanicsModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case TimeStepSolverType::_static: {
options.non_linear_solver_type = NonLinearSolverType::_linear;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_pseudo_time;
options.solution_type["displacement"] = IntegrationScheme::_not_defined;
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleInternalForce() {
for (auto type : mesh.elementTypes(_spatial_dimension = _all_dimensions,
_element_kind = _ek_structural)) {
assembleInternalForce(type, _not_ghost);
// assembleInternalForce(type, _ghost);
}
}
/* -------------------------------------------------------------------------- */
-void StructuralMechanicsModel::assembleInternalForce(const ElementType & type,
+void StructuralMechanicsModel::assembleInternalForce(ElementType type,
GhostType gt) {
auto & fem = getFEEngine();
auto & sigma = stress(type, gt);
auto ndof = getNbDegreeOfFreedom(type);
auto nb_nodes = mesh.getNbNodesPerElement(type);
auto ndof_per_elem = ndof * nb_nodes;
Array<Real> BtSigma(fem.getNbIntegrationPoints(type) *
mesh.getNbElement(type),
ndof_per_elem, "BtSigma");
fem.computeBtD(sigma, BtSigma, type, gt);
Array<Real> intBtSigma(0, ndof_per_elem, "intBtSigma");
fem.integrate(BtSigma, intBtSigma, ndof_per_elem, type, gt);
BtSigma.resize(0);
getDOFManager().assembleElementalArrayLocalArray(intBtSigma, *internal_force,
type, gt, 1);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/structural_mechanics/structural_mechanics_model.hh b/src/model/structural_mechanics/structural_mechanics_model.hh
index 726cf29d8..b5e3b833b 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.hh
+++ b/src/model/structural_mechanics/structural_mechanics_model.hh
@@ -1,310 +1,309 @@
/**
* @file structural_mechanics_model.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Tue Feb 20 2018
*
* @brief Particular implementation of the structural elements in the
* StructuralMechanicsModel
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "boundary_condition.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__
-#define __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__
+#ifndef AKANTU_STRUCTURAL_MECHANICS_MODEL_HH_
+#define AKANTU_STRUCTURAL_MECHANICS_MODEL_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class Material;
class MaterialSelector;
class DumperIOHelper;
class NonLocalManager;
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeStructural;
} // namespace akantu
namespace akantu {
struct StructuralMaterial {
Real E{0};
Real A{1};
Real I{0};
Real Iz{0};
Real Iy{0};
Real GJ{0};
Real rho{0};
Real t{0};
Real nu{0};
};
class StructuralMechanicsModel : public Model {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MyFEEngineType =
FEEngineTemplate<IntegratorGauss, ShapeStructural, _ek_structural>;
- StructuralMechanicsModel(Mesh & mesh,
- UInt spatial_dimension = _all_dimensions,
+ StructuralMechanicsModel(Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "structural_mechanics_model",
const MemoryID & memory_id = 0);
- virtual ~StructuralMechanicsModel();
+ ~StructuralMechanicsModel() override;
/// Init full model
void initFullImpl(const ModelOptions & options) override;
/// Init boundary FEEngine
void initFEEngineBoundary() override;
/* ------------------------------------------------------------------------ */
/* Virtual methods from SolverCallback */
/* ------------------------------------------------------------------------ */
/// get the type of matrix needed
- MatrixType getMatrixType(const ID &) override;
+ MatrixType getMatrixType(const ID & matrix_id) override;
/// callback to assemble a Matrix
- void assembleMatrix(const ID &) override;
+ void assembleMatrix(const ID & matrix_id) override;
/// callback to assemble a lumped Matrix
- void assembleLumpedMatrix(const ID &) override;
+ void assembleLumpedMatrix(const ID & matrix_id) override;
/// callback to assemble the residual (rhs)
void assembleResidual() override;
/* ------------------------------------------------------------------------ */
/* Virtual methods from Model */
/* ------------------------------------------------------------------------ */
protected:
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
- UInt getNbDegreeOfFreedom(const ElementType & type) const;
+ static UInt getNbDegreeOfFreedom(ElementType type);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
- void initSolver(TimeStepSolverType, NonLinearSolverType) override;
+ void initSolver(TimeStepSolverType time_step_solver_type,
+ NonLinearSolverType non_linear_solver_type) override;
/// initialize the model
void initModel() override;
/// compute the stresses per elements
void computeStresses();
/// compute the nodal forces
void assembleInternalForce();
/// compute the nodal forces for an element type
- void assembleInternalForce(const ElementType & type, GhostType gt);
+ void assembleInternalForce(ElementType type, GhostType gt);
/// assemble the stiffness matrix
void assembleStiffnessMatrix();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
/// TODO remove
- void computeRotationMatrix(const ElementType & type);
+ void computeRotationMatrix(ElementType type);
protected:
/// compute Rotation Matrices
template <const ElementType type>
void computeRotationMatrix(__attribute__((unused)) Array<Real> & rotations) {}
/* ------------------------------------------------------------------------ */
/* Mass (structural_mechanics_model_mass.cc) */
/* ------------------------------------------------------------------------ */
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMass(GhostType ghost_type);
/// computes rho
void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);
/// finish the computation of residual to solve in increment
void updateResidualInternal();
/* ------------------------------------------------------------------------ */
private:
template <ElementType type> void assembleStiffnessMatrix();
template <ElementType type> void assembleMass();
template <ElementType type> void computeStressOnQuad();
template <ElementType type>
void computeTangentModuli(Array<Real> & tangent_moduli);
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
- const UInt & spatial_dimension,
- const ElementKind & kind) override;
+ UInt spatial_dimension, ElementKind kind) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// set the value of the time step
// void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// return the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the StructuralMechanicsModel::displacement vector
AKANTU_GET_MACRO(Displacement, *displacement_rotation, Array<Real> &);
/// get the StructuralMechanicsModel::velocity vector
AKANTU_GET_MACRO(Velocity, *velocity, Array<Real> &);
/// get the StructuralMechanicsModel::acceleration vector, updated
/// by
/// StructuralMechanicsModel::updateAcceleration
AKANTU_GET_MACRO(Acceleration, *acceleration, Array<Real> &);
/// get the StructuralMechanicsModel::external_force vector
AKANTU_GET_MACRO(ExternalForce, *external_force, Array<Real> &);
/// get the StructuralMechanicsModel::internal_force vector (boundary forces)
AKANTU_GET_MACRO(InternalForce, *internal_force, Array<Real> &);
/// get the StructuralMechanicsModel::boundary vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(RotationMatrix, rotation_matrix, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Stress, stress, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(ElementMaterial, element_material, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Set_ID, set_ID, UInt);
void addMaterial(StructuralMaterial & material) {
materials.push_back(material);
}
const StructuralMaterial & getMaterial(const Element & element) const {
return materials[element_material(element)];
}
/* ------------------------------------------------------------------------ */
/* Boundaries (structural_mechanics_model_boundary.cc) */
/* ------------------------------------------------------------------------ */
public:
/// Compute Linear load function set in global axis
template <ElementType type>
void computeForcesByGlobalTractionArray(const Array<Real> & tractions);
/// Compute Linear load function set in local axis
template <ElementType type>
void computeForcesByLocalTractionArray(const Array<Real> & tractions);
/// compute force vector from a function(x,y,momentum) that describe stresses
// template <ElementType type>
// void computeForcesFromFunction(BoundaryFunction in_function,
// BoundaryFunctionType function_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// time step
Real time_step;
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
Array<Real> * displacement_rotation{nullptr};
/// velocities array
Array<Real> * velocity{nullptr};
/// accelerations array
Array<Real> * acceleration{nullptr};
/// forces array
Array<Real> * internal_force{nullptr};
/// forces array
Array<Real> * external_force{nullptr};
/// lumped mass array
Array<Real> * mass{nullptr};
/// boundaries array
Array<bool> * blocked_dofs{nullptr};
/// stress array
ElementTypeMapArray<Real> stress;
ElementTypeMapArray<UInt> element_material;
// Define sets of beams
ElementTypeMapArray<UInt> set_ID;
/// number of degre of freedom
UInt nb_degree_of_freedom;
// Rotation matrix
ElementTypeMapArray<Real> rotation_matrix;
// /// analysis method check the list in akantu::AnalysisMethod
// AnalysisMethod method;
/// flag defining if the increment must be computed or not
bool increment_flag;
/* ------------------------------------------------------------------------ */
std::vector<StructuralMaterial> materials;
};
} // namespace akantu
-#endif /* __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__ */
+#endif /* AKANTU_STRUCTURAL_MECHANICS_MODEL_HH_ */
diff --git a/src/model/structural_mechanics/structural_mechanics_model_inline_impl.hh b/src/model/structural_mechanics/structural_mechanics_model_inline_impl.hh
index dcba28e64..bbe416c12 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_inline_impl.hh
+++ b/src/model/structural_mechanics/structural_mechanics_model_inline_impl.hh
@@ -1,370 +1,370 @@
/**
* @file structural_mechanics_model_inline_impl.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of inline functions of StructuralMechanicsModel
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_HH__
-#define __AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_HH__
+#ifndef AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_HH_
+#define AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt
-StructuralMechanicsModel::getNbDegreeOfFreedom(const ElementType & type) const {
+StructuralMechanicsModel::getNbDegreeOfFreedom(ElementType type) {
UInt ndof = 0;
#define GET_(type) ndof = ElementClass<type>::getNbDegreeOfFreedom()
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_, _ek_structural);
#undef GET_
return ndof;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeTangentModuli(
Array<Real> & /*tangent_moduli*/) {
AKANTU_TO_IMPLEMENT();
}
} // namespace akantu
#include "structural_element_bernoulli_beam_2.hh"
#include "structural_element_bernoulli_beam_3.hh"
#include "structural_element_kirchhoff_shell.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
auto nb_element = getFEEngine().getMesh().getNbElement(type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
auto tangent_size = ElementClass<type>::getNbStressComponents();
auto tangent_moduli = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points, tangent_size * tangent_size,
"tangent_stiffness_matrix");
computeTangentModuli<type>(*tangent_moduli);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = nb_degree_of_freedom * nb_nodes_per_element;
auto bt_d_b = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points, bt_d_b_size * bt_d_b_size, "B^t*D*B");
const auto & b = getFEEngine().getShapesDerivatives(type);
Matrix<Real> BtD(bt_d_b_size, tangent_size);
for (auto && tuple :
zip(make_view(b, tangent_size, bt_d_b_size),
make_view(*tangent_moduli, tangent_size, tangent_size),
make_view(*bt_d_b, bt_d_b_size, bt_d_b_size))) {
auto & B = std::get<0>(tuple);
auto & D = std::get<1>(tuple);
auto & BtDB = std::get<2>(tuple);
BtD.mul<true, false>(B, D);
BtDB.template mul<false, false>(BtD, B);
}
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto int_bt_d_b = std::make_unique<Array<Real>>(
nb_element, bt_d_b_size * bt_d_b_size, "int_B^t*D*B");
getFEEngine().integrate(*bt_d_b, *int_bt_d_b, bt_d_b_size * bt_d_b_size,
type);
getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *int_bt_d_b, type, _not_ghost, _symmetric);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeStressOnQuad() {
AKANTU_DEBUG_IN();
Array<Real> & sigma = stress(type, _not_ghost);
auto nb_element = mesh.getNbElement(type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
auto tangent_size = ElementClass<type>::getNbStressComponents();
auto tangent_moduli = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points, tangent_size * tangent_size,
"tangent_stiffness_matrix");
computeTangentModuli<type>(*tangent_moduli);
/// compute DB
auto d_b_size = nb_degree_of_freedom * nb_nodes_per_element;
auto d_b = std::make_unique<Array<Real>>(nb_element * nb_quadrature_points,
d_b_size * tangent_size, "D*B");
const auto & b = getFEEngine().getShapesDerivatives(type);
auto B = b.begin(tangent_size, d_b_size);
auto D = tangent_moduli->begin(tangent_size, tangent_size);
auto D_B = d_b->begin(tangent_size, d_b_size);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q, ++B, ++D, ++D_B) {
D_B->template mul<false, false>(*D, *B);
}
}
/// compute DBu
D_B = d_b->begin(tangent_size, d_b_size);
auto DBu = sigma.begin(tangent_size);
Array<Real> u_el(0, d_b_size);
FEEngine::extractNodalToElementField(mesh, *displacement_rotation, u_el,
type);
auto ug = u_el.begin(d_b_size);
// No need to rotate because B is post-multiplied
for (UInt e = 0; e < nb_element; ++e, ++ug) {
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_B, ++DBu) {
DBu->template mul<false>(*D_B, *ug);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeForcesByLocalTractionArray(
const Array<Real> & /*tractions*/) {
AKANTU_DEBUG_IN();
#if 0
UInt nb_element = getFEEngine().getMesh().getNbElement(type);
UInt nb_nodes_per_element =
getFEEngine().getMesh().getNbNodesPerElement(type);
UInt nb_quad = getFEEngine().getNbIntegrationPoints(type);
// check dimension match
AKANTU_DEBUG_ASSERT(
Mesh::getSpatialDimension(type) == getFEEngine().getElementDimension(),
"element type dimension does not match the dimension of boundaries : "
<< getFEEngine().getElementDimension()
<< " != " << Mesh::getSpatialDimension(type));
// check size of the vector
AKANTU_DEBUG_ASSERT(
tractions.size() == nb_quad * nb_element,
"the size of the vector should be the total number of quadrature points");
// check number of components
AKANTU_DEBUG_ASSERT(tractions.getNbComponent() == nb_degree_of_freedom,
"the number of components should be the spatial "
"dimension of the problem");
Array<Real> Nvoigt(nb_element * nb_quad, nb_degree_of_freedom *
nb_degree_of_freedom *
nb_nodes_per_element);
transferNMatrixToSymVoigtNMatrix<type>(Nvoigt);
Array<Real>::const_matrix_iterator N_it = Nvoigt.begin(
nb_degree_of_freedom, nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::const_matrix_iterator T_it =
rotation_matrix(type).begin(nb_degree_of_freedom * nb_nodes_per_element,
nb_degree_of_freedom * nb_nodes_per_element);
auto te_it =
tractions.begin(nb_degree_of_freedom);
Array<Real> funct(nb_element * nb_quad,
nb_degree_of_freedom * nb_nodes_per_element, 0.);
Array<Real>::iterator<Vector<Real>> Fe_it =
funct.begin(nb_degree_of_freedom * nb_nodes_per_element);
Vector<Real> fe(nb_degree_of_freedom * nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e, ++T_it) {
const Matrix<Real> & T = *T_it;
for (UInt q = 0; q < nb_quad; ++q, ++N_it, ++te_it, ++Fe_it) {
const Matrix<Real> & N = *N_it;
const Vector<Real> & te = *te_it;
Vector<Real> & Fe = *Fe_it;
// compute N^t tl
fe.mul<true>(N, te);
// turn N^t tl back in the global referential
Fe.mul<true>(T, fe);
}
}
// allocate the vector that will contain the integrated values
std::stringstream name;
name << id << type << ":integral_boundary";
Array<Real> int_funct(nb_element, nb_degree_of_freedom * nb_nodes_per_element,
name.str());
// do the integration
getFEEngine().integrate(funct, int_funct,
nb_degree_of_freedom * nb_nodes_per_element, type);
// assemble the result into force vector
getFEEngine().assembleArray(int_funct, *force_momentum,
dof_synchronizer->getLocalDOFEquationNumbers(),
nb_degree_of_freedom, type);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeForcesByGlobalTractionArray(
const Array<Real> & /*traction_global*/) {
AKANTU_DEBUG_IN();
#if 0
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad = getFEEngine().getNbIntegrationPoints(type);
UInt nb_nodes_per_element =
getFEEngine().getMesh().getNbNodesPerElement(type);
std::stringstream name;
name << id << ":structuralmechanics:imposed_linear_load";
Array<Real> traction_local(nb_element * nb_quad, nb_degree_of_freedom,
name.str());
Array<Real>::const_matrix_iterator T_it =
rotation_matrix(type).begin(nb_degree_of_freedom * nb_nodes_per_element,
nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::const_iterator<Vector<Real>> Te_it =
traction_global.begin(nb_degree_of_freedom);
Array<Real>::iterator<Vector<Real>> te_it =
traction_local.begin(nb_degree_of_freedom);
Matrix<Real> R(nb_degree_of_freedom, nb_degree_of_freedom);
for (UInt e = 0; e < nb_element; ++e, ++T_it) {
const Matrix<Real> & T = *T_it;
for (UInt i = 0; i < nb_degree_of_freedom; ++i)
for (UInt j = 0; j < nb_degree_of_freedom; ++j)
R(i, j) = T(i, j);
for (UInt q = 0; q < nb_quad; ++q, ++Te_it, ++te_it) {
const Vector<Real> & Te = *Te_it;
Vector<Real> & te = *te_it;
// turn the traction in the local referential
te.mul<false>(R, Te);
}
}
computeForcesByLocalTractionArray<type>(traction_local);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @param myf pointer to a function that fills a vector/tensor with respect to
* passed coordinates
*/
#if 0
template <ElementType type>
inline void StructuralMechanicsModel::computeForcesFromFunction(
BoundaryFunction myf, BoundaryFunctionType function_type) {
/** function type is
** _bft_forces : linear load is given
** _bft_stress : stress function is given -> Not already done for this kind
*of model
*/
std::stringstream name;
name << id << ":structuralmechanics:imposed_linear_load";
Array<Real> lin_load(0, nb_degree_of_freedom, name.str());
- name.clear();
+ name.zero();
UInt offset = nb_degree_of_freedom;
// prepare the loop over element types
UInt nb_quad = getFEEngine().getNbIntegrationPoints(type);
UInt nb_element = getFEEngine().getMesh().getNbElement(type);
- name.clear();
+ name.zero();
name << id << ":structuralmechanics:quad_coords";
Array<Real> quad_coords(nb_element * nb_quad, spatial_dimension,
"quad_coords");
getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.interpolateOnIntegrationPoints<type>(getFEEngine().getMesh().getNodes(),
quad_coords, spatial_dimension);
getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.interpolateOnIntegrationPoints<type>(
getFEEngine().getMesh().getNodes(), quad_coords, spatial_dimension,
_not_ghost, empty_filter, true, 0, 1, 1);
if (spatial_dimension == 3)
getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.interpolateOnIntegrationPoints<type>(
getFEEngine().getMesh().getNodes(), quad_coords, spatial_dimension,
_not_ghost, empty_filter, true, 0, 2, 2);
lin_load.resize(nb_element * nb_quad);
Real * imposed_val = lin_load.storage();
/// sigma/load on each quadrature points
Real * qcoord = quad_coords.storage();
for (UInt el = 0; el < nb_element; ++el) {
for (UInt q = 0; q < nb_quad; ++q) {
myf(qcoord, imposed_val, NULL, 0);
imposed_val += offset;
qcoord += spatial_dimension;
}
}
switch (function_type) {
case _bft_traction_local:
computeForcesByLocalTractionArray<type>(lin_load);
break;
case _bft_traction:
computeForcesByGlobalTractionArray<type>(lin_load);
break;
default:
break;
}
}
#endif
} // namespace akantu
-#endif /* __AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_HH__ */
+#endif /* AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_HH_ */
diff --git a/src/model/structural_mechanics/structural_mechanics_model_mass.cc b/src/model/structural_mechanics/structural_mechanics_model_mass.cc
index c556016d2..52bea77c2 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_mass.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model_mass.cc
@@ -1,78 +1,78 @@
/**
* @file structural_mechanics_model_mass.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 07 2014
* @date last modification: Fri Dec 15 2017
*
* @brief function handling mass computation
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "material.hh"
#include "shape_structural.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ComputeRhoFunctorStruct {
public:
explicit ComputeRhoFunctorStruct(const StructuralMechanicsModel & model)
: model(model){};
void operator()(Matrix<Real> & rho, const Element & element) const {
Real mat_rho = model.getMaterial(element).rho;
rho.set(mat_rho);
}
private:
const StructuralMechanicsModel & model;
};
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleMass() {
AKANTU_DEBUG_IN();
assembleMass(_not_ghost);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleMass(GhostType ghost_type) {
AKANTU_DEBUG_IN();
- MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
+ auto & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctorStruct compute_rho(*this);
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_structural)) {
fem.assembleFieldMatrix(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/solver/petsc_wrapper.hh b/src/solver/petsc_wrapper.hh
index c3c848790..d9379a7b3 100644
--- a/src/solver/petsc_wrapper.hh
+++ b/src/solver/petsc_wrapper.hh
@@ -1,79 +1,79 @@
/**
* @file petsc_wrapper.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Sat Feb 03 2018
*
* @brief Wrapper of PETSc structures
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PETSC_WRAPPER_HH__
-#define __AKANTU_PETSC_WRAPPER_HH__
+#ifndef AKANTU_PETSC_WRAPPER_HH_
+#define AKANTU_PETSC_WRAPPER_HH_
/* -------------------------------------------------------------------------- */
#include <mpi.h>
#include <petscao.h>
#include <petscis.h>
#include <petscksp.h>
#include <petscmat.h>
#include <petscvec.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
struct PETScMatrixWrapper {
Mat mat;
AO ao;
ISLocalToGlobalMapping mapping;
/// MPI communicator for PETSc commands
MPI_Comm communicator;
};
/* -------------------------------------------------------------------------- */
struct PETScSolverWrapper {
KSP ksp;
Vec solution;
Vec rhs;
// MPI communicator for PETSc commands
MPI_Comm communicator;
};
#if not defined(PETSC_CLANGUAGE_CXX)
extern int aka_PETScError(int ierr);
#define CHKERRXX(x) \
do { \
int error = aka_PETScError(x); \
if (error != 0) { \
AKANTU_EXCEPTION("Error in PETSC"); \
} \
} while (0)
#endif
} // namespace akantu
-#endif /* __AKANTU_PETSC_WRAPPER_HH__ */
+#endif /* AKANTU_PETSC_WRAPPER_HH_ */
diff --git a/src/solver/solver_petsc.cc b/src/solver/solver_petsc.cc
index 5ba8b943f..3ab4cef60 100644
--- a/src/solver/solver_petsc.cc
+++ b/src/solver/solver_petsc.cc
@@ -1,1074 +1,91 @@
/**
* @file solver_petsc.cc
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 13 2014
* @date last modification: Sun Aug 13 2017
*
* @brief Solver class implementation for the petsc solver
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solver_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
#include "solver_vector_petsc.hh"
#include "sparse_matrix_petsc.hh"
/* -------------------------------------------------------------------------- */
#include <petscksp.h>
//#include <petscsys.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SolverPETSc::SolverPETSc(DOFManagerPETSc & dof_manager, const ID & matrix_id,
const ID & id, const MemoryID & memory_id)
: SparseSolver(dof_manager, matrix_id, id, memory_id),
- dof_manager(dof_manager), matrix(dof_manager.getMatrix(matrix_id)),
- is_petsc_data_initialized(false) {
- auto mpi_comm = dof_manager.getMPIComm();
+ dof_manager(dof_manager), matrix(dof_manager.getMatrix(matrix_id)) {
+ auto && mpi_comm = dof_manager.getMPIComm();
/// create a solver context
PETSc_call(KSPCreate, mpi_comm, &this->ksp);
}
/* -------------------------------------------------------------------------- */
SolverPETSc::~SolverPETSc() {
- AKANTU_DEBUG_IN();
-
- if (ksp)
+ if (ksp != nullptr) {
PETSc_call(KSPDestroy, &ksp);
-
- AKANTU_DEBUG_OUT();
+ }
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::setOperators() {
// set the matrix that defines the linear system and the matrix for
// preconditioning (here they are the same)
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
PETSc_call(KSPSetOperators, ksp, this->matrix.getMat(),
this->matrix.getMat());
#else
PETSc_call(KSPSetOperators, ksp, this->matrix.getMat(), this->matrix.getMat(),
SAME_NONZERO_PATTERN);
#endif
// If this is not called the solution vector is zeroed in the call to
// KSPSolve().
PETSc_call(KSPSetInitialGuessNonzero, ksp, PETSC_TRUE);
PETSc_call(KSPSetFromOptions, ksp);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::solve() {
Vec & rhs(this->dof_manager.getResidual());
Vec & solution(this->dof_manager.getSolution());
PETSc_call(KSPSolve, ksp, rhs, solution);
}
-// /* --------------------------------------------------------------------------
-// */
-// void SolverPETSc::solve(Array<Real> & solution) {
-// AKANTU_DEBUG_IN();
-
-// this->solution = &solution;
-// this->solve();
-
-// PetscErrorCode ierr;
-// PETScMatrix * petsc_matrix = static_cast<PETScMatrix *>(this->matrix);
-
-// // ierr = VecGetOwnershipRange(this->petsc_solver_wrapper->solution,
-// // solution_begin, solution_end); CHKERRXX(ierr);
-// // ierr = VecGetArray(this->petsc_solver_wrapper->solution, PetscScalar
-// // **array); CHKERRXX(ierr);
-// UInt nb_component = solution.getNbComponent();
-// UInt size = solution.size();
-
-// for (UInt i = 0; i < size; ++i) {
-// for (UInt j = 0; j < nb_component; ++j) {
-// UInt i_local = i * nb_component + j;
-// if (this->matrix->getDOFSynchronizer().isLocalOrMasterDOF(i_local)) {
-// Int i_global =
-// this->matrix->getDOFSynchronizer().getDOFGlobalID(i_local);
-// ierr =
-// AOApplicationToPetsc(petsc_matrix->getPETScMatrixWrapper()->ao,
-// 1, &(i_global));
-// CHKERRXX(ierr);
-// ierr = VecGetValues(this->petsc_solver_wrapper->solution, 1,
-// &i_global,
-// &solution(i, j));
-// CHKERRXX(ierr);
-// }
-// }
-// }
-// synch_registry->synchronize(SynchronizationTag::_solver_solution);
-
-// AKANTU_DEBUG_OUT();
-// }
-
-/* -------------------------------------------------------------------------- */
-// void finalize_petsc() {
-
-// static bool finalized = false;
-// if (!finalized) {
-
-// cout<<"*** INFO *** PETSc is finalizing..."<<endl;
-// // finalize PETSc
-// PetscErrorCode ierr = PetscFinalize();CHKERRCONTINUE(ierr);
-// finalized = true;
-// }
-// }
-
-// SolverPETSc::sparse_vector_type
-// SolverPETSc::operator()(const SolverPETSc::sparse_matrix_type& AA,
-// const SolverPETSc::sparse_vector_type& bb) {
-
-// #ifdef CPPUTILS_VERBOSE
-// // parallel output stream
-// Output_stream out;
-// // timer
-// cpputils::ctimer timer;
-// out<<"Inside PETSc solver: "<<timer<<endl;
-// #endif
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Inside operator()(const sparse_matrix_type&, const
-// sparse_vector_type&)... "<<timer<<endl;
-// #endif
-
-// assert(AA.rows() == bb.size());
-
-// // KSP ksp; //!< linear solver context
-
-// Vec b; /* RHS */
-// PC pc; /* preconditioner context */
-// PetscErrorCode ierr;
-// PetscInt nlocal;
-// PetscInt n = bb.size();
-// VecScatter ctx;
-
-// /*
-// Create vectors. Note that we form 1 vector from scratch and
-// then duplicate as needed. For this simple case let PETSc decide how
-// many elements of the vector are stored on each processor. The second
-// argument to VecSetSizes() below causes PETSc to decide.
-// */
-// ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRCONTINUE(ierr);
-// ierr = VecSetSizes(b,PETSC_DECIDE,n);CHKERRCONTINUE(ierr);
-// ierr = VecSetFromOptions(b);CHKERRCONTINUE(ierr);
-// if (!allocated_) {
-// ierr = VecDuplicate(b,&x_);CHKERRCONTINUE(ierr);
-// } else
-// VecZeroEntries(x_);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Vectors created... "<<timer<<endl;
-// #endif
-
-// /* Set hight-hand-side vector */
-// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
-// bb.map_.end(); ++it) {
-// int row = it->first;
-// ierr = VecSetValues(b, 1, &row, &it->second, ADD_VALUES);
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Right hand side set... "<<timer<<endl;
-// #endif
-
-// /*
-// Assemble vector, using the 2-step process:
-// VecAssemblyBegin(), VecAssemblyEnd()
-// Computations can be done while messages are in transition
-// by placing code between these two statements.
-// */
-// ierr = VecAssemblyBegin(b);CHKERRCONTINUE(ierr);
-// ierr = VecAssemblyEnd(b);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Right-hand-side vector assembled... "<<timer<<endl;
-
-// ierr = VecView(b,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
-
-// Vec b_all;
-// ierr = VecScatterCreateToAll(b, &ctx, &b_all);CHKERRCONTINUE(ierr);
-// ierr =
-// VecScatterBegin(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
-// ierr =
-// VecScatterEnd(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
-
-// value_type nrm;
-// VecNorm(b_all,NORM_2,&nrm);
-// out<<" Norm of right hand side... "<<nrm<<endl;
-// #endif
-
-// /* Identify the starting and ending mesh points on each
-// processor for the interior part of the mesh. We let PETSc decide
-// above. */
-
-// // PetscInt rstart,rend;
-// // ierr = VecGetOwnershipRange(x_,&rstart,&rend);CHKERRCONTINUE(ierr);
-// ierr = VecGetLocalSize(x_,&nlocal);CHKERRCONTINUE(ierr);
-
-// /*
-// Create matrix. When using MatCreate(), the matrix format can
-// be specified at runtime.
-
-// Performance tuning note: For problems of substantial size,
-// preallocation of matrix memory is crucial for attaining good
-// performance. See the matrix chapter of the users manual for details.
-
-// We pass in nlocal as the "local" size of the matrix to force it
-// to have the same parallel layout as the vector created above.
-// */
-// if (!allocated_) {
-
-// ierr = MatCreate(PETSC_COMM_WORLD,&A_);CHKERRCONTINUE(ierr);
-// ierr = MatSetSizes(A_,nlocal,nlocal,n,n);CHKERRCONTINUE(ierr);
-// ierr = MatSetFromOptions(A_);CHKERRCONTINUE(ierr);
-// ierr = MatSetUp(A_);CHKERRCONTINUE(ierr);
-// } else {
-// // zero-out matrix
-// MatZeroEntries(A_);
-// }
-
-// /*
-// Assemble matrix.
-
-// The linear system is distributed across the processors by
-// chunks of contiguous rows, which correspond to contiguous
-// sections of the mesh on which the problem is discretized.
-// For matrix assembly, each processor contributes entries for
-// the part that it owns locally.
-// */
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Zeroed-out sparse matrix entries... "<<timer<<endl;
-// #endif
-
-// for (sparse_matrix_type::const_hash_iterator it = AA.map_.begin(); it !=
-// AA.map_.end(); ++it) {
-
-// // get subscripts
-// std::pair<size_t,size_t> subs = AA.unhash(it->first);
-// PetscInt row = subs.first;
-// PetscInt col = subs.second;
-// ierr = MatSetValues(A_, 1, &row, 1, &col, &it->second,
-// ADD_VALUES);CHKERRCONTINUE(ierr);
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Filled sparse matrix... "<<timer<<endl;
-// #endif
-
-// /* Assemble the matrix */
-// ierr = MatAssemblyBegin(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
-// ierr = MatAssemblyEnd(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
-
-// if (!allocated_) {
-// // set after the first MatAssemblyEnd
-// // ierr = MatSetOption(A_, MAT_NEW_NONZERO_LOCATIONS,
-// PETSC_FALSE);CHKERRCONTINUE(ierr);
-// ierr = MatSetOption(A_, MAT_NEW_NONZERO_ALLOCATION_ERR,
-// PETSC_FALSE);CHKERRCONTINUE(ierr);
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Sparse matrix assembled... "<<timer<<endl;
-// // view matrix
-// MatView(A_, PETSC_VIEWER_STDOUT_WORLD);
-
-// MatNorm(A_,NORM_FROBENIUS,&nrm);
-// out<<" Norm of stiffness matrix... "<<nrm<<endl;
-// #endif
-
-// /*
-// Set operators. Here the matrix that defines the linear system
-// also serves as the preconditioning matrix.
-// */
-// // ierr =
-// KSPSetOperators(ksp,A_,A_,DIFFERENT_NONZERO_PATTERN);CHKERRCONTINUE(ierr);
-// ierr =
-// KSPSetOperators(ksp_,A_,A_,SAME_NONZERO_PATTERN);CHKERRCONTINUE(ierr);
-
-// //
-// // /*
-// // Set runtime options, e.g.,
-// // -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
-// // These options will override those specified above as long as
-// // KSPSetFromOptions() is called _after_ any other customization
-// // routines.
-// // */
-// // ierr = KSPSetFromOptions(ksp);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Solving system... "<<timer<<endl;
-// #endif
-
-// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-// Solve the linear system
-// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
-// /*
-// Solve linear system
-// */
-// ierr = KSPSolve(ksp_,b,x_);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-
-// /*
-// View solver info; we could instead use the option -ksp_view to
-// print this info to the screen at the conclusion of KSPSolve().
-// */
-// ierr = KSPView(ksp_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
-
-// int iter;
-// KSPGetIterationNumber(ksp_, &iter);
-// out<<" System solved in "<<iter<<" iterations... "<<timer<<endl;
-// KSPConvergedReason reason;
-// ierr = KSPGetConvergedReason(ksp_,&reason);CHKERRCONTINUE(ierr);
-// if (reason < 0)
-// out<<"*** WARNING *** PETSc solver diverged with flag ";
-// else
-// out<<"*** INFO *** PETSc solver converged with flag ";
-
-// if (reason == KSP_CONVERGED_RTOL)
-// out<<"KSP_CONVERGED_RTOL"<<endl;
-// else if (reason == KSP_CONVERGED_ATOL)
-// out<<"KSP_CONVERGED_ATOL"<<endl;
-// else if (reason == KSP_CONVERGED_ITS)
-// out<<"KSP_CONVERGED_ITS"<<endl;
-// else if (reason == KSP_CONVERGED_CG_NEG_CURVE)
-// out<<"KSP_CONVERGED_CG_NEG_CURVE"<<endl;
-// else if (reason == KSP_CONVERGED_CG_CONSTRAINED)
-// out<<"KSP_CONVERGED_CG_CONSTRAINED"<<endl;
-// else if (reason == KSP_CONVERGED_STEP_LENGTH)
-// out<<"KSP_CONVERGED_STEP_LENGTH"<<endl;
-// else if (reason == KSP_CONVERGED_HAPPY_BREAKDOWN)
-// out<<"KSP_CONVERGED_HAPPY_BREAKDOWN"<<endl;
-// else if (reason == KSP_DIVERGED_NULL)
-// out<<"KSP_DIVERGED_NULL"<<endl;
-// else if (reason == KSP_DIVERGED_ITS)
-// out<<"KSP_DIVERGED_ITS"<<endl;
-// else if (reason == KSP_DIVERGED_DTOL)
-// out<<"KSP_DIVERGED_DTOL"<<endl;
-// else if (reason == KSP_DIVERGED_BREAKDOWN)
-// out<<"KSP_DIVERGED_BREAKDOWN"<<endl;
-// else if (reason == KSP_DIVERGED_BREAKDOWN_BICG)
-// out<<"KSP_DIVERGED_BREAKDOWN_BICG"<<endl;
-// else if (reason == KSP_DIVERGED_NONSYMMETRIC)
-// out<<"KSP_DIVERGED_NONSYMMETRIC"<<endl;
-// else if (reason == KSP_DIVERGED_INDEFINITE_PC)
-// out<<"KSP_DIVERGED_INDEFINITE_PC"<<endl;
-// else if (reason == KSP_DIVERGED_NAN)
-// out<<"KSP_DIVERGED_NAN"<<endl;
-// else if (reason == KSP_DIVERGED_INDEFINITE_MAT)
-// out<<"KSP_DIVERGED_INDEFINITE_MAT"<<endl;
-// else if (reason == KSP_CONVERGED_ITERATING)
-// out<<"KSP_CONVERGED_ITERATING"<<endl;
-
-// PetscReal rnorm;
-// ierr = KSPGetResidualNorm(ksp_,&rnorm);CHKERRCONTINUE(ierr);
-
-// out<<"PETSc last residual norm computed: "<<rnorm<<endl;
-
-// ierr = VecView(x_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
-
-// VecNorm(x_,NORM_2,&nrm);
-// out<<" Norm of solution vector... "<<nrm<<endl;
-
-// #endif
-
-// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-// Check solution and clean up
-// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
-
-// Vec x_all;
-
-// ierr = VecScatterCreateToAll(x_, &ctx, &x_all);CHKERRCONTINUE(ierr);
-// ierr =
-// VecScatterBegin(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
-// ierr =
-// VecScatterEnd(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Solution vector scattered... "<<timer<<endl;
-// VecNorm(x_all,NORM_2,&nrm);
-// out<<" Norm of scattered vector... "<<nrm<<endl;
-// // ierr = VecView(x_all,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
-// #endif
-
-// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-// Get values from solution and store them in the object that will be
-// returned
-// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
-
-// sparse_vector_type xx(bb.size());
-
-// /* Set solution vector */
-// double zero = 0.;
-// double val;
-// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
-// bb.map_.end(); ++it) {
-// int row = it->first;
-// ierr = VecGetValues(x_all, 1, &row, &val);
-// if (val != zero)
-// xx[row] = val;
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Solution vector copied... "<<timer<<endl;
-// // out<<" Norm of copied solution vector... "<<norm(xx,
-// Insert_t)<<endl;
-// #endif
-
-// /*
-// Free work space. All PETSc objects should be destroyed when they
-// are no longer needed.
-// */
-// ierr = VecDestroy(&b);CHKERRCONTINUE(ierr);
-// // ierr = KSPDestroy(&ksp);CHKERRCONTINUE(ierr);
-
-// // set allocated flag
-// if (!allocated_) {
-// allocated_ = true;
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Temporary data structures destroyed... "<<timer<<endl;
-// #endif
-
-// return xx;
-// }
-
-// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const
-// SolverPETSc::sparse_matrix_type& KKpf, const SolverPETSc::sparse_matrix_type&
-// KKpp, const SolverPETSc::sparse_vector_type& UUp) {
-
-// #ifdef CPPUTILS_VERBOSE
-// // parallel output stream
-// Output_stream out;
-// // timer
-// cpputils::ctimer timer;
-// out<<"Inside SolverPETSc::operator()(const sparse_matrix&, const
-// sparse_matrix&, const sparse_vector&). "<<timer<<endl;
-// #endif
-
-// Mat Kpf, Kpp;
-// Vec Up, Pf, Pp;
-
-// PetscErrorCode ierr =
-// MatCreate(PETSC_COMM_WORLD,&Kpf);CHKERRCONTINUE(ierr);
-// ierr = MatCreate(PETSC_COMM_WORLD,&Kpp);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Allocating memory... "<<timer<<endl;
-// #endif
-
-// ierr = MatSetFromOptions(Kpf);CHKERRCONTINUE(ierr);
-// ierr = MatSetFromOptions(Kpp);CHKERRCONTINUE(ierr);
-
-// ierr = MatSetSizes(Kpf,PETSC_DECIDE,PETSC_DECIDE, KKpf.rows(),
-// KKpf.columns());CHKERRCONTINUE(ierr);
-// ierr = MatSetSizes(Kpp,PETSC_DECIDE,PETSC_DECIDE, KKpp.rows(),
-// KKpp.columns());CHKERRCONTINUE(ierr);
-
-// // get number of non-zeros in both diagonal and non-diagonal portions of
-// the matrix
-
-// std::pair<size_t,size_t> Kpf_nz = KKpf.non_zero_off_diagonal();
-// std::pair<size_t,size_t> Kpp_nz = KKpp.non_zero_off_diagonal();
-
-// ierr = MatMPIAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL,
-// Kpf_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
-// ierr = MatMPIAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL,
-// Kpp_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
-// ierr = MatSeqAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL);
-// CHKERRCONTINUE(ierr);
-// ierr = MatSeqAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL);
-// CHKERRCONTINUE(ierr);
-
-// for (sparse_matrix_type::const_hash_iterator it = KKpf.map_.begin(); it !=
-// KKpf.map_.end(); ++it) {
-
-// // get subscripts
-// std::pair<size_t,size_t> subs = KKpf.unhash(it->first);
-// int row = subs.first;
-// int col = subs.second;
-// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second,
-// ADD_VALUES);CHKERRCONTINUE(ierr);
-// }
-
-// for (sparse_matrix_type::const_hash_iterator it = KKpp.map_.begin(); it !=
-// KKpp.map_.end(); ++it) {
-
-// // get subscripts
-// std::pair<size_t,size_t> subs = KKpp.unhash(it->first);
-// int row = subs.first;
-// int col = subs.second;
-// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second,
-// ADD_VALUES);CHKERRCONTINUE(ierr);
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Filled sparse matrices... "<<timer<<endl;
-// #endif
-
-// /*
-// Assemble matrix, using the 2-step process:
-// MatAssemblyBegin(), MatAssemblyEnd()
-// Computations can be done while messages are in transition
-// by placing code between these two statements.
-// */
-// ierr = MatAssemblyBegin(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
-// ierr = MatAssemblyBegin(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
-// ierr = MatAssemblyEnd(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
-// ierr = MatAssemblyEnd(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Sparse matrices assembled... "<<timer<<endl;
-// #endif
-
-// ierr = VecCreate(PETSC_COMM_WORLD,&Up);CHKERRCONTINUE(ierr);
-// ierr = VecSetSizes(Up,PETSC_DECIDE, UUp.size());CHKERRCONTINUE(ierr);
-// ierr = VecSetFromOptions(Up);CHKERRCONTINUE(ierr);
-
-// ierr = VecCreate(PETSC_COMM_WORLD,&Pf);CHKERRCONTINUE(ierr);
-// ierr = VecSetSizes(Pf,PETSC_DECIDE, KKpf.rows());CHKERRCONTINUE(ierr);
-// ierr = VecSetFromOptions(Pf);CHKERRCONTINUE(ierr);
-// ierr = VecDuplicate(Pf,&Pp);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Vectors created... "<<timer<<endl;
-// #endif
-
-// /* Set hight-hand-side vector */
-// for (sparse_vector_type::const_hash_iterator it = UUp.map_.begin(); it !=
-// UUp.map_.end(); ++it) {
-// int row = it->first;
-// ierr = VecSetValues(Up, 1, &row, &it->second, ADD_VALUES);
-// }
-
-// /*
-// Assemble vector, using the 2-step process:
-// VecAssemblyBegin(), VecAssemblyEnd()
-// Computations can be done while messages are in transition
-// by placing code between these two statements.
-// */
-// ierr = VecAssemblyBegin(Up);CHKERRCONTINUE(ierr);
-// ierr = VecAssemblyEnd(Up);CHKERRCONTINUE(ierr);
-
-// // add Kpf*Uf
-// ierr = MatMult(Kpf, x_, Pf);
-
-// // add Kpp*Up
-// ierr = MatMultAdd(Kpp, Up, Pf, Pp);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Matrices multiplied... "<<timer<<endl;
-// #endif
-
-// VecScatter ctx;
-// Vec Pp_all;
-
-// ierr = VecScatterCreateToAll(Pp, &ctx, &Pp_all);CHKERRCONTINUE(ierr);
-// ierr =
-// VecScatterBegin(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
-// ierr =
-// VecScatterEnd(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Vector scattered... "<<timer<<endl;
-// #endif
-
-// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-// Get values from solution and store them in the object that will be
-// returned
-// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
-
-// sparse_vector_type pp(KKpf.rows());
-
-// // get reaction vector
-// for (int i=0; i<KKpf.rows(); ++i) {
-
-// PetscScalar v;
-// ierr = VecGetValues(Pp_all, 1, &i, &v);
-// if (v != PetscScalar())
-// pp[i] = v;
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Vector copied... "<<timer<<endl;
-// #endif
-
-// ierr = MatDestroy(&Kpf);CHKERRCONTINUE(ierr);
-// ierr = MatDestroy(&Kpp);CHKERRCONTINUE(ierr);
-// ierr = VecDestroy(&Up);CHKERRCONTINUE(ierr);
-// ierr = VecDestroy(&Pf);CHKERRCONTINUE(ierr);
-// ierr = VecDestroy(&Pp);CHKERRCONTINUE(ierr);
-// ierr = VecDestroy(&Pp_all);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Temporary data structures destroyed... "<<timer<<endl;
-// #endif
-
-// return pp;
-// }
-
-// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const
-// SolverPETSc::sparse_vector_type& aa, const SolverPETSc::sparse_vector_type&
-// bb) {
-
-// assert(aa.size() == bb.size());
-
-// #ifdef CPPUTILS_VERBOSE
-// // parallel output stream
-// Output_stream out;
-// // timer
-// cpputils::ctimer timer;
-// out<<"Inside SolverPETSc::operator()(const sparse_vector&, const
-// sparse_vector&). "<<timer<<endl;
-// #endif
-
-// Vec r;
-
-// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
-// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
-// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Vectors created... "<<timer<<endl;
-// #endif
-
-// // set values
-// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
-// aa.map_.end(); ++it) {
-// int row = it->first;
-// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
-// }
-// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
-// bb.map_.end(); ++it) {
-// int row = it->first;
-// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
-// }
-
-// /*
-// Assemble vector, using the 2-step process:
-// VecAssemblyBegin(), VecAssemblyEnd()
-// Computations can be done while messages are in transition
-// by placing code between these two statements.
-// */
-// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
-// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);
-
-// sparse_vector_type rr(aa.size());
-
-// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
-// aa.map_.end(); ++it) {
-// int row = it->first;
-// ierr = VecGetValues(r, 1, &row, &rr[row]);
-// }
-// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
-// bb.map_.end(); ++it) {
-// int row = it->first;
-// ierr = VecGetValues(r, 1, &row, &rr[row]);
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Vector copied... "<<timer<<endl;
-// #endif
-
-// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Temporary data structures destroyed... "<<timer<<endl;
-// #endif
-
-// return rr;
-// }
-
-// SolverPETSc::value_type SolverPETSc::norm(const
-// SolverPETSc::sparse_matrix_type& aa, Element_insertion_type flag) {
-
-// #ifdef CPPUTILS_VERBOSE
-// // parallel output stream
-// Output_stream out;
-// // timer
-// cpputils::ctimer timer;
-// out<<"Inside SolverPETSc::norm(const sparse_matrix&). "<<timer<<endl;
-// #endif
-
-// Mat r;
-
-// PetscErrorCode ierr = MatCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
-// ierr = MatSetSizes(r,PETSC_DECIDE,PETSC_DECIDE, aa.rows(),
-// aa.columns());CHKERRCONTINUE(ierr);
-// ierr = MatSetFromOptions(r);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Matrix created... "<<timer<<endl;
-// #endif
-
-// // set values
-// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
-// aa.map_.end(); ++it) {
-// // get subscripts
-// std::pair<size_t,size_t> subs = aa.unhash(it->first);
-// int row = subs.first;
-// int col = subs.second;
-
-// if (flag == Add_t)
-// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, ADD_VALUES);
-// else if (flag == Insert_t)
-// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, INSERT_VALUES);
-// CHKERRCONTINUE(ierr);
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Matrix filled..."<<timer<<endl;
-// #endif
-
-// /*
-// Assemble vector, using the 2-step process:
-// VecAssemblyBegin(), VecAssemblyEnd()
-// Computations can be done while messages are in transition
-// by placing code between these two statements.
-// */
-// ierr = MatAssemblyBegin(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
-// ierr = MatAssemblyEnd(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
-
-// value_type nrm;
-
-// MatNorm(r,NORM_FROBENIUS,&nrm);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Norm computed... "<<timer<<endl;
-// #endif
-
-// ierr = MatDestroy(&r);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Temporary data structures destroyed... "<<timer<<endl;
-// #endif
-
-// return nrm;
-// }
-
-// SolverPETSc::value_type SolverPETSc::norm(const
-// SolverPETSc::sparse_vector_type& aa, Element_insertion_type flag) {
-
-// #ifdef CPPUTILS_VERBOSE
-// // parallel output stream
-// Output_stream out;
-// // timer
-// cpputils::ctimer timer;
-// out<<"Inside SolverPETSc::norm(const sparse_vector&). "<<timer<<endl;
-// #endif
-
-// Vec r;
-
-// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
-// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
-// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Vector created... "<<timer<<endl;
-// #endif
-
-// // set values
-// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
-// aa.map_.end(); ++it) {
-// int row = it->first;
-// if (flag == Add_t)
-// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
-// else if (flag == Insert_t)
-// ierr = VecSetValues(r, 1, &row, &it->second, INSERT_VALUES);
-// CHKERRCONTINUE(ierr);
-// }
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Vector filled..."<<timer<<endl;
-// #endif
-
-// /*
-// Assemble vector, using the 2-step process:
-// VecAssemblyBegin(), VecAssemblyEnd()
-// Computations can be done while messages are in transition
-// by placing code between these two statements.
-// */
-// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
-// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);
-
-// value_type nrm;
-
-// VecNorm(r,NORM_2,&nrm);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Norm computed... "<<timer<<endl;
-// #endif
-
-// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);
-
-// #ifdef CPPUTILS_VERBOSE
-// out<<" Temporary data structures destroyed... "<<timer<<endl;
-// #endif
-
-// return nrm;
-
-// }
-
-// //
-// ///*
-// -------------------------------------------------------------------------- */
-// //SolverMumps::SolverMumps(SparseMatrix & matrix,
-// // const ID & id,
-// // const MemoryID & memory_id) :
-// //Solver(matrix, id, memory_id), is_mumps_data_initialized(false),
-// rhs_is_local(true) {
-// // AKANTU_DEBUG_IN();
-// //
-// //#ifdef AKANTU_USE_MPI
-// // parallel_method = SolverMumpsOptions::_fully_distributed;
-// //#else //AKANTU_USE_MPI
-// // parallel_method = SolverMumpsOptions::_master_slave_distributed;
-// //#endif //AKANTU_USE_MPI
-// //
-// // CommunicatorEventHandler & comm_event_handler = *this;
-// //
-// // communicator.registerEventHandler(comm_event_handler);
-// //
-// // AKANTU_DEBUG_OUT();
-// //}
-// //
-// ///*
-// -------------------------------------------------------------------------- */
-// //SolverMumps::~SolverMumps() {
-// // AKANTU_DEBUG_IN();
-// //
-// // AKANTU_DEBUG_OUT();
-// //}
-// //
-// ///*
-// -------------------------------------------------------------------------- */
-// //void SolverMumps::destroyMumpsData() {
-// // AKANTU_DEBUG_IN();
-// //
-// // if(is_mumps_data_initialized) {
-// // mumps_data.job = _smj_destroy; // destroy
-// // dmumps_c(&mumps_data);
-// // is_mumps_data_initialized = false;
-// // }
-// //
-// // AKANTU_DEBUG_OUT();
-// //}
-// //
-// ///*
-// -------------------------------------------------------------------------- */
-// //void SolverMumps::onCommunicatorFinalize(const StaticCommunicator & comm) {
-// // AKANTU_DEBUG_IN();
-// //
-// // try{
-// // const StaticCommunicatorMPI & comm_mpi =
-// // dynamic_cast<const StaticCommunicatorMPI
-// &>(comm.getRealStaticCommunicator());
-// // if(mumps_data.comm_fortran ==
-// MPI_Comm_c2f(comm_mpi.getMPICommunicator()))
-// // destroyMumpsData();
-// // } catch(...) {}
-// //
-// // AKANTU_DEBUG_OUT();
-// //}
-// //
-// ///*
-// -------------------------------------------------------------------------- */
-// //void SolverMumps::initMumpsData(SolverMumpsOptions::ParallelMethod
-// parallel_method) {
-// // switch(parallel_method) {
-// // case SolverMumpsOptions::_fully_distributed:
-// // icntl(18) = 3; //fully distributed
-// // icntl(28) = 0; //automatic choice
-// //
-// // mumps_data.nz_loc = matrix->getNbNonZero();
-// // mumps_data.irn_loc = matrix->getIRN().values;
-// // mumps_data.jcn_loc = matrix->getJCN().values;
-// // break;
-// // case SolverMumpsOptions::_master_slave_distributed:
-// // if(prank == 0) {
-// // mumps_data.nz = matrix->getNbNonZero();
-// // mumps_data.irn = matrix->getIRN().values;
-// // mumps_data.jcn = matrix->getJCN().values;
-// // } else {
-// // mumps_data.nz = 0;
-// // mumps_data.irn = NULL;
-// // mumps_data.jcn = NULL;
-// //
-// // icntl(18) = 0; //centralized
-// // icntl(28) = 0; //sequential analysis
-// // }
-// // break;
-// // }
-// //}
-// //
-// ///*
-// -------------------------------------------------------------------------- */
-// //void SolverMumps::initialize(SolverOptions & options) {
-// // AKANTU_DEBUG_IN();
-// //
-// // mumps_data.par = 1;
-// //
-// // if(SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions
-// *>(&options)) {
-// // if(opt->parallel_method ==
-// SolverMumpsOptions::_master_slave_distributed) {
-// // mumps_data.par = 0;
-// // }
-// // }
-// //
-// // mumps_data.sym = 2 * (matrix->getSparseMatrixType() == _symmetric);
-// // prank = communicator.whoAmI();
-// //#ifdef AKANTU_USE_MPI
-// // mumps_data.comm_fortran = MPI_Comm_c2f(dynamic_cast<const
-// StaticCommunicatorMPI
-// &>(communicator.getRealStaticCommunicator()).getMPICommunicator());
-// //#endif
-// //
-// // if(AKANTU_DEBUG_TEST(dblTrace)) {
-// // icntl(1) = 2;
-// // icntl(2) = 2;
-// // icntl(3) = 2;
-// // icntl(4) = 4;
-// // }
-// //
-// // mumps_data.job = _smj_initialize; //initialize
-// // dmumps_c(&mumps_data);
-// // is_mumps_data_initialized = true;
-// //
-// // /*
-// ------------------------------------------------------------------------ */
-// // UInt size = matrix->size();
-// //
-// // if(prank == 0) {
-// // std::stringstream sstr_rhs; sstr_rhs << id << ":rhs";
-// // rhs = &(alloc<Real>(sstr_rhs.str(), size, 1, REAL_INIT_VALUE));
-// // } else {
-// // rhs = NULL;
-// // }
-// //
-// // /// No outputs
-// // icntl(1) = 0;
-// // icntl(2) = 0;
-// // icntl(3) = 0;
-// // icntl(4) = 0;
-// // mumps_data.nz_alloc = 0;
-// //
-// // if (AKANTU_DEBUG_TEST(dblDump)) icntl(4) = 4;
-// //
-// // mumps_data.n = size;
-// //
-// // if(AKANTU_DEBUG_TEST(dblDump)) {
-// // strcpy(mumps_data.write_problem, "mumps_matrix.mtx");
-// // }
-// //
-// // /*
-// ------------------------------------------------------------------------ */
-// // // Default Scaling
-// // icntl(8) = 77;
-// //
-// // icntl(5) = 0; // Assembled matrix
-// //
-// // SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions *>(&options);
-// // if(opt)
-// // parallel_method = opt->parallel_method;
-// //
-// // initMumpsData(parallel_method);
-// //
-// // mumps_data.job = _smj_analyze; //analyze
-// // dmumps_c(&mumps_data);
-// //
-// // AKANTU_DEBUG_OUT();
-// //}
-// //
-// ///*
-// -------------------------------------------------------------------------- */
-// //void SolverMumps::setRHS(Array<Real> & rhs) {
-// // if(prank == 0) {
-// // matrix->getDOFSynchronizer().gather(rhs, 0, this->rhs);
-// // } else {
-// // matrix->getDOFSynchronizer().gather(rhs, 0);
-// // }
-// //}
-// //
-// ///*
-// -------------------------------------------------------------------------- */
-// //void SolverMumps::solve() {
-// // AKANTU_DEBUG_IN();
-// //
-// // if(parallel_method == SolverMumpsOptions::_fully_distributed)
-// // mumps_data.a_loc = matrix->getA().values;
-// // else
-// // if(prank == 0) {
-// // mumps_data.a = matrix->getA().values;
-// // }
-// //
-// // if(prank == 0) {
-// // mumps_data.rhs = rhs->values;
-// // }
-// //
-// // /// Default centralized dense second member
-// // icntl(20) = 0;
-// // icntl(21) = 0;
-// //
-// // mumps_data.job = _smj_factorize_solve; //solve
-// // dmumps_c(&mumps_data);
-// //
-// // AKANTU_DEBUG_ASSERT(info(1) != -10, "Singular matrix");
-// // AKANTU_DEBUG_ASSERT(info(1) == 0,
-// // "Error in mumps during solve process, check mumps
-// user guide INFO(1) ="
-// // << info(1));
-// //
-// // AKANTU_DEBUG_OUT();
-// //}
-// //
-// ///*
-// -------------------------------------------------------------------------- */
-// //void SolverMumps::solve(Array<Real> & solution) {
-// // AKANTU_DEBUG_IN();
-// //
-// // solve();
-// //
-// // if(prank == 0) {
-// // matrix->getDOFSynchronizer().scatter(solution, 0, this->rhs);
-// // } else {
-// // matrix->getDOFSynchronizer().scatter(solution, 0);
-// // }
-// //
-// // AKANTU_DEBUG_OUT();
-// //}
-
} // namespace akantu
diff --git a/src/solver/solver_petsc.hh b/src/solver/solver_petsc.hh
index 81d52191f..046966621 100644
--- a/src/solver/solver_petsc.hh
+++ b/src/solver/solver_petsc.hh
@@ -1,177 +1,81 @@
/**
* @file solver_petsc.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 13 2014
* @date last modification: Mon Jun 19 2017
*
* @brief Solver class interface for the petsc solver
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_solver.hh"
/* -------------------------------------------------------------------------- */
#include <petscksp.h>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLVER_PETSC_HH__
-#define __AKANTU_SOLVER_PETSC_HH__
+#ifndef AKANTU_SOLVER_PETSC_HH_
+#define AKANTU_SOLVER_PETSC_HH_
namespace akantu {
class SparseMatrixPETSc;
class DOFManagerPETSc;
} // namespace akantu
namespace akantu {
class SolverPETSc : public SparseSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SolverPETSc(DOFManagerPETSc & dof_manager, const ID & matrix_id,
const ID & id = "solver_petsc", const MemoryID & memory_id = 0);
- virtual ~SolverPETSc();
+ ~SolverPETSc() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create the solver context and set the matrices
virtual void setOperators();
- virtual void solve();
+ void solve() override;
private:
/// DOFManager correctly typed
DOFManagerPETSc & dof_manager;
/// PETSc linear solver
KSP ksp;
/// Matrix defining the system of equations
SparseMatrixPETSc & matrix;
-
- /// specify if the petsc_data is initialized or not
- bool is_petsc_data_initialized;
};
-// SolverPETSc(int argc, char *argv[]) : allocated_(false) {
-
-// /*
-// Set linear solver defaults for this problem (optional).
-// - By extracting the KSP and PC contexts from the KSP context,
-// we can then directly call any KSP and PC routines to set
-// various options.
-// - The following four statements are optional; all of these
-// parameters could alternatively be specified at runtime via
-// KSPSetFromOptions();
-// */
-// // ierr = KSPGetPC(ksp_,&pc);CHKERRCONTINUE(ierr);
-// // ierr = PCSetType(pc,PCILU);CHKERRCONTINUE(ierr);
-// // ierr = PCSetType(pc,PCJACOBI);CHKERRCONTINUE(ierr);
-// ierr =
-// KSPSetTolerances(ksp_,1.e-5,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRCONTINUE(ierr);
-// }
-
-// //! Overload operator() to solve system of linear equations
-// sparse_vector_type operator()(const sparse_matrix_type& AA, const
-// sparse_vector_type& bb);
-
-// //! Overload operator() to obtain reaction vector
-// sparse_vector_type operator()(const sparse_matrix_type& Kpf, const
-// sparse_matrix_type& Kpp, const sparse_vector_type& Up);
-
-// //! Overload operator() to obtain the addition two vectors
-// sparse_vector_type operator()(const sparse_vector_type& aa, const
-// sparse_vector_type& bb);
-
-// value_type norm(const sparse_matrix_type& aa, Element_insertion_type it =
-// Add_t);
-
-// value_type norm(const sparse_vector_type& aa, Element_insertion_type it =
-// Add_t);
-
-// // NOTE: the destructor will return an error if it is called after
-// MPI_Finalize is
-// // called because it uses collect communication to free-up allocated
-// memory.
-// ~SolverPETSc() {
-
-// static bool exit = false;
-// if (!exit) {
-// // add finalize PETSc function at exit
-// atexit(finalize);
-// exit = true;
-// }
-
-// if (allocated_) {
-// PetscErrorCode ierr = MatDestroy(&A_);CHKERRCONTINUE(ierr);
-// ierr = VecDestroy(&x_);CHKERRCONTINUE(ierr);
-// ierr = KSPDestroy(&ksp_);CHKERRCONTINUE(ierr);
-// }
-// }
-
-// /* from the PETSc library, these are the options that can be passed
-// to the command line
-
-// Options Database Keys
-
-// -options_table - Calls PetscOptionsView()
-// -options_left - Prints unused options that remain in
-// the
-// database
-// -objects_left - Prints list of all objects that have not
-// been freed
-// -mpidump - Calls PetscMPIDump()
-// -malloc_dump - Calls PetscMallocDump()
-// -malloc_info - Prints total memory usage
-// -malloc_log - Prints summary of memory usage
-
-// Options Database Keys for Profiling
-
-// -log_summary [filename] - Prints summary of flop and timing
-// information to screen.
-// If the filename is specified the summary is written to the file. See
-// PetscLogView().
-// -log_summary_python [filename] - Prints data on of flop and timing
-// usage
-// to a file or screen.
-// -log_all [filename] - Logs extensive profiling information
-// See
-// PetscLogDump().
-// -log [filename] - Logs basic profiline information See
-// PetscLogDump().
-// -log_sync - Log the synchronization in scatters,
-// inner products and norms
-// -log_mpe [filename] - Creates a logfile viewable by the utility
-// Upshot/Nupshot (in MPICH distribution)
-// }
-// }
-// };
} // namespace akantu
-#endif /* __AKANTU_SOLVER_PETSC_HH__ */
+#endif /* AKANTU_SOLVER_PETSC_HH_ */
diff --git a/src/solver/solver_vector.hh b/src/solver/solver_vector.hh
index 8fb95f0c9..d413cd56a 100644
--- a/src/solver/solver_vector.hh
+++ b/src/solver/solver_vector.hh
@@ -1,86 +1,87 @@
/**
* @file solver_vector.hh
*
* @author Nicolas Richart
*
* @date creation Tue Jan 01 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLVER_VECTOR_HH__
-#define __AKANTU_SOLVER_VECTOR_HH__
+#ifndef AKANTU_SOLVER_VECTOR_HH_
+#define AKANTU_SOLVER_VECTOR_HH_
namespace akantu {
class DOFManager;
}
namespace akantu {
class SolverVector {
public:
SolverVector(DOFManager & dof_manager, const ID & id = "solver_vector")
: id(id), _dof_manager(dof_manager) {}
SolverVector(const SolverVector & vector, const ID & id = "solver_vector")
: id(id), _dof_manager(vector._dof_manager) {}
virtual ~SolverVector() = default;
// resize the vector to the size of the problem
virtual void resize() = 0;
// clear the vector
- virtual void clear() = 0;
+ virtual void set(Real val) = 0;
+ void zero() { this->set({}); }
virtual operator const Array<Real> &() const = 0;
virtual Int size() const = 0;
virtual Int localSize() const = 0;
virtual SolverVector & operator+(const SolverVector & y) = 0;
virtual SolverVector & operator=(const SolverVector & y) = 0;
UInt & release() { return release_; }
UInt release() const { return release_; }
virtual void printself(std::ostream & stream, int indent = 0) const = 0;
protected:
ID id;
/// Underlying dof manager
DOFManager & _dof_manager;
UInt release_{0};
};
inline std::ostream & operator<<(std::ostream & stream, SolverVector & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
-#endif /* __AKANTU_SOLVER_VECTOR_HH__ */
+#endif /* AKANTU_SOLVER_VECTOR_HH_ */
diff --git a/src/solver/solver_vector_default.hh b/src/solver/solver_vector_default.hh
index 4368e7b4f..915d5a4d3 100644
--- a/src/solver/solver_vector_default.hh
+++ b/src/solver/solver_vector_default.hh
@@ -1,140 +1,140 @@
/**
* @file solver_vector_default.hh
*
* @author Nicolas Richart
*
* @date creation Tue Jan 01 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solver_vector.hh"
/* -------------------------------------------------------------------------- */
#include <utility>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLVER_VECTOR_DEFAULT_HH__
-#define __AKANTU_SOLVER_VECTOR_DEFAULT_HH__
+#ifndef AKANTU_SOLVER_VECTOR_DEFAULT_HH_
+#define AKANTU_SOLVER_VECTOR_DEFAULT_HH_
namespace akantu {
class DOFManagerDefault;
} // namespace akantu
namespace akantu {
class SolverVectorArray : public SolverVector {
public:
SolverVectorArray(DOFManagerDefault & dof_manager, const ID & id);
SolverVectorArray(const SolverVectorArray & vector, const ID & id);
- virtual ~SolverVectorArray() = default;
+ ~SolverVectorArray() override = default;
virtual Array<Real> & getVector() = 0;
virtual const Array<Real> & getVector() const = 0;
void printself(std::ostream & stream, int indent = 0) const override {
std::string space(indent, AKANTU_INDENT);
stream << space << "SolverVectorArray [" << std::endl;
stream << space << " + id: " << id << std::endl;
this->getVector().printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
};
/* -------------------------------------------------------------------------- */
template <class Array_> class SolverVectorArrayTmpl : public SolverVectorArray {
public:
SolverVectorArrayTmpl(DOFManagerDefault & dof_manager, Array_ & vector,
const ID & id = "solver_vector_default")
: SolverVectorArray(dof_manager, id), dof_manager(dof_manager),
vector(vector) {}
template <class A = Array_,
std::enable_if_t<not std::is_reference<A>::value> * = nullptr>
SolverVectorArrayTmpl(DOFManagerDefault & dof_manager,
const ID & id = "solver_vector_default")
: SolverVectorArray(dof_manager, id), dof_manager(dof_manager),
vector(0, 1, id + ":vector") {}
SolverVectorArrayTmpl(const SolverVectorArrayTmpl & vector,
const ID & id = "solver_vector_default")
: SolverVectorArray(vector, id), dof_manager(vector.dof_manager),
vector(vector.vector) {}
operator const Array<Real> &() const override { return getVector(); };
virtual operator Array<Real> &() { return getVector(); };
SolverVector & operator+(const SolverVector & y) override;
SolverVector & operator=(const SolverVector & y) override;
void resize() override {
static_assert(not std::is_const<std::remove_reference_t<Array_>>::value,
"Cannot resize a const Array");
this->vector.resize(this->localSize(), 0.);
++this->release_;
}
- void clear() override {
- static_assert(not std::is_const<std::remove_reference_t<Array_>>::value,
+ void set(Real val) override {
+ static_assert(not std::is_const<std::remove_reference_t<Array_>>::value,
"Cannot clear a const Array");
- this->vector.clear();
+ this->vector.set(val);
++this->release_;
}
public:
Array<Real> & getVector() override { return vector; }
const Array<Real> & getVector() const override { return vector; }
Int size() const override;
Int localSize() const override;
virtual Array<Real> & getGlobalVector() { return this->vector; }
virtual void setGlobalVector(const Array<Real> & solution) {
this->vector.copy(solution);
}
protected:
DOFManagerDefault & dof_manager;
Array_ vector;
template <class A> friend class SolverVectorArrayTmpl;
};
/* -------------------------------------------------------------------------- */
using SolverVectorDefault = SolverVectorArrayTmpl<Array<Real>>;
/* -------------------------------------------------------------------------- */
template <class Array>
using SolverVectorDefaultWrap = SolverVectorArrayTmpl<Array &>;
template <class Array>
decltype(auto) make_solver_vector_default_wrap(DOFManagerDefault & dof_manager,
Array & vector) {
return SolverVectorDefaultWrap<Array>(dof_manager, vector);
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "solver_vector_default_tmpl.hh"
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_SOLVER_VECTOR_DEFAULT_HH__ */
+#endif /* AKANTU_SOLVER_VECTOR_DEFAULT_HH_ */
diff --git a/src/solver/solver_vector_default_tmpl.hh b/src/solver/solver_vector_default_tmpl.hh
index 22b14cdca..6e2cdb9cb 100644
--- a/src/solver/solver_vector_default_tmpl.hh
+++ b/src/solver/solver_vector_default_tmpl.hh
@@ -1,83 +1,83 @@
/**
* @file solver_vector_default_tmpl.hh
*
* @author Nicolas Richart
*
* @date creation Tue Jan 01 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
#include "solver_vector_default.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLVER_VECTOR_DEFAULT_TMPL_HH__
-#define __AKANTU_SOLVER_VECTOR_DEFAULT_TMPL_HH__
+#ifndef AKANTU_SOLVER_VECTOR_DEFAULT_TMPL_HH_
+#define AKANTU_SOLVER_VECTOR_DEFAULT_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline SolverVectorArray::SolverVectorArray(DOFManagerDefault & dof_manager,
const ID & id)
: SolverVector(dof_manager, id) {}
/* -------------------------------------------------------------------------- */
inline SolverVectorArray::SolverVectorArray(const SolverVectorArray & vector,
const ID & id)
: SolverVector(vector, id) {}
/* -------------------------------------------------------------------------- */
template <class Array_>
SolverVector & SolverVectorArrayTmpl<Array_>::
operator+(const SolverVector & y) {
const auto & y_ = aka::as_type<SolverVectorArray>(y);
this->vector += y_.getVector();
++this->release_;
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Array_>
SolverVector & SolverVectorArrayTmpl<Array_>::
operator=(const SolverVector & y) {
const auto & y_ = aka::as_type<SolverVectorArray>(y);
this->vector.copy(y_.getVector());
this->release_ = y.release();
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Array_> inline Int SolverVectorArrayTmpl<Array_>::size() const {
return this->dof_manager.getSystemSize();
}
/* -------------------------------------------------------------------------- */
template <class Array_>
inline Int SolverVectorArrayTmpl<Array_>::localSize() const {
return dof_manager.getLocalSystemSize();
}
} // namespace akantu
-#endif /* __AKANTU_SOLVER_VECTOR_DEFAULT_TMPL_HH__ */
+#endif /* AKANTU_SOLVER_VECTOR_DEFAULT_TMPL_HH_ */
diff --git a/src/solver/solver_vector_distributed.hh b/src/solver/solver_vector_distributed.hh
index 9e8a71ef5..d2c2d3c05 100644
--- a/src/solver/solver_vector_distributed.hh
+++ b/src/solver/solver_vector_distributed.hh
@@ -1,55 +1,55 @@
/**
* @file solver_vector_distributed.hh
*
* @author Nicolas Richart
*
* @date creation Tue Jan 01 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solver_vector_default.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLVER_VECTOR_DISTRIBUTED_HH__
-#define __AKANTU_SOLVER_VECTOR_DISTRIBUTED_HH__
+#ifndef AKANTU_SOLVER_VECTOR_DISTRIBUTED_HH_
+#define AKANTU_SOLVER_VECTOR_DISTRIBUTED_HH_
namespace akantu {
class SolverVectorDistributed : public SolverVectorDefault {
public:
SolverVectorDistributed(DOFManagerDefault & dof_manager,
const ID & id = "solver_vector_mumps");
SolverVectorDistributed(const SolverVectorDefault & vector,
const ID & id = "solver_vector_mumps");
Array<Real> & getGlobalVector() override;
- void setGlobalVector(const Array<Real> & global_vector) override;
+ void setGlobalVector(const Array<Real> & solution) override;
protected:
// full vector in case it needs to be centralized on master
std::unique_ptr<Array<Real>> global_vector;
};
} // namespace akantu
-#endif /* __AKANTU_SOLVER_VECTOR_DISTRIBUTED_HH__ */
+#endif /* AKANTU_SOLVER_VECTOR_DISTRIBUTED_HH_ */
diff --git a/src/solver/solver_vector_petsc.cc b/src/solver/solver_vector_petsc.cc
index b21dafa81..ec791614e 100644
--- a/src/solver/solver_vector_petsc.cc
+++ b/src/solver/solver_vector_petsc.cc
@@ -1,286 +1,289 @@
/**
* @file solver_vector_petsc.cc
*
* @author Nicolas Richart
*
* @date creation Tue Jan 01 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solver_vector_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
#include <petscvec.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::SolverVectorPETSc(DOFManagerPETSc & dof_manager,
const ID & id)
: SolverVector(dof_manager, id), dof_manager(dof_manager) {
auto && mpi_comm = dof_manager.getMPIComm();
PETSc_call(VecCreate, mpi_comm, &x);
detail::PETScSetName(x, id);
PETSc_call(VecSetFromOptions, x);
auto local_system_size = dof_manager.getLocalSystemSize();
auto nb_local_dofs = dof_manager.getPureLocalSystemSize();
PETSc_call(VecSetSizes, x, nb_local_dofs, PETSC_DECIDE);
VecType vec_type;
PETSc_call(VecGetType, x, &vec_type);
if (std::string(vec_type) == std::string(VECMPI)) {
- PetscInt lowest_gidx, highest_gidx;
+ PetscInt lowest_gidx;
+ PetscInt highest_gidx;
PETSc_call(VecGetOwnershipRange, x, &lowest_gidx, &highest_gidx);
std::vector<PetscInt> ghost_idx;
for (auto && d : arange(local_system_size)) {
int gidx = dof_manager.localToGlobalEquationNumber(d);
if (gidx != -1) {
if ((gidx < lowest_gidx) or (gidx >= highest_gidx)) {
ghost_idx.push_back(gidx);
}
}
}
PETSc_call(VecMPISetGhost, x, ghost_idx.size(), ghost_idx.data());
} else {
std::vector<int> idx(nb_local_dofs);
std::iota(idx.begin(), idx.end(), 0);
ISLocalToGlobalMapping is;
PETSc_call(ISLocalToGlobalMappingCreate, PETSC_COMM_SELF, 1, idx.size(),
idx.data(), PETSC_COPY_VALUES, &is);
PETSc_call(VecSetLocalToGlobalMapping, x, is);
PETSc_call(ISLocalToGlobalMappingDestroy, &is);
}
}
/* -------------------------------------------------------------------------- */
-SolverVectorPETSc::SolverVectorPETSc(const SolverVectorPETSc & vector,
- const ID & id)
+SolverVectorPETSc::SolverVectorPETSc( // NOLINT(bugprone-copy-constructor-init)
+ const SolverVectorPETSc & vector, const ID & id)
: SolverVector(vector, id), dof_manager(vector.dof_manager) {
- if (vector.x) {
+ if (vector.x != nullptr) {
PETSc_call(VecDuplicate, vector.x, &x);
PETSc_call(VecCopy, vector.x, x);
detail::PETScSetName(x, id);
}
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "SolverVectorPETSc [" << std::endl;
stream << space << " + id: " << id << std::endl;
PETSc_call(PetscViewerPushFormat, PETSC_VIEWER_STDOUT_WORLD,
PETSC_VIEWER_ASCII_INDEX);
PETSc_call(VecView, x, PETSC_VIEWER_STDOUT_WORLD);
PETSc_call(PetscViewerPopFormat, PETSC_VIEWER_STDOUT_WORLD);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::SolverVectorPETSc(Vec x, DOFManagerPETSc & dof_manager,
const ID & id)
: SolverVector(dof_manager, id), dof_manager(dof_manager) {
PETSc_call(VecDuplicate, x, &this->x);
PETSc_call(VecCopy, x, this->x);
detail::PETScSetName(x, id);
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::~SolverVectorPETSc() {
- if (x) {
+ if (x != nullptr) {
PETSc_call(VecDestroy, &x);
}
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::resize() {
// the arrays are destroyed and recreated in the dof manager
// resize is so not implemented
}
/* -------------------------------------------------------------------------- */
-void SolverVectorPETSc::clear() {
- PETSc_call(VecSet, x, 0.);
+void SolverVectorPETSc::set(Real val) {
+ PETSc_call(VecSet, x, val);
applyModifications();
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::applyModifications() {
PETSc_call(VecAssemblyBegin, x);
PETSc_call(VecAssemblyEnd, x);
updateGhost();
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::updateGhost() {
Vec x_ghosted{nullptr};
PETSc_call(VecGhostGetLocalForm, x, &x_ghosted);
- if (x_ghosted) {
+ if (x_ghosted != nullptr) {
PETSc_call(VecGhostUpdateBegin, x, INSERT_VALUES, SCATTER_FORWARD);
PETSc_call(VecGhostUpdateEnd, x, INSERT_VALUES, SCATTER_FORWARD);
}
PETSc_call(VecGhostRestoreLocalForm, x, &x_ghosted);
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::getValues(const Array<Int> & idx,
Array<Real> & values) const {
- if (idx.size() == 0)
+ if (idx.empty()) {
return;
+ }
ISLocalToGlobalMapping is_ltog_map;
PETSc_call(VecGetLocalToGlobalMapping, x, &is_ltog_map);
PetscInt n;
Array<PetscInt> lidx(idx.size());
PETSc_call(ISGlobalToLocalMappingApply, is_ltog_map, IS_GTOLM_MASK,
idx.size(), idx.storage(), &n, lidx.storage());
getValuesLocal(lidx, values);
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::getValuesLocal(const Array<Int> & idx,
Array<Real> & values) const {
- if (idx.size() == 0)
+ if (idx.empty()) {
return;
+ }
Vec x_ghosted{nullptr};
PETSc_call(VecGhostGetLocalForm, x, &x_ghosted);
// VecScatterBegin(scatter, x, x_local, INSERT_VALUES, SCATTER_FORWARD);
// VecScatterEnd(scatter, x, x_local, INSERT_VALUES, SCATTER_FORWARD);
- if (not x_ghosted) {
+ if (x_ghosted == nullptr) {
const PetscScalar * array;
PETSc_call(VecGetArrayRead, x, &array);
for (auto && data : zip(idx, make_view(values))) {
auto i = std::get<0>(data);
if (i != -1) {
std::get<1>(data) = array[i];
}
}
PETSc_call(VecRestoreArrayRead, x, &array);
return;
}
PETSc_call(VecSetOption, x_ghosted, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE);
PETSc_call(VecGetValues, x_ghosted, idx.size(), idx.storage(),
values.storage());
PETSc_call(VecGhostRestoreLocalForm, x, &x_ghosted);
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::addValues(const Array<Int> & gidx,
const Array<Real> & values,
Real scale_factor) {
Real * to_add = values.storage();
Array<Real> scaled_array;
if (scale_factor != 1.) {
scaled_array.copy(values, false);
scaled_array *= scale_factor;
to_add = scaled_array.storage();
}
PETSc_call(VecSetOption, x, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE);
PETSc_call(VecSetValues, x, gidx.size(), gidx.storage(), to_add, ADD_VALUES);
applyModifications();
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::addValuesLocal(const Array<Int> & lidx,
const Array<Real> & values,
Real scale_factor) {
Vec x_ghosted{nullptr};
PETSc_call(VecGhostGetLocalForm, x, &x_ghosted);
- if (not x_ghosted) {
+ if (x_ghosted == nullptr) {
Real * to_add = values.storage();
Array<Real> scaled_array;
if (scale_factor != 1.) {
scaled_array.copy(values, false);
scaled_array *= scale_factor;
to_add = scaled_array.storage();
}
PETSc_call(VecSetOption, x, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE);
PETSc_call(VecSetValuesLocal, x, lidx.size(), lidx.storage(), to_add,
ADD_VALUES);
return;
}
PETSc_call(VecGhostRestoreLocalForm, x, &x_ghosted);
ISLocalToGlobalMapping is_ltog_map;
PETSc_call(VecGetLocalToGlobalMapping, x, &is_ltog_map);
Array<Int> gidx(lidx.size());
PETSc_call(ISLocalToGlobalMappingApply, is_ltog_map, lidx.size(),
lidx.storage(), gidx.storage());
addValues(gidx, values, scale_factor);
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::operator const Array<Real> &() const {
const_cast<Array<Real> &>(cache).resize(local_size());
auto xl = internal::make_petsc_local_vector(x);
auto cachep = internal::make_petsc_wraped_vector(this->cache);
PETSc_call(VecCopy, cachep, xl);
return cache;
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc & SolverVectorPETSc::operator=(const SolverVectorPETSc & y) {
if (size() != y.size()) {
PETSc_call(VecDuplicate, y, &x);
}
PETSc_call(VecCopy, y.x, x);
release_ = y.release_;
return *this;
}
/* -------------------------------------------------------------------------- */
SolverVector & SolverVectorPETSc::operator=(const SolverVector & y) {
const auto & y_ = aka::as_type<SolverVectorPETSc>(y);
return operator=(y_);
}
/* -------------------------------------------------------------------------- */
SolverVector & SolverVectorPETSc::operator+(const SolverVector & y) {
- auto & y_ = aka::as_type<SolverVectorPETSc>(y);
+ const auto & y_ = aka::as_type<SolverVectorPETSc>(y);
PETSc_call(VecAXPY, x, 1., y_.x);
release_ = y_.release_;
return *this;
}
} // namespace akantu
diff --git a/src/solver/solver_vector_petsc.hh b/src/solver/solver_vector_petsc.hh
index e40ff7ab4..d34999f04 100644
--- a/src/solver/solver_vector_petsc.hh
+++ b/src/solver/solver_vector_petsc.hh
@@ -1,204 +1,204 @@
/**
* @file solver_vector_petsc.hh
*
* @author Nicolas Richart
*
* @date creation Tue Jan 01 2019
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_petsc.hh"
#include "solver_vector.hh"
/* -------------------------------------------------------------------------- */
#include <petscvec.h>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLVER_VECTOR_PETSC_HH__
-#define __AKANTU_SOLVER_VECTOR_PETSC_HH__
+#ifndef AKANTU_SOLVER_VECTOR_PETSC_HH_
+#define AKANTU_SOLVER_VECTOR_PETSC_HH_
namespace akantu {
class DOFManagerPETSc;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
namespace internal {
/* ------------------------------------------------------------------------ */
class PETScVector {
public:
virtual ~PETScVector() = default;
operator Vec &() { return x; }
operator const Vec &() const { return x; }
Int size() const {
PetscInt n;
PETSc_call(VecGetSize, x, &n);
return n;
}
Int local_size() const {
PetscInt n;
PETSc_call(VecGetLocalSize, x, &n);
return n;
}
AKANTU_GET_MACRO_NOT_CONST(Vec, x, auto &);
AKANTU_GET_MACRO(Vec, x, const auto &);
protected:
Vec x{nullptr};
};
} // namespace internal
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class SolverVectorPETSc : public SolverVector, public internal::PETScVector {
public:
SolverVectorPETSc(DOFManagerPETSc & dof_manager,
const ID & id = "solver_vector_petsc");
SolverVectorPETSc(const SolverVectorPETSc & vector,
const ID & id = "solver_vector_petsc");
- SolverVectorPETSc(Vec vec, DOFManagerPETSc & dof_manager,
+ SolverVectorPETSc(Vec x, DOFManagerPETSc & dof_manager,
const ID & id = "solver_vector_petsc");
~SolverVectorPETSc() override;
// resize the vector to the size of the problem
void resize() override;
- void clear() override;
+ void set(Real val) override;
operator const Array<Real> &() const override;
SolverVector & operator+(const SolverVector & y) override;
SolverVector & operator=(const SolverVector & y) override;
SolverVectorPETSc & operator=(const SolverVectorPETSc & y);
/// get values using processors global indexes
void getValues(const Array<Int> & idx, Array<Real> & values) const;
/// get values using processors local indexes
void getValuesLocal(const Array<Int> & idx, Array<Real> & values) const;
/// adding values to the vector using the global indices
void addValues(const Array<Int> & gidx, const Array<Real> & values,
Real scale_factor = 1.);
/// adding values to the vector using the local indices
void addValuesLocal(const Array<Int> & lidx, const Array<Real> & values,
Real scale_factor = 1.);
Int size() const override { return internal::PETScVector::size(); }
Int localSize() const override { return internal::PETScVector::local_size(); }
void printself(std::ostream & stream, int indent = 0) const override;
protected:
void applyModifications();
void updateGhost();
protected:
DOFManagerPETSc & dof_manager;
// used for the conversion operator
Array<Real> cache;
};
/* -------------------------------------------------------------------------- */
namespace internal {
/* ------------------------------------------------------------------------ */
template <class Array> class PETScWrapedVector : public PETScVector {
public:
PETScWrapedVector(Array && array) : array(array) {
PETSc_call(VecCreateSeqWithArray, PETSC_COMM_SELF, 1, array.size(),
array.storage(), &x);
}
- ~PETScWrapedVector() { PETSc_call(VecDestroy, &x); }
+ ~PETScWrapedVector() override { PETSc_call(VecDestroy, &x); }
private:
Array array;
};
/* ------------------------------------------------------------------------ */
template <bool read_only> class PETScLocalVector : public PETScVector {
public:
PETScLocalVector(const Vec & g) : g(g) {
PETSc_call(VecGetLocalVectorRead, g, x);
}
PETScLocalVector(const SolverVectorPETSc & g)
: PETScLocalVector(g.getVec()) {}
- ~PETScLocalVector() {
+ ~PETScLocalVector() override {
PETSc_call(VecRestoreLocalVectorRead, g, x);
PETSc_call(VecDestroy, &x);
}
private:
const Vec & g;
};
template <> class PETScLocalVector<false> : public PETScVector {
public:
PETScLocalVector(Vec & g) : g(g) {
PETSc_call(VecGetLocalVectorRead, g, x);
}
PETScLocalVector(SolverVectorPETSc & g) : PETScLocalVector(g.getVec()) {}
- ~PETScLocalVector() {
+ ~PETScLocalVector() override {
PETSc_call(VecRestoreLocalVectorRead, g, x);
PETSc_call(VecDestroy, &x);
}
private:
Vec & g;
};
/* ------------------------------------------------------------------------ */
template <class Array>
decltype(auto) make_petsc_wraped_vector(Array && array) {
return PETScWrapedVector<Array>(std::forward<Array>(array));
}
template <
typename V,
std::enable_if_t<std::is_same<Vec, std::decay_t<V>>::value> * = nullptr>
decltype(auto) make_petsc_local_vector(V && vec) {
constexpr auto read_only = std::is_const<std::remove_reference_t<V>>::value;
return PETScLocalVector<read_only>(vec);
}
template <typename V, std::enable_if_t<std::is_base_of<
SolverVector, std::decay_t<V>>::value> * = nullptr>
decltype(auto) make_petsc_local_vector(V && vec) {
constexpr auto read_only = std::is_const<std::remove_reference_t<V>>::value;
return PETScLocalVector<read_only>(
dynamic_cast<std::conditional_t<read_only, const SolverVectorPETSc,
SolverVectorPETSc> &>(vec));
}
} // namespace internal
} // namespace akantu
-#endif /* __AKANTU_SOLVER_VECTOR_PETSC_HH__ */
+#endif /* AKANTU_SOLVER_VECTOR_PETSC_HH_ */
diff --git a/src/solver/sparse_matrix.hh b/src/solver/sparse_matrix.hh
index b65a88853..3e2fa09d4 100644
--- a/src/solver/sparse_matrix.hh
+++ b/src/solver/sparse_matrix.hh
@@ -1,161 +1,163 @@
/**
* @file sparse_matrix.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Tue Feb 20 2018
*
* @brief sparse matrix storage class (distributed assembled matrix)
* This is a COO format (Coordinate List)
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SPARSE_MATRIX_HH__
-#define __AKANTU_SPARSE_MATRIX_HH__
+#ifndef AKANTU_SPARSE_MATRIX_HH_
+#define AKANTU_SPARSE_MATRIX_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManager;
class TermsToAssemble;
class SolverVector;
} // namespace akantu
namespace akantu {
class SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrix(DOFManager & dof_manager, const MatrixType & matrix_type,
const ID & id = "sparse_matrix");
SparseMatrix(const SparseMatrix & matrix, const ID & id = "sparse_matrix");
virtual ~SparseMatrix();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
virtual void clearProfile();
/// set the matrix to 0
- virtual void clear() = 0;
+ virtual void set(Real val) = 0;
+
+ virtual void zero() { this->set(0); }
/// add a non-zero element to the profile
virtual UInt add(UInt i, UInt j) = 0;
/// assemble a local matrix in the sparse one
virtual void add(UInt i, UInt j, Real value) = 0;
/// save the profil in a file using the MatrixMarket file format
virtual void saveProfile(const std::string & /* filename */) const {
AKANTU_TO_IMPLEMENT();
}
/// save the matrix in a file using the MatrixMarket file format
virtual void saveMatrix(const std::string & /* filename */) const {
AKANTU_TO_IMPLEMENT();
};
/// multiply the matrix by a coefficient
virtual void mul(Real alpha) = 0;
/// add matrices
- virtual void add(const SparseMatrix & matrix, Real alpha = 1.);
+ virtual void add(const SparseMatrix & B, Real alpha = 1.);
/// Equivalent of *gemv in blas
virtual void matVecMul(const SolverVector & x, SolverVector & y,
Real alpha = 1., Real beta = 0.) const = 0;
/// modify the matrix to "remove" the blocked dof
virtual void applyBoundary(Real block_val = 1.) = 0;
/// copy the profile of another matrix
virtual void copyProfile(const SparseMatrix & other) = 0;
/// operator *=
SparseMatrix & operator*=(Real alpha) {
this->mul(alpha);
return *this;
}
protected:
/// This is the revert of add \f[B += \alpha * *this\f];
virtual void addMeTo(SparseMatrix & B, Real alpha) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the values at potition i, j
virtual inline Real operator()(UInt /*i*/, UInt /*j*/) const {
AKANTU_TO_IMPLEMENT();
}
/// return the values at potition i, j
virtual inline Real & operator()(UInt /*i*/, UInt /*j*/) {
AKANTU_TO_IMPLEMENT();
}
AKANTU_GET_MACRO(NbNonZero, nb_non_zero, UInt);
UInt size() const { return size_; }
AKANTU_GET_MACRO(MatrixType, matrix_type, const MatrixType &);
virtual UInt getRelease() const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ID id;
/// Underlying dof manager
DOFManager & _dof_manager;
/// sparce matrix type
MatrixType matrix_type;
/// Size of the matrix
UInt size_;
/// number of processors
UInt nb_proc;
/// number of non zero element
UInt nb_non_zero;
};
// Array<Real> & operator*=(Array<Real> & vect, const SparseMatrix & mat);
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_inline_impl.hh"
-#endif /* __AKANTU_SPARSE_MATRIX_HH__ */
+#endif /* AKANTU_SPARSE_MATRIX_HH_ */
diff --git a/src/solver/sparse_matrix_aij.cc b/src/solver/sparse_matrix_aij.cc
index c9855c00d..c6551625a 100644
--- a/src/solver/sparse_matrix_aij.cc
+++ b/src/solver/sparse_matrix_aij.cc
@@ -1,293 +1,300 @@
/**
* @file sparse_matrix_aij.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Aug 21 2015
* @date last modification: Mon Dec 04 2017
*
* @brief Implementation of the AIJ sparse matrix
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij.hh"
#include "aka_iterators.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "solver_vector_default.hh"
#include "terms_to_assemble.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::SparseMatrixAIJ(DOFManagerDefault & dof_manager,
const MatrixType & matrix_type, const ID & id)
: SparseMatrix(dof_manager, matrix_type, id), dof_manager(dof_manager),
irn(0, 1, id + ":irn"), jcn(0, 1, id + ":jcn"), a(0, 1, id + ":a") {}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::SparseMatrixAIJ(const SparseMatrixAIJ & matrix, const ID & id)
: SparseMatrix(matrix, id), dof_manager(matrix.dof_manager),
irn(matrix.irn, id + ":irn"), jcn(matrix.jcn, id + ":jcn"),
a(matrix.a, id + ":a") {}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::~SparseMatrixAIJ() = default;
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::applyBoundary(Real block_val) {
AKANTU_DEBUG_IN();
const auto & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
auto begin = blocked_dofs.begin();
auto end = blocked_dofs.end();
auto is_blocked = [&](auto && i) -> bool {
auto il = this->dof_manager.globalToLocalEquationNumber(i);
return std::binary_search(begin, end, il);
};
for (auto && ij_a : zip(irn, jcn, a)) {
UInt ni = std::get<0>(ij_a) - 1;
UInt nj = std::get<1>(ij_a) - 1;
if (is_blocked(ni) or is_blocked(nj)) {
std::get<2>(ij_a) =
std::get<0>(ij_a) != std::get<1>(ij_a)
? 0.
: this->dof_manager.isLocalOrMasterDOF(
this->dof_manager.globalToLocalEquationNumber(ni))
? block_val
: 0.;
}
}
this->value_release++;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::saveProfile(const std::string & filename) const {
AKANTU_DEBUG_IN();
std::ofstream outfile;
outfile.open(filename.c_str());
UInt m = this->size_;
auto & comm = dof_manager.getCommunicator();
// write header
if (comm.whoAmI() == 0) {
outfile << "%%MatrixMarket matrix coordinate pattern";
- if (this->matrix_type == _symmetric)
+ if (this->matrix_type == _symmetric) {
outfile << " symmetric";
- else
+ } else {
outfile << " general";
+ }
outfile << std::endl;
outfile << m << " " << m << " " << this->nb_non_zero << std::endl;
}
for (auto p : arange(comm.getNbProc())) {
// write content
if (comm.whoAmI() == p) {
for (UInt i = 0; i < this->nb_non_zero; ++i) {
outfile << this->irn.storage()[i] << " " << this->jcn.storage()[i]
<< " 1" << std::endl;
}
}
comm.barrier();
}
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
auto & comm = dof_manager.getCommunicator();
// open and set the properties of the stream
std::ofstream outfile;
if (0 == comm.whoAmI()) {
outfile.open(filename.c_str());
} else {
outfile.open(filename.c_str(), std::ios_base::app);
}
outfile.precision(std::numeric_limits<Real>::digits10);
// write header
decltype(nb_non_zero) nnz = this->nb_non_zero;
comm.allReduce(nnz);
if (comm.whoAmI() == 0) {
outfile << "%%MatrixMarket matrix coordinate real";
- if (this->matrix_type == _symmetric)
+ if (this->matrix_type == _symmetric) {
outfile << " symmetric";
- else
+ } else {
outfile << " general";
+ }
outfile << std::endl;
outfile << this->size_ << " " << this->size_ << " " << nnz << std::endl;
}
for (auto p : arange(comm.getNbProc())) {
// write content
if (comm.whoAmI() == p) {
for (UInt i = 0; i < this->nb_non_zero; ++i) {
outfile << this->irn(i) << " " << this->jcn(i) << " " << this->a(i)
<< std::endl;
}
}
comm.barrier();
}
// time to end
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::matVecMul(const Array<Real> & x, Array<Real> & y,
Real alpha, Real beta) const {
AKANTU_DEBUG_IN();
y *= beta;
auto i_it = this->irn.begin();
auto j_it = this->jcn.begin();
auto a_it = this->a.begin();
auto a_end = this->a.end();
auto x_it = x.begin_reinterpret(x.size() * x.getNbComponent());
auto y_it = y.begin_reinterpret(x.size() * x.getNbComponent());
for (; a_it != a_end; ++i_it, ++j_it, ++a_it) {
Int i = this->dof_manager.globalToLocalEquationNumber(*i_it - 1);
Int j = this->dof_manager.globalToLocalEquationNumber(*j_it - 1);
const Real & A = *a_it;
y_it[i] += alpha * A * x_it[j];
- if ((this->matrix_type == _symmetric) && (i != j))
+ if ((this->matrix_type == _symmetric) && (i != j)) {
y_it[j] += alpha * A * x_it[i];
+ }
}
- if (this->dof_manager.hasSynchronizer())
+ if (this->dof_manager.hasSynchronizer()) {
this->dof_manager.getSynchronizer().reduceSynchronizeArray<AddOperation>(y);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::matVecMul(const SolverVector & _x, SolverVector & _y,
Real alpha, Real beta) const {
AKANTU_DEBUG_IN();
auto && x = aka::as_type<SolverVectorArray>(_x).getVector();
auto && y = aka::as_type<SolverVectorArray>(_y).getVector();
this->matVecMul(x, y, alpha, beta);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::copyContent(const SparseMatrix & matrix) {
AKANTU_DEBUG_IN();
const auto & mat = aka::as_type<SparseMatrixAIJ>(matrix);
AKANTU_DEBUG_ASSERT(nb_non_zero == mat.getNbNonZero(),
"The to matrix don't have the same profiles");
memcpy(a.storage(), mat.getA().storage(), nb_non_zero * sizeof(Real));
this->value_release++;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::copyProfile(const SparseMatrix & other) {
- auto & A = aka::as_type<SparseMatrixAIJ>(other);
+ const auto & A = aka::as_type<SparseMatrixAIJ>(other);
SparseMatrix::clearProfile();
this->irn.copy(A.irn);
this->jcn.copy(A.jcn);
this->irn_jcn_k.clear();
- UInt i, j, k;
+ UInt i;
+ UInt j;
+ UInt k;
for (auto && data : enumerate(irn, jcn)) {
std::tie(k, i, j) = data;
this->irn_jcn_k[this->key(i - 1, j - 1)] = k;
}
this->nb_non_zero = this->irn.size();
this->a.resize(this->nb_non_zero);
this->a.set(0.);
this->size_ = A.size_;
this->profile_release = A.profile_release;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
template <class MatrixType>
void SparseMatrixAIJ::addMeToTemplated(MatrixType & B, Real alpha) const {
- UInt i, j;
+ UInt i;
+ UInt j;
Real A_ij;
for (auto && tuple : zip(irn, jcn, a)) {
std::tie(i, j, A_ij) = tuple;
B.add(i - 1, j - 1, alpha * A_ij);
}
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::addMeTo(SparseMatrix & B, Real alpha) const {
if (aka::is_of_type<SparseMatrixAIJ>(B)) {
this->addMeToTemplated<SparseMatrixAIJ>(aka::as_type<SparseMatrixAIJ>(B),
alpha);
} else {
// this->addMeToTemplated<SparseMatrix>(*this, alpha);
}
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::mul(Real alpha) {
this->a *= alpha;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
-void SparseMatrixAIJ::clear() {
- a.set(0.);
+void SparseMatrixAIJ::set(Real val) {
+ a.set(val);
this->value_release++;
}
} // namespace akantu
diff --git a/src/solver/sparse_matrix_aij.hh b/src/solver/sparse_matrix_aij.hh
index 3523aa669..da344b028 100644
--- a/src/solver/sparse_matrix_aij.hh
+++ b/src/solver/sparse_matrix_aij.hh
@@ -1,197 +1,198 @@
/**
* @file sparse_matrix_aij.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Wed Nov 08 2017
*
* @brief AIJ implementation of the SparseMatrix (this the format used by
* Mumps)
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SPARSE_MATRIX_AIJ_HH__
-#define __AKANTU_SPARSE_MATRIX_AIJ_HH__
+#ifndef AKANTU_SPARSE_MATRIX_AIJ_HH_
+#define AKANTU_SPARSE_MATRIX_AIJ_HH_
namespace akantu {
class DOFManagerDefault;
class TermsToAssemble;
} // namespace akantu
namespace akantu {
class SparseMatrixAIJ : public SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrixAIJ(DOFManagerDefault & dof_manager,
const MatrixType & matrix_type,
const ID & id = "sparse_matrix_aij");
SparseMatrixAIJ(const SparseMatrixAIJ & matrix,
const ID & id = "sparse_matrix_aij");
~SparseMatrixAIJ() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
inline void clearProfile() override;
/// add a non-zero element
inline UInt add(UInt i, UInt j) override;
/// set the matrix to 0
- void clear() override;
+ void set(Real val) override;
/// assemble a local matrix in the sparse one
inline void add(UInt i, UInt j, Real value) override;
/// add a block of values
inline void addValues(const Vector<Int> & is, const Vector<Int> & js,
const Matrix<Real> & values, MatrixType values_type);
/// set the size of the matrix
void resize(UInt size) { this->size_ = size; }
/// modify the matrix to "remove" the blocked dof
void applyBoundary(Real block_val = 1.) override;
/// save the profil in a file using the MatrixMarket file format
void saveProfile(const std::string & filename) const override;
/// save the matrix in a file using the MatrixMarket file format
void saveMatrix(const std::string & filename) const override;
/// copy assuming the profile are the same
virtual void copyContent(const SparseMatrix & matrix);
/// multiply the matrix by a scalar
void mul(Real alpha) override;
/// Equivalent of *gemv in blas
void matVecMul(const SolverVector & x, SolverVector & y, Real alpha = 1.,
Real beta = 0.) const override;
void matVecMul(const Array<Real> & x, Array<Real> & y, Real alpha = 1.,
Real beta = 0.) const;
/// copy the profile of another matrix
void copyProfile(const SparseMatrix & other) override;
/* ------------------------------------------------------------------------ */
/// accessor to A_{ij} - if (i, j) not present it returns 0
inline Real operator()(UInt i, UInt j) const override;
/// accessor to A_{ij} - if (i, j) not present it fails, (i, j) should be
/// first added to the profile
inline Real & operator()(UInt i, UInt j) override;
protected:
void addMeTo(SparseMatrix & B, Real alpha) const override;
inline void addSymmetricValuesToSymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values);
inline void addUnsymmetricValuesToSymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values);
inline void addValuesToUnsymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values);
private:
/// This is just to inline the addToMatrix function
template <class MatrixType>
void addMeToTemplated(MatrixType & B, Real alpha) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(IRN, irn, const Array<Int> &);
AKANTU_GET_MACRO(JCN, jcn, const Array<Int> &);
AKANTU_GET_MACRO(A, a, const Array<Real> &);
/// The release changes at each call of a function that changes the profile,
/// it in increasing but could overflow so it should be checked as
/// (my_release != release) and not as (my_release < release)
AKANTU_GET_MACRO(ProfileRelease, profile_release, UInt);
AKANTU_GET_MACRO(ValueRelease, value_release, UInt);
UInt getRelease() const override { return value_release; }
protected:
using KeyCOO = std::pair<UInt, UInt>;
using coordinate_list_map = std::unordered_map<KeyCOO, UInt>;
/// get the pair corresponding to (i, j)
inline KeyCOO key(UInt i, UInt j) const {
- if (this->matrix_type == _symmetric && (i > j))
+ if (this->matrix_type == _symmetric && (i > j)) {
return std::make_pair(j, i);
+ }
return std::make_pair(i, j);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// row indexes
Array<Int> irn;
/// column indexes
Array<Int> jcn;
/// values : A[k] = Matrix[irn[k]][jcn[k]]
Array<Real> a;
/// Profile release
UInt profile_release{1};
/// Value release
UInt value_release{1};
/// map for (i, j) -> k correspondence
coordinate_list_map irn_jcn_k;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij_inline_impl.hh"
-#endif /* __AKANTU_SPARSE_MATRIX_AIJ_HH__ */
+#endif /* AKANTU_SPARSE_MATRIX_AIJ_HH_ */
diff --git a/src/solver/sparse_matrix_aij_inline_impl.hh b/src/solver/sparse_matrix_aij_inline_impl.hh
index c38609595..397d5eebd 100644
--- a/src/solver/sparse_matrix_aij_inline_impl.hh
+++ b/src/solver/sparse_matrix_aij_inline_impl.hh
@@ -1,188 +1,194 @@
/**
* @file sparse_matrix_aij_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Aug 21 2015
* @date last modification: Wed Nov 08 2017
*
* @brief Implementation of inline functions of SparseMatrixAIJ
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_HH__
-#define __AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_HH__
+#ifndef AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_HH_
+#define AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_HH_
namespace akantu {
inline UInt SparseMatrixAIJ::add(UInt i, UInt j) {
KeyCOO jcn_irn = this->key(i, j);
auto it = this->irn_jcn_k.find(jcn_irn);
- if (!(it == this->irn_jcn_k.end()))
+ if (!(it == this->irn_jcn_k.end())) {
return it->second;
+ }
- if (i + 1 > this->size_)
+ if (i + 1 > this->size_) {
this->size_ = i + 1;
- if (j + 1 > this->size_)
+ }
+ if (j + 1 > this->size_) {
this->size_ = j + 1;
+ }
this->irn.push_back(i + 1);
this->jcn.push_back(j + 1);
this->a.push_back(0.);
this->irn_jcn_k[jcn_irn] = this->nb_non_zero;
(this->nb_non_zero)++;
this->profile_release++;
this->value_release++;
return (this->nb_non_zero - 1);
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::clearProfile() {
SparseMatrix::clearProfile();
this->irn_jcn_k.clear();
- this->irn.resize(0);
- this->jcn.resize(0);
- this->a.resize(0);
+ this->irn.clear();
+ this->jcn.clear();
+ this->a.clear();
this->size_ = 0;
this->nb_non_zero = 0;
this->profile_release++;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::add(UInt i, UInt j, Real value) {
UInt idx = this->add(i, j);
this->a(idx) += value;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
inline Real SparseMatrixAIJ::operator()(UInt i, UInt j) const {
KeyCOO jcn_irn = this->key(i, j);
auto irn_jcn_k_it = this->irn_jcn_k.find(jcn_irn);
- if (irn_jcn_k_it == this->irn_jcn_k.end())
+ if (irn_jcn_k_it == this->irn_jcn_k.end()) {
return 0.;
+ }
return this->a(irn_jcn_k_it->second);
}
/* -------------------------------------------------------------------------- */
inline Real & SparseMatrixAIJ::operator()(UInt i, UInt j) {
KeyCOO jcn_irn = this->key(i, j);
auto irn_jcn_k_it = this->irn_jcn_k.find(jcn_irn);
AKANTU_DEBUG_ASSERT(irn_jcn_k_it != this->irn_jcn_k.end(),
"Couple (i,j) = (" << i << "," << j
<< ") does not exist in the profile");
// it may change the profile so it is considered as a change
this->value_release++;
return this->a(irn_jcn_k_it->second);
}
/* -------------------------------------------------------------------------- */
inline void
SparseMatrixAIJ::addSymmetricValuesToSymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values) {
for (UInt i = 0; i < values.rows(); ++i) {
UInt c_irn = is(i);
if (c_irn < size_) {
for (UInt j = i; j < values.cols(); ++j) {
UInt c_jcn = js(j);
if (c_jcn < size_) {
operator()(c_irn, c_jcn) += values(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void
SparseMatrixAIJ::addUnsymmetricValuesToSymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values) {
for (UInt i = 0; i < values.rows(); ++i) {
UInt c_irn = is(i);
if (c_irn < size_) {
for (UInt j = 0; j < values.cols(); ++j) {
UInt c_jcn = js(j);
if (c_jcn < size_) {
if (c_jcn >= c_irn) {
operator()(c_irn, c_jcn) += values(i, j);
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void
SparseMatrixAIJ::addValuesToUnsymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values) {
for (UInt i = 0; i < values.rows(); ++i) {
UInt c_irn = is(i);
if (c_irn < size_) {
for (UInt j = 0; j < values.cols(); ++j) {
UInt c_jcn = js(j);
if (c_jcn < size_) {
operator()(c_irn, c_jcn) += values(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::addValues(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values,
MatrixType values_type) {
- if (getMatrixType() == _symmetric)
- if (values_type == _symmetric)
+ if (getMatrixType() == _symmetric) {
+ if (values_type == _symmetric) {
this->addSymmetricValuesToSymmetric(is, js, values);
- else
+ } else {
this->addUnsymmetricValuesToSymmetric(is, js, values);
- else
+ }
+ } else {
this->addValuesToUnsymmetric(is, js, values);
+ }
}
} // namespace akantu
-#endif /* __AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_HH__ */
+#endif /* AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_HH_ */
diff --git a/src/solver/sparse_matrix_petsc.cc b/src/solver/sparse_matrix_petsc.cc
index 5b2dbb874..9f857b14d 100644
--- a/src/solver/sparse_matrix_petsc.cc
+++ b/src/solver/sparse_matrix_petsc.cc
@@ -1,284 +1,286 @@
/**
* @file sparse_matrix_petsc.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Sat Feb 03 2018
*
* @brief Implementation of PETSc matrix class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
#include "solver_vector_petsc.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::SparseMatrixPETSc(DOFManagerPETSc & dof_manager,
const MatrixType & matrix_type,
const ID & id)
: SparseMatrix(dof_manager, matrix_type, id), dof_manager(dof_manager) {
AKANTU_DEBUG_IN();
- auto mpi_comm = dof_manager.getMPIComm();
+ auto && mpi_comm = dof_manager.getMPIComm();
PETSc_call(MatCreate, mpi_comm, &mat);
detail::PETScSetName(mat, id);
resize();
PETSc_call(MatSetFromOptions, mat);
PETSc_call(MatSetUp, mat);
PETSc_call(MatSetOption, mat, MAT_ROW_ORIENTED, PETSC_TRUE);
PETSc_call(MatSetOption, mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE);
- if (matrix_type == _symmetric)
+ if (matrix_type == _symmetric) {
PETSc_call(MatSetOption, mat, MAT_SYMMETRIC, PETSC_TRUE);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::SparseMatrixPETSc(const SparseMatrixPETSc & matrix,
const ID & id)
: SparseMatrix(matrix, id), dof_manager(matrix.dof_manager) {
PETSc_call(MatDuplicate, matrix.mat, MAT_COPY_VALUES, &mat);
detail::PETScSetName(mat, id);
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::~SparseMatrixPETSc() {
AKANTU_DEBUG_IN();
- if (mat)
+ if (mat != nullptr) {
PETSc_call(MatDestroy, &mat);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::resize() {
auto local_size = dof_manager.getPureLocalSystemSize();
PETSc_call(MatSetSizes, mat, local_size, local_size, size_, size_);
auto & is_ltog_mapping = dof_manager.getISLocalToGlobalMapping();
PETSc_call(MatSetLocalToGlobalMapping, mat, is_ltog_mapping, is_ltog_mapping);
}
/* -------------------------------------------------------------------------- */
/**
* Method to save the nonzero pattern and the values stored at each position
* @param filename name of the file in which the information will be stored
*/
void SparseMatrixPETSc::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
- auto mpi_comm = dof_manager.getMPIComm();
+ auto && mpi_comm = dof_manager.getMPIComm();
/// create Petsc viewer
PetscViewer viewer;
PETSc_call(PetscViewerASCIIOpen, mpi_comm, filename.c_str(), &viewer);
PETSc_call(PetscViewerPushFormat, viewer, PETSC_VIEWER_ASCII_MATRIXMARKET);
PETSc_call(MatView, mat, viewer);
PETSc_call(PetscViewerPopFormat, viewer);
PETSc_call(PetscViewerDestroy, &viewer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// Equivalent of *gemv in blas
void SparseMatrixPETSc::matVecMul(const SolverVector & _x, SolverVector & _y,
Real alpha, Real beta) const {
- auto & x = aka::as_type<SolverVectorPETSc>(_x);
+ const auto & x = aka::as_type<SolverVectorPETSc>(_x);
auto & y = aka::as_type<SolverVectorPETSc>(_y);
// y = alpha A x + beta y
SolverVectorPETSc w(x, this->id + ":tmp");
// w = A x
if (release == 0) {
PETSc_call(VecZeroEntries, w);
} else {
PETSc_call(MatMult, mat, x, w);
}
if (alpha != 1.) {
// w = alpha w
PETSc_call(VecScale, w, alpha);
}
// y = w + beta y
PETSc_call(VecAYPX, y, beta, w);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addMeToImpl(SparseMatrixPETSc & B, Real alpha) const {
PETSc_call(MatAXPY, B.mat, alpha, mat, SAME_NONZERO_PATTERN);
B.release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addMeTo(SparseMatrix & B, Real alpha) const {
if (aka::is_of_type<SparseMatrixPETSc>(B)) {
auto & B_petsc = aka::as_type<SparseMatrixPETSc>(B);
this->addMeToImpl(B_petsc, alpha);
} else {
AKANTU_TO_IMPLEMENT();
// this->addMeToTemplated<SparseMatrix>(*this, alpha);
}
}
/* -------------------------------------------------------------------------- */
/**
* MatSetValues() generally caches the values. The matrix is ready to
* use only after MatAssemblyBegin() and MatAssemblyEnd() have been
* called. (http://www.mcs.anl.gov/petsc/)
*/
void SparseMatrixPETSc::applyModifications() {
this->beginAssembly();
this->endAssembly();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::beginAssembly() {
PETSc_call(MatAssemblyBegin, mat, MAT_FINAL_ASSEMBLY);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::endAssembly() {
PETSc_call(MatAssemblyEnd, mat, MAT_FINAL_ASSEMBLY);
PETSc_call(MatSetOption, mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_FALSE);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::copyProfile(const SparseMatrix & other) {
- auto & A = aka::as_type<SparseMatrixPETSc>(other);
+ const auto & A = aka::as_type<SparseMatrixPETSc>(other);
MatDestroy(&mat);
MatDuplicate(A.mat, MAT_DO_NOT_COPY_VALUES, &mat);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::applyBoundary(Real block_val) {
AKANTU_DEBUG_IN();
const auto & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
// std::vector<PetscInt> rows;
// for (auto && data : enumerate(blocked)) {
// if (std::get<1>(data)) {
// rows.push_back(std::get<0>(data));
// }
// }
// applyModifications();
static int c = 0;
saveMatrix("before_blocked_" + std::to_string(c) + ".mtx");
PETSc_call(MatZeroRowsColumnsLocal, mat, blocked_dofs.size(),
blocked_dofs.storage(), block_val, nullptr, nullptr);
saveMatrix("after_blocked_" + std::to_string(c) + ".mtx");
++c;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::mul(Real alpha) {
PETSc_call(MatScale, mat, alpha);
this->release++;
}
/* -------------------------------------------------------------------------- */
-void SparseMatrixPETSc::clear() {
+void SparseMatrixPETSc::zero() {
PETSc_call(MatZeroEntries, mat);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::clearProfile() {
SparseMatrix::clearProfile();
PETSc_call(MatResetPreallocation, mat);
PETSc_call(MatSetOption, mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE);
// PETSc_call(MatSetOption, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
// PETSc_call(MatSetOption, MAT_NEW_NONZERO_ALLOCATIONS, PETSC_TRUE);
// PETSc_call(MatSetOption, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
- clear();
+ this->zero();
}
/* -------------------------------------------------------------------------- */
UInt SparseMatrixPETSc::add(UInt i, UInt j) {
PETSc_call(MatSetValue, mat, i, j, 0, ADD_VALUES);
return 0;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::add(UInt i, UInt j, Real val) {
PETSc_call(MatSetValue, mat, i, j, val, ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(UInt i, UInt j) {
PETSc_call(MatSetValueLocal, mat, i, j, 0, ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(UInt i, UInt j, Real val) {
PETSc_call(MatSetValueLocal, mat, i, j, val, ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(const Vector<Int> & rows,
const Vector<Int> & cols,
- const Matrix<Real> & vals) {
+ const Matrix<Real> & values) {
PETSc_call(MatSetValuesLocal, mat, rows.size(), rows.storage(), cols.size(),
- cols.storage(), vals.storage(), ADD_VALUES);
+ cols.storage(), values.storage(), ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addValues(const Vector<Int> & rows,
const Vector<Int> & cols,
- const Matrix<Real> & vals, MatrixType type) {
- if (type == _unsymmetric and matrix_type == _symmetric) {
+ const Matrix<Real> & values, MatrixType values_type) {
+ if (values_type == _unsymmetric and matrix_type == _symmetric) {
PETSc_call(MatSetOption, mat, MAT_SYMMETRIC, PETSC_FALSE);
PETSc_call(MatSetOption, mat, MAT_STRUCTURALLY_SYMMETRIC, PETSC_FALSE);
}
PETSc_call(MatSetValues, mat, rows.size(), rows.storage(), cols.size(),
- cols.storage(), vals.storage(), ADD_VALUES);
+ cols.storage(), values.storage(), ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/solver/sparse_matrix_petsc.hh b/src/solver/sparse_matrix_petsc.hh
index 6f422f609..a52c4f5e3 100644
--- a/src/solver/sparse_matrix_petsc.hh
+++ b/src/solver/sparse_matrix_petsc.hh
@@ -1,158 +1,159 @@
/**
* @file sparse_matrix_petsc.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 06 2018
*
* @brief Interface for PETSc matrices
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PETSC_MATRIX_HH__
-#define __AKANTU_PETSC_MATRIX_HH__
+#ifndef AKANTU_PETSC_MATRIX_HH_
+#define AKANTU_PETSC_MATRIX_HH_
/* -------------------------------------------------------------------------- */
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <petscmat.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManagerPETSc;
}
namespace akantu {
class SparseMatrixPETSc : public SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrixPETSc(DOFManagerPETSc & dof_manager,
const MatrixType & matrix_type,
const ID & id = "sparse_matrix_petsc");
SparseMatrixPETSc(const SparseMatrixPETSc & matrix,
const ID & id = "sparse_matrix_petsc");
- virtual ~SparseMatrixPETSc();
+ ~SparseMatrixPETSc() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set the matrix to 0
- void clear() override;
+ void zero() override;
+ void set(Real /*val*/) override {
+ AKANTU_TO_IMPLEMENT();
+ }
void clearProfile() override;
/// add a non-zero element to the profile
UInt add(UInt i, UInt j) override;
/// assemble a local matrix in the sparse one
void add(UInt i, UInt j, Real value) override;
void addLocal(UInt i, UInt j);
void addLocal(UInt i, UInt j, Real val);
void addLocal(const Vector<Int> & rows, const Vector<Int> & cols,
- const Matrix<Real> & vals);
+ const Matrix<Real> & values);
/// add a block of values
- void addValues(const Vector<Int> & is, const Vector<Int> & js,
+ void addValues(const Vector<Int> & rows, const Vector<Int> & cols,
const Matrix<Real> & values, MatrixType values_type);
/// save the profil in a file using the MatrixMarket file format
// void saveProfile(__attribute__((unused)) const std::string &) const
// override {
// AKANTU_DEBUG_TO_IMPLEMENT();
// }
/// save the matrix in a file using the MatrixMarket file format
void saveMatrix(const std::string & filename) const override;
/// multiply the matrix by a coefficient
void mul(Real alpha) override;
/// Equivalent of *gemv in blas
void matVecMul(const SolverVector & x, SolverVector & y, Real alpha = 1.,
Real beta = 0.) const override;
/// modify the matrix to "remove" the blocked dof
void applyBoundary(Real block_val = 1.) override;
/// copy the profile of a matrix
void copyProfile(const SparseMatrix & other) override;
void applyModifications();
void resize();
protected:
void addMeTo(SparseMatrix & B, Real alpha) const override;
/// This is the specific implementation
void addMeToImpl(SparseMatrixPETSc & B, Real alpha) const;
void beginAssembly();
void endAssembly();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the values at potition i, j
- virtual inline Real operator()(__attribute__((unused)) UInt i,
- __attribute__((unused)) UInt j) const {
+ inline Real operator()(UInt /*i*/, UInt /*j*/) const override {
AKANTU_TO_IMPLEMENT();
}
/// return the values at potition i, j
- virtual inline Real & operator()(__attribute__((unused)) UInt i,
- __attribute__((unused)) UInt j) {
+ inline Real & operator()(UInt /*i*/, UInt /*j*/) override {
AKANTU_TO_IMPLEMENT();
}
- virtual UInt getRelease() const override { return release; };
+ UInt getRelease() const override { return release; };
operator Mat &() { return mat; }
operator const Mat &() const { return mat; }
AKANTU_GET_MACRO(Mat, mat, const Mat &);
AKANTU_GET_MACRO_NOT_CONST(Mat, mat, Mat &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// DOFManagerPETSc that contains the numbering for petsc
DOFManagerPETSc & dof_manager;
/// store the PETSc matrix
Mat mat;
/// matrix release
UInt release{0};
};
} // namespace akantu
-#endif /* __AKANTU_PETSC_MATRIX_HH__ */
+#endif /* AKANTU_PETSC_MATRIX_HH_ */
diff --git a/src/solver/sparse_solver.hh b/src/solver/sparse_solver.hh
index 4653da8e6..99f99006e 100644
--- a/src/solver/sparse_solver.hh
+++ b/src/solver/sparse_solver.hh
@@ -1,129 +1,129 @@
/**
* @file sparse_solver.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 24 2018
*
* @brief interface for solvers
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "communicator_event_handler.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLVER_HH__
-#define __AKANTU_SOLVER_HH__
+#ifndef AKANTU_SOLVER_HH_
+#define AKANTU_SOLVER_HH_
namespace akantu {
enum SolverParallelMethod {
_not_parallel,
_fully_distributed,
_master_slave_distributed
};
class DOFManager;
} // namespace akantu
namespace akantu {
class SparseSolver : protected Memory,
public Parsable,
public CommunicatorEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseSolver(DOFManager & dof_manager, const ID & matrix_id,
const ID & id = "solver", const MemoryID & memory_id = 0);
~SparseSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the solver
virtual void initialize() = 0;
virtual void analysis(){};
virtual void factorize(){};
virtual void solve(){};
protected:
virtual void destroyInternalData(){};
public:
virtual void beforeStaticSolverDestroy();
void createSynchronizerRegistry();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
void onCommunicatorFinalize() override;
// inline virtual UInt getNbDataForDOFs(const Array<UInt> & dofs,
// SynchronizationTag tag) const;
// inline virtual void packDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag) const;
// inline virtual void unpackDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// manager handling the dofs for this SparseMatrix solver
DOFManager & _dof_manager;
/// The id of the associated matrix
ID matrix_id;
/// How to parallelize the solve
SolverParallelMethod parallel_method;
/// Communicator used by the solver
Communicator & communicator;
};
namespace debug {
class SingularMatrixException : public Exception {
public:
SingularMatrixException(const SparseMatrix & matrix)
: Exception("Solver encountered singular matrix"), matrix(matrix) {}
const SparseMatrix & matrix;
};
} // namespace debug
} // namespace akantu
-#endif /* __AKANTU_SOLVER_HH__ */
+#endif /* AKANTU_SOLVER_HH_ */
diff --git a/src/solver/sparse_solver_mumps.cc b/src/solver/sparse_solver_mumps.cc
index d91a1d58e..7a5d5a168 100644
--- a/src/solver/sparse_solver_mumps.cc
+++ b/src/solver/sparse_solver_mumps.cc
@@ -1,452 +1,455 @@
/**
* @file sparse_solver_mumps.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Tue Feb 20 2018
*
* @brief implem of SparseSolverMumps class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*
* @subsection Ctrl_param Control parameters
*
* ICNTL(1),
* ICNTL(2),
* ICNTL(3) : output streams for error, diagnostics, and global messages
*
* ICNTL(4) : verbose level : 0 no message - 4 all messages
*
* ICNTL(5) : type of matrix, 0 assembled, 1 elementary
*
* ICNTL(6) : control the permutation and scaling(default 7) see mumps doc for
* more information
*
* ICNTL(7) : determine the pivot order (default 7) see mumps doc for more
* information
*
* ICNTL(8) : describe the scaling method used
*
* ICNTL(9) : 1 solve A x = b, 0 solve At x = b
*
* ICNTL(10) : number of iterative refinement when NRHS = 1
*
* ICNTL(11) : > 0 return statistics
*
* ICNTL(12) : only used for SYM = 2, ordering strategy
*
* ICNTL(13) :
*
* ICNTL(14) : percentage of increase of the estimated working space
*
* ICNTL(15-17) : not used
*
* ICNTL(18) : only used if ICNTL(5) = 0, 0 matrix centralized, 1 structure on
* host and mumps give the mapping, 2 structure on host and distributed matrix
* for facto, 3 distributed matrix
*
* ICNTL(19) : > 0, Shur complement returned
*
* ICNTL(20) : 0 rhs dense, 1 rhs sparse
*
* ICNTL(21) : 0 solution in rhs, 1 solution distributed in ISOL_loc and SOL_loc
* allocated by user
*
* ICNTL(22) : 0 in-core, 1 out-of-core
*
* ICNTL(23) : maximum memory allocatable by mumps pre proc
*
* ICNTL(24) : controls the detection of "null pivot rows"
*
* ICNTL(25) :
*
* ICNTL(26) :
*
* ICNTL(27) :
*
* ICNTL(28) : 0 automatic choice, 1 sequential analysis, 2 parallel analysis
*
* ICNTL(29) : 0 automatic choice, 1 PT-Scotch, 2 ParMetis
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "solver_vector_default.hh"
#include "sparse_matrix_aij.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// static std::ostream & operator <<(std::ostream & stream, const DMUMPS_STRUC_C
// & _this) {
// stream << "DMUMPS Data [" << std::endl;
// stream << " + job : " << _this.job << std::endl;
// stream << " + par : " << _this.par << std::endl;
// stream << " + sym : " << _this.sym << std::endl;
// stream << " + comm_fortran : " << _this.comm_fortran << std::endl;
// stream << " + nz : " << _this.nz << std::endl;
// stream << " + irn : " << _this.irn << std::endl;
// stream << " + jcn : " << _this.jcn << std::endl;
// stream << " + nz_loc : " << _this.nz_loc << std::endl;
// stream << " + irn_loc : " << _this.irn_loc << std::endl;
// stream << " + jcn_loc : " << _this.jcn_loc << std::endl;
// stream << "]";
// return stream;
// }
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseSolverMumps::SparseSolverMumps(DOFManagerDefault & dof_manager,
const ID & matrix_id, const ID & id,
const MemoryID & memory_id)
: SparseSolver(dof_manager, matrix_id, id, memory_id),
dof_manager(dof_manager), master_rhs_solution(0, 1) {
AKANTU_DEBUG_IN();
this->prank = communicator.whoAmI();
#ifdef AKANTU_USE_MPI
this->parallel_method = _fully_distributed;
#else // AKANTU_USE_MPI
this->parallel_method = _not_parallel;
#endif // AKANTU_USE_MPI
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseSolverMumps::~SparseSolverMumps() {
AKANTU_DEBUG_IN();
mumpsDataDestroy();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::mumpsDataDestroy() {
#ifdef AKANTU_USE_MPI
int finalized = 0;
MPI_Finalized(&finalized);
- if (finalized) // Da fuck !?
+ if (finalized != 0) { // Da fuck !?
return;
+ }
#endif
if (this->is_initialized) {
this->mumps_data.job = _smj_destroy; // destroy
dmumps_c(&this->mumps_data);
this->is_initialized = false;
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::destroyInternalData() { mumpsDataDestroy(); }
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::checkInitialized() {
- if (this->is_initialized)
+ if (this->is_initialized) {
return;
+ }
this->initialize();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::setOutputLevel() {
// Output setup
icntl(1) = 0; // error output
icntl(2) = 0; // diagnostics output
icntl(3) = 0; // information
icntl(4) = 0;
#if !defined(AKANTU_NDEBUG)
DebugLevel dbg_lvl = debug::debugger.getDebugLevel();
if (AKANTU_DEBUG_TEST(dblDump)) {
strcpy(this->mumps_data.write_problem, "mumps_matrix.mtx");
}
// clang-format off
icntl(1) = (dbg_lvl >= dblWarning) ? 6 : 0;
icntl(3) = (dbg_lvl >= dblInfo) ? 6 : 0;
icntl(2) = (dbg_lvl >= dblTrace) ? 6 : 0;
icntl(4) =
dbg_lvl >= dblDump ? 4 :
dbg_lvl >= dblTrace ? 3 :
dbg_lvl >= dblInfo ? 2 :
dbg_lvl >= dblWarning ? 1 :
0;
// clang-format on
#endif
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::initMumpsData() {
auto & A = dof_manager.getMatrix(matrix_id);
// Default Scaling
icntl(8) = 77;
// Assembled matrix
icntl(5) = 0;
/// Default centralized dense second member
icntl(20) = 0;
icntl(21) = 0;
// automatic choice for analysis
icntl(28) = 0;
UInt size = A.size();
if (prank == 0) {
this->master_rhs_solution.resize(size);
}
this->mumps_data.nz_alloc = 0;
this->mumps_data.n = size;
switch (this->parallel_method) {
case _fully_distributed:
icntl(18) = 3; // fully distributed
this->mumps_data.nz_loc = A.getNbNonZero();
this->mumps_data.irn_loc = A.getIRN().storage();
this->mumps_data.jcn_loc = A.getJCN().storage();
break;
case _not_parallel:
case _master_slave_distributed:
icntl(18) = 0; // centralized
if (prank == 0) {
this->mumps_data.nz = A.getNbNonZero();
this->mumps_data.irn = A.getIRN().storage();
this->mumps_data.jcn = A.getJCN().storage();
} else {
this->mumps_data.nz = 0;
this->mumps_data.irn = nullptr;
this->mumps_data.jcn = nullptr;
}
break;
default:
AKANTU_ERROR("This case should not happen!!");
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::initialize() {
AKANTU_DEBUG_IN();
this->mumps_data.par = 1; // The host is part of computations
switch (this->parallel_method) {
case _not_parallel:
break;
case _master_slave_distributed:
this->mumps_data.par = 0; // The host is not part of the computations
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it */
case _fully_distributed:
#ifdef AKANTU_USE_MPI
const auto & mpi_data =
aka::as_type<MPICommunicatorData>(communicator.getCommunicatorData());
MPI_Comm mpi_comm = mpi_data.getMPICommunicator();
this->mumps_data.comm_fortran = MPI_Comm_c2f(mpi_comm);
#else
AKANTU_ERROR(
"You cannot use parallel method to solve without activating MPI");
#endif
break;
}
const auto & A = dof_manager.getMatrix(matrix_id);
- this->mumps_data.sym = 2 * (A.getMatrixType() == _symmetric);
+ this->mumps_data.sym = 2 * static_cast<int>(A.getMatrixType() == _symmetric);
this->prank = communicator.whoAmI();
this->setOutputLevel();
this->mumps_data.job = _smj_initialize; // initialize
dmumps_c(&this->mumps_data);
this->setOutputLevel();
this->is_initialized = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::analysis() {
AKANTU_DEBUG_IN();
initMumpsData();
this->mumps_data.job = _smj_analyze; // analyze
dmumps_c(&this->mumps_data);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::factorize() {
AKANTU_DEBUG_IN();
auto & A = dof_manager.getMatrix(matrix_id);
- if (parallel_method == _fully_distributed)
+ if (parallel_method == _fully_distributed) {
this->mumps_data.a_loc = A.getA().storage();
- else {
- if (prank == 0)
+ } else {
+ if (prank == 0) {
this->mumps_data.a = A.getA().storage();
+ }
}
this->mumps_data.job = _smj_factorize; // factorize
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solve(Array<Real> & x, const Array<Real> & b) {
auto & synch = this->dof_manager.getSynchronizer();
if (this->prank == 0) {
this->master_rhs_solution.resize(this->dof_manager.getSystemSize());
synch.gather(b, this->master_rhs_solution);
} else {
synch.gather(b);
}
this->solveInternal();
if (this->prank == 0) {
synch.scatter(x, this->master_rhs_solution);
} else {
synch.scatter(x);
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solve() {
this->master_rhs_solution.copy(
aka::as_type<SolverVectorDefault>(this->dof_manager.getResidual())
.getGlobalVector());
this->solveInternal();
aka::as_type<SolverVectorDefault>(this->dof_manager.getSolution())
.setGlobalVector(this->master_rhs_solution);
this->dof_manager.splitSolutionPerDOFs();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solveInternal() {
AKANTU_DEBUG_IN();
this->checkInitialized();
const auto & A = dof_manager.getMatrix(matrix_id);
this->setOutputLevel();
if (this->last_profile_release != A.getProfileRelease()) {
this->analysis();
this->last_profile_release = A.getProfileRelease();
}
if (AKANTU_DEBUG_TEST(dblDump)) {
A.saveMatrix("solver_mumps" + std::to_string(prank) + ".mtx");
}
if (this->last_value_release != A.getValueRelease()) {
this->factorize();
this->last_value_release = A.getValueRelease();
}
if (prank == 0) {
this->mumps_data.rhs = this->master_rhs_solution.storage();
}
this->mumps_data.job = _smj_solve; // solve
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::printError() {
Vector<Int> _info_v(2);
_info_v[0] = info(1); // to get errors
_info_v[1] = -info(1); // to get warnings
dof_manager.getCommunicator().allReduce(_info_v, SynchronizerOperation::_min);
_info_v[1] = -_info_v[1];
if (_info_v[0] < 0) { // < 0 is an error
switch (_info_v[0]) {
case -10: {
AKANTU_CUSTOM_EXCEPTION(
debug::SingularMatrixException(dof_manager.getMatrix(matrix_id)));
break;
}
case -9: {
icntl(14) += 10;
if (icntl(14) != 90) {
// std::cout << "Dynamic memory increase of 10%" << std::endl;
AKANTU_DEBUG_WARNING("MUMPS dynamic memory is insufficient it will be "
"increased allowed to use 10% more");
// change releases to force a recompute
this->last_value_release--;
this->last_profile_release--;
this->solve();
} else {
AKANTU_ERROR("The MUMPS workarray is too small INFO(2)="
<< info(2) << "No further increase possible");
}
break;
}
default:
AKANTU_ERROR("Error in mumps during solve process, check mumps "
"user guide INFO(1) = "
<< _info_v[1]);
}
} else if (_info_v[1] > 0) {
AKANTU_DEBUG_WARNING("Warning in mumps during solve process, check mumps "
"user guide INFO(1) = "
<< _info_v[1]);
}
}
} // namespace akantu
diff --git a/src/solver/sparse_solver_mumps.hh b/src/solver/sparse_solver_mumps.hh
index fe966bd50..8adfe8845 100644
--- a/src/solver/sparse_solver_mumps.hh
+++ b/src/solver/sparse_solver_mumps.hh
@@ -1,156 +1,156 @@
/**
* @file sparse_solver_mumps.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Solver class implementation for the mumps solver
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_solver.hh"
/* -------------------------------------------------------------------------- */
#include <dmumps_c.h>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SOLVER_MUMPS_HH__
-#define __AKANTU_SOLVER_MUMPS_HH__
+#ifndef AKANTU_SOLVER_MUMPS_HH_
+#define AKANTU_SOLVER_MUMPS_HH_
namespace akantu {
class DOFManagerDefault;
class SparseMatrixAIJ;
} // namespace akantu
namespace akantu {
class SparseSolverMumps : public SparseSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseSolverMumps(DOFManagerDefault & dof_manager, const ID & matrix_id,
const ID & id = "sparse_solver_mumps",
const MemoryID & memory_id = 0);
~SparseSolverMumps() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build the profile and do the analysis part
void initialize() override;
/// analysis (symbolic facto + permutations)
void analysis() override;
/// factorize the matrix
void factorize() override;
/// solve the system
virtual void solve(Array<Real> & x, const Array<Real> & b);
/// solve using residual and solution from the dof_manager
void solve() override;
private:
/// print the error if any happened in mumps
void printError();
/// solve the system with master_rhs_solution as b and x
void solveInternal();
/// set internal values;
void initMumpsData();
/// set the level of verbosity of mumps based on the debug level of akantu
void setOutputLevel();
protected:
/// de-initialize the internal data
void destroyInternalData() override;
/// check if initialized and except if it is not the case
void checkInitialized();
private:
void mumpsDataDestroy();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
private:
/// access the control variable
inline Int & icntl(UInt i) { return mumps_data.icntl[i - 1]; }
/// access the results info
inline Int & info(UInt i) { return mumps_data.info[i - 1]; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// DOFManager used by the Mumps implementation of the SparseSolver
DOFManagerDefault & dof_manager;
/// Full right hand side on the master processors and solution after solve
Array<Real> master_rhs_solution;
/// mumps data
DMUMPS_STRUC_C mumps_data;
/// Rank of the current process
UInt prank;
/// matrix release at last solve
UInt last_profile_release{UInt(-1)};
/// matrix release at last solve
UInt last_value_release{UInt(-1)};
/// check if the solver data are initialized
bool is_initialized{false};
/* ------------------------------------------------------------------------ */
/* Local types */
/* ------------------------------------------------------------------------ */
private:
SolverParallelMethod parallel_method;
// bool rhs_is_local;
enum SolverMumpsJob {
_smj_initialize = -1,
_smj_analyze = 1,
_smj_factorize = 2,
_smj_solve = 3,
_smj_analyze_factorize = 4,
_smj_factorize_solve = 5,
_smj_complete = 6, // analyze, factorize, solve
_smj_destroy = -2
};
};
} // namespace akantu
-#endif /* __AKANTU_SOLVER_MUMPS_HH__ */
+#endif /* AKANTU_SOLVER_MUMPS_HH_ */
diff --git a/src/solver/terms_to_assemble.hh b/src/solver/terms_to_assemble.hh
index bd5f93e8d..bf5227e79 100644
--- a/src/solver/terms_to_assemble.hh
+++ b/src/solver/terms_to_assemble.hh
@@ -1,99 +1,99 @@
/**
* @file terms_to_assemble.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief List of terms to assemble to a matrix
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TERMS_TO_ASSEMBLE_HH__
-#define __AKANTU_TERMS_TO_ASSEMBLE_HH__
+#ifndef AKANTU_TERMS_TO_ASSEMBLE_HH_
+#define AKANTU_TERMS_TO_ASSEMBLE_HH_
namespace akantu {
class TermsToAssemble {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TermsToAssemble() = default;
virtual ~TermsToAssemble() = default;
class TermToAssemble {
public:
TermToAssemble(UInt i, UInt j) : _i(i), _j(j), val(0.) {}
inline TermToAssemble & operator=(Real val) {
this->val = val;
return *this;
}
inline TermToAssemble operator+=(Real val) {
this->val += val;
return *this;
}
inline operator Real() const { return val; }
inline UInt i() const { return _i; }
inline UInt j() const { return _j; }
private:
UInt _i, _j;
Real val;
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline TermToAssemble & operator()(UInt i, UInt j) {
terms.emplace_back(i, j);
return terms.back();
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
private:
using TermsContainer = std::vector<TermToAssemble>;
public:
using const_terms_iterator = TermsContainer::const_iterator;
const_terms_iterator begin() const { return terms.begin(); }
const_terms_iterator end() const { return terms.end(); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
TermsContainer terms;
};
} // namespace akantu
-#endif /* __AKANTU_TERMS_TO_ASSEMBLE_HH__ */
+#endif /* AKANTU_TERMS_TO_ASSEMBLE_HH_ */
diff --git a/src/synchronizer/communication_buffer.hh b/src/synchronizer/communication_buffer.hh
index 0ec160856..5a0a5b98a 100644
--- a/src/synchronizer/communication_buffer.hh
+++ b/src/synchronizer/communication_buffer.hh
@@ -1,180 +1,181 @@
/**
* @file communication_buffer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Buffer for packing and unpacking data
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#include <array>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COMMUNICATION_BUFFER_HH__
-#define __AKANTU_COMMUNICATION_BUFFER_HH__
+#ifndef AKANTU_COMMUNICATION_BUFFER_HH_
+#define AKANTU_COMMUNICATION_BUFFER_HH_
namespace akantu {
template <bool is_static = true> class CommunicationBufferTemplated {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit CommunicationBufferTemplated(UInt size) : buffer(size, 1, char()) {
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
};
CommunicationBufferTemplated() : CommunicationBufferTemplated(0) {}
CommunicationBufferTemplated(const CommunicationBufferTemplated & other) =
delete;
CommunicationBufferTemplated &
operator=(const CommunicationBufferTemplated & other) = delete;
- CommunicationBufferTemplated(CommunicationBufferTemplated && other) = default;
+ CommunicationBufferTemplated(CommunicationBufferTemplated && other) noexcept =
+ default;
virtual ~CommunicationBufferTemplated() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// reset to "empty"
inline void reset();
/// resize the internal buffer do not allocate on dynamic buffers
inline void resize(UInt size);
/// resize the internal buffer allocate always
inline void reserve(UInt size);
/// clear buffer context
- inline void clear();
+ inline void zero();
private:
inline void packResize(UInt size);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline char * storage() { return buffer.storage(); };
inline const char * storage() const { return buffer.storage(); };
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
/// printing tool
- template <typename T> inline std::string extractStream(UInt packet_size);
+ template <typename T> inline std::string extractStream(UInt block_size);
/// packing data
template <typename T>
inline CommunicationBufferTemplated & operator<<(const T & to_pack);
template <typename T>
inline CommunicationBufferTemplated & operator<<(const Vector<T> & to_pack);
template <typename T>
inline CommunicationBufferTemplated & operator<<(const Matrix<T> & to_pack);
template <typename T>
inline CommunicationBufferTemplated &
operator<<(const std::vector<T> & to_pack);
/// unpacking data
template <typename T>
inline CommunicationBufferTemplated & operator>>(T & to_unpack);
template <typename T>
inline CommunicationBufferTemplated & operator>>(Vector<T> & to_unpack);
template <typename T>
inline CommunicationBufferTemplated & operator>>(Matrix<T> & to_unpack);
template <typename T>
inline CommunicationBufferTemplated & operator>>(std::vector<T> & to_unpack);
inline CommunicationBufferTemplated & operator<<(const std::string & to_pack);
inline CommunicationBufferTemplated & operator>>(std::string & to_unpack);
private:
template <typename T> inline void packIterable(T & to_pack);
- template <typename T> inline void unpackIterable(T & to_pack);
+ template <typename T> inline void unpackIterable(T & to_unpack);
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
template <typename T> static inline UInt sizeInBuffer(const T & data);
template <typename T> static inline UInt sizeInBuffer(const Vector<T> & data);
template <typename T> static inline UInt sizeInBuffer(const Matrix<T> & data);
template <typename T>
static inline UInt sizeInBuffer(const std::vector<T> & data);
static inline UInt sizeInBuffer(const std::string & data);
/// return the size in bytes of the stored values
inline UInt getPackedSize() const { return ptr_pack - buffer.storage(); };
/// return the size in bytes of data left to be unpacked
inline UInt getLeftToUnpack() const {
return buffer.size() - (ptr_unpack - buffer.storage());
};
/// return the global size allocated
inline UInt size() const { return buffer.size(); };
/// is the buffer empty
inline bool empty() const {
return (getPackedSize() == 0) and (getLeftToUnpack() == 0);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// current position for packing
char * ptr_pack;
/// current position for unpacking
char * ptr_unpack;
/// storing buffer
Array<char> buffer;
};
using CommunicationBuffer = CommunicationBufferTemplated<true>;
using DynamicCommunicationBuffer = CommunicationBufferTemplated<false>;
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "communication_buffer_inline_impl.hh"
-#endif /* __AKANTU_COMMUNICATION_BUFFER_HH__ */
+#endif /* AKANTU_COMMUNICATION_BUFFER_HH_ */
diff --git a/src/synchronizer/communication_buffer_inline_impl.hh b/src/synchronizer/communication_buffer_inline_impl.hh
index b19470124..80945ee0c 100644
--- a/src/synchronizer/communication_buffer_inline_impl.hh
+++ b/src/synchronizer/communication_buffer_inline_impl.hh
@@ -1,337 +1,328 @@
/**
* @file communication_buffer_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 14 2011
* @date last modification: Wed Nov 08 2017
*
* @brief CommunicationBuffer inline implementation
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
+#include <cstring>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
-inline UInt CommunicationBufferTemplated<is_static>::sizeInBuffer(const T &) {
+inline UInt
+CommunicationBufferTemplated<is_static>::sizeInBuffer(const T & /*unused*/) {
return sizeof(T);
}
template <bool is_static>
template <typename T>
inline UInt
CommunicationBufferTemplated<is_static>::sizeInBuffer(const Vector<T> & data) {
UInt size = data.size() * sizeof(T);
return size;
}
template <bool is_static>
template <typename T>
inline UInt
CommunicationBufferTemplated<is_static>::sizeInBuffer(const Matrix<T> & data) {
UInt size = data.size() * sizeof(T);
return size;
}
template <bool is_static>
template <typename T>
inline UInt CommunicationBufferTemplated<is_static>::sizeInBuffer(
const std::vector<T> & data) {
UInt size = data.size() * sizeof(T) + sizeof(size_t);
return size;
}
template <bool is_static>
inline UInt CommunicationBufferTemplated<is_static>::sizeInBuffer(
const std::string & data) {
UInt size = data.size() * sizeof(std::string::value_type) + sizeof(size_t);
return size;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::packResize(UInt size) {
if (not is_static) {
char * values = buffer.storage();
auto nb_packed = ptr_pack - values;
- if (buffer.size() > nb_packed + size)
+ if (buffer.size() > nb_packed + size) {
return;
+ }
buffer.resize(nb_packed + size);
ptr_pack = buffer.storage() + nb_packed;
ptr_unpack = buffer.storage() + (ptr_unpack - values);
}
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(const T & to_pack) {
UInt size = sizeInBuffer(to_pack);
packResize(size);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_pack + size),
"Packing too much data in the CommunicationBufferTemplated");
- memcpy(ptr_pack, reinterpret_cast<const char *>(&to_pack), size);
+ std::memcpy(ptr_pack, reinterpret_cast<const char *>(&to_pack), size);
ptr_pack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(T & to_unpack) {
UInt size = sizeInBuffer(to_unpack);
alignas(alignof(T)) std::array<char, sizeof(T)> aligned_ptr;
memcpy(aligned_ptr.data(), ptr_unpack, size);
auto * tmp = reinterpret_cast<T *>(aligned_ptr.data());
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_unpack + size),
"Unpacking too much data in the CommunicationBufferTemplated");
to_unpack = *tmp;
// memcpy(reinterpret_cast<char *>(&to_unpack), ptr_unpack, size);
ptr_unpack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
/* Specialization */
/* -------------------------------------------------------------------------- */
/**
* Vector
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(const Vector<T> & to_pack) {
UInt size = sizeInBuffer(to_pack);
packResize(size);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_pack + size),
"Packing too much data in the CommunicationBufferTemplated");
memcpy(ptr_pack, to_pack.storage(), size);
ptr_pack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(Vector<T> & to_unpack) {
UInt size = sizeInBuffer(to_unpack);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_unpack + size),
"Unpacking too much data in the CommunicationBufferTemplated");
memcpy(to_unpack.storage(), ptr_unpack, size);
ptr_unpack += size;
return *this;
}
/**
* Matrix
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(const Matrix<T> & to_pack) {
UInt size = sizeInBuffer(to_pack);
packResize(size);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_pack + size),
"Packing too much data in the CommunicationBufferTemplated");
memcpy(ptr_pack, to_pack.storage(), size);
ptr_pack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(Matrix<T> & to_unpack) {
UInt size = sizeInBuffer(to_unpack);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_unpack + size),
"Unpacking too much data in the CommunicationBufferTemplated");
memcpy(to_unpack.storage(), ptr_unpack, size);
ptr_unpack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline void CommunicationBufferTemplated<is_static>::packIterable(T & to_pack) {
operator<<(size_t(to_pack.size()));
auto it = to_pack.begin();
auto end = to_pack.end();
- for (; it != end; ++it)
+ for (; it != end; ++it) {
operator<<(*it);
+ }
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline void
CommunicationBufferTemplated<is_static>::unpackIterable(T & to_unpack) {
size_t size;
operator>>(size);
to_unpack.resize(size);
auto it = to_unpack.begin();
auto end = to_unpack.end();
- for (; it != end; ++it)
+ for (; it != end; ++it) {
operator>>(*it);
+ }
}
/**
* std::vector<T>
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(
const std::vector<T> & to_pack) {
packIterable(to_pack);
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(
std::vector<T> & to_unpack) {
unpackIterable(to_unpack);
return *this;
}
/**
* std::string
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(
const std::string & to_pack) {
packIterable(to_pack);
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(std::string & to_unpack) {
unpackIterable(to_unpack);
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline std::string
CommunicationBufferTemplated<is_static>::extractStream(UInt block_size) {
std::stringstream str;
auto * ptr = reinterpret_cast<T *>(buffer.storage());
UInt sz = buffer.size() / sizeof(T);
UInt sz_block = block_size / sizeof(T);
UInt n_block = 0;
for (UInt i = 0; i < sz; ++i) {
if (i % sz_block == 0) {
str << std::endl << n_block << " ";
++n_block;
}
str << *ptr << " ";
++ptr;
}
return str.str();
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::resize(UInt size) {
if (!is_static) {
buffer.resize(0, 0);
} else {
buffer.resize(size, 0);
}
reset();
#ifndef AKANTU_NDEBUG
- clear();
+ zero();
#endif
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::reserve(UInt size) {
char * values = buffer.storage();
auto nb_packed = ptr_pack - values;
buffer.resize(size);
ptr_pack = buffer.storage() + nb_packed;
ptr_unpack = buffer.storage() + (ptr_unpack - values);
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
-inline void CommunicationBufferTemplated<is_static>::clear() {
- buffer.clear();
+inline void CommunicationBufferTemplated<is_static>::zero() {
+ buffer.zero();
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::reset() {
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
}
-/* -------------------------------------------------------------------------- */
-// template<bool is_static>
-// inline CommunicationBufferTemplated<is_static> &
-// CommunicationBufferTemplated<is_static>::packMeshData (const MeshData &
-// to_pack, const ElementType & type) {
-
-// UInt size = to_pack.size();
-// operator<<(size);
-// typename std::vector<T>::iterator it = to_pack.begin();
-// typename std::vector<T>::iterator end = to_pack.end();
-// for(;it != end; ++it) operator<<(*it);
-// return *this;
-
-//}
} // namespace akantu
diff --git a/src/synchronizer/communication_descriptor.hh b/src/synchronizer/communication_descriptor.hh
index 245c420a3..78369f0e1 100644
--- a/src/synchronizer/communication_descriptor.hh
+++ b/src/synchronizer/communication_descriptor.hh
@@ -1,153 +1,153 @@
/**
* @file communication_descriptor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 07 2016
* @date last modification: Thu Jan 25 2018
*
* @brief Implementation of the helper classes for the synchronizer
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "communication_request.hh"
#include "communication_tag.hh"
#include "data_accessor.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COMMUNICATION_DESCRIPTOR_HH__
-#define __AKANTU_COMMUNICATION_DESCRIPTOR_HH__
+#ifndef AKANTU_COMMUNICATION_DESCRIPTOR_HH_
+#define AKANTU_COMMUNICATION_DESCRIPTOR_HH_
namespace akantu {
/* ------------------------------------------------------------------------ */
enum CommunicationSendRecv { _send, _recv, _csr_not_defined };
/* -------------------------------------------------------------------------- */
struct CommunicationSRType {
using type = CommunicationSendRecv;
static const type _begin_ = _send;
static const type _end_ = _csr_not_defined;
};
using send_recv_t = safe_enum<CommunicationSRType>;
namespace {
send_recv_t iterate_send_recv{};
}
/* ------------------------------------------------------------------------ */
class Communication {
public:
explicit Communication(const CommunicationSendRecv & type = _csr_not_defined)
: _type(type) {}
Communication(const Communication &) = delete;
Communication & operator=(const Communication &) = delete;
void resize(UInt size) {
this->_size = size;
this->_buffer.resize(size);
}
inline const CommunicationSendRecv & type() const { return this->_type; }
inline const UInt & size() const { return this->_size; }
inline const CommunicationRequest & request() const { return this->_request; }
inline CommunicationRequest & request() { return this->_request; }
inline const CommunicationBuffer & buffer() const { return this->_buffer; }
inline CommunicationBuffer & buffer() { return this->_buffer; }
private:
UInt _size{0};
CommunicationBuffer _buffer;
CommunicationRequest _request;
CommunicationSendRecv _type;
};
template <class Entity> class Communications;
/* ------------------------------------------------------------------------ */
template <class Entity> class CommunicationDescriptor {
public:
CommunicationDescriptor(Communication & communication, Array<Entity> & scheme,
Communications<Entity> & communications,
const SynchronizationTag & tag, UInt proc);
CommunicationDescriptor(const CommunicationDescriptor &) = default;
CommunicationDescriptor &
operator=(const CommunicationDescriptor &) = default;
/// get the quantity of data in the buffer
UInt getNbData() { return communication.size(); }
/// set the quantity of data in the buffer
void setNbData(UInt size) { communication.resize(size); }
/// get the corresponding tag
const SynchronizationTag & getTag() const { return tag; }
/// get the data buffer
CommunicationBuffer & getBuffer();
/// get the corresponding request
CommunicationRequest & getRequest();
/// get the communication scheme
const Array<Entity> & getScheme();
/// reset the buffer before pack or after unpack
void resetBuffer();
/// pack data for entities in the buffer
void packData(const DataAccessor<Entity> & accessor);
/// unpack data for entities from the buffer
void unpackData(DataAccessor<Entity> & accessor);
/// posts asynchronous send requests
void postSend(int hash_id);
/// posts asynchronous receive requests
void postRecv(int hash_id);
/// free the request
void freeRequest();
UInt getProc() { return proc; }
protected:
Communication & communication;
const Array<Entity> & scheme;
Communications<Entity> & communications;
const SynchronizationTag & tag;
UInt proc;
UInt rank;
UInt counter;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "communication_descriptor_tmpl.hh"
-#endif /* __AKANTU_COMMUNICATION_DESCRIPTOR_HH__ */
+#endif /* AKANTU_COMMUNICATION_DESCRIPTOR_HH_ */
diff --git a/src/synchronizer/communication_descriptor_tmpl.hh b/src/synchronizer/communication_descriptor_tmpl.hh
index 16a76d14e..24369fe01 100644
--- a/src/synchronizer/communication_descriptor_tmpl.hh
+++ b/src/synchronizer/communication_descriptor_tmpl.hh
@@ -1,151 +1,151 @@
/**
* @file communication_descriptor_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 07 2016
* @date last modification: Thu Jan 25 2018
*
* @brief implementation of CommunicationDescriptor
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_descriptor.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH__
-#define __AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH__
+#ifndef AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH_
+#define AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Implementations */
/* -------------------------------------------------------------------------- */
template <class Entity>
CommunicationDescriptor<Entity>::CommunicationDescriptor(
Communication & communication, Array<Entity> & scheme,
Communications<Entity> & communications, const SynchronizationTag & tag,
UInt proc)
: communication(communication), scheme(scheme),
communications(communications), tag(tag), proc(proc),
rank(communications.getCommunicator().whoAmI()) {
counter = communications.getCounter(tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
CommunicationBuffer & CommunicationDescriptor<Entity>::getBuffer() {
return communication.buffer();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
CommunicationRequest & CommunicationDescriptor<Entity>::getRequest() {
return communication.request();
}
/* -------------------------------------------------------------------------- */
template <class Entity> void CommunicationDescriptor<Entity>::freeRequest() {
const auto & comm = communications.getCommunicator();
// comm.test(communication.request());
comm.freeCommunicationRequest(communication.request());
communications.decrementPending(tag, communication.type());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
const Array<Entity> & CommunicationDescriptor<Entity>::getScheme() {
return scheme;
}
template <class Entity> void CommunicationDescriptor<Entity>::resetBuffer() {
this->communication.buffer().reset();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::packData(
const DataAccessor<Entity> & accessor) {
AKANTU_DEBUG_ASSERT(
communication.type() == _send,
"Cannot pack data on communication that is not of type _send");
accessor.packData(communication.buffer(), scheme, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::unpackData(
DataAccessor<Entity> & accessor) {
AKANTU_DEBUG_ASSERT(
communication.type() == _recv,
"Cannot unpack data from communication that is not of type _recv");
accessor.unpackData(communication.buffer(), scheme, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::postSend(int hash_id) {
AKANTU_DEBUG_ASSERT(communication.type() == _send,
"Cannot send a communication that is not of type _send");
Tag comm_tag = Tag::genTag(rank, counter, tag, hash_id);
AKANTU_DEBUG_ASSERT(communication.buffer().getPackedSize() ==
communication.size(),
"a problem have been introduced with "
<< "false sent sizes declaration "
<< communication.buffer().getPackedSize()
<< " != " << communication.size());
AKANTU_DEBUG_INFO("Posting send to proc " << proc << " (tag: " << tag << " - "
<< communication.size()
<< " data to send) "
<< " [ " << comm_tag << " ]");
CommunicationRequest & request = communication.request();
request = communications.getCommunicator().asyncSend(communication.buffer(),
proc, comm_tag);
communications.incrementPending(tag, communication.type());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::postRecv(int hash_id) {
AKANTU_DEBUG_ASSERT(communication.type() == _recv,
"Cannot receive data for communication ("
<< communication.type()
<< ")that is not of type _recv");
Tag comm_tag = Tag::genTag(proc, counter, tag, hash_id);
AKANTU_DEBUG_INFO("Posting receive from proc "
<< proc << " (tag: " << tag << " - " << communication.size()
<< " data to receive) "
<< " [ " << comm_tag << " ]");
CommunicationRequest & request = communication.request();
request = communications.getCommunicator().asyncReceive(
communication.buffer(), proc, comm_tag);
communications.incrementPending(tag, communication.type());
}
} // namespace akantu
-#endif /* __AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH__ */
+#endif /* AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH_ */
diff --git a/src/synchronizer/communication_request.hh b/src/synchronizer/communication_request.hh
index 04a64af1b..58e88bd22 100644
--- a/src/synchronizer/communication_request.hh
+++ b/src/synchronizer/communication_request.hh
@@ -1,111 +1,111 @@
/**
* @file communication_request.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Wed Nov 08 2017
*
* @brief empty class just for inheritance
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_REAL_STATIC_COMMUNICATOR_HH__
-#define __AKANTU_REAL_STATIC_COMMUNICATOR_HH__
+#ifndef AKANTU_REAL_STATIC_COMMUNICATOR_HH_
+#define AKANTU_REAL_STATIC_COMMUNICATOR_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
class InternalCommunicationRequest {
public:
InternalCommunicationRequest(UInt source, UInt dest);
virtual ~InternalCommunicationRequest();
virtual void printself(std::ostream & stream, int indent = 0) const;
AKANTU_GET_MACRO(Source, source, UInt);
AKANTU_GET_MACRO(Destination, destination, UInt);
private:
UInt source;
UInt destination;
UInt id;
static UInt counter;
};
/* -------------------------------------------------------------------------- */
class CommunicationRequest {
public:
CommunicationRequest(
std::shared_ptr<InternalCommunicationRequest> request = nullptr)
: request(std::move(request)) {}
virtual ~CommunicationRequest() = default;
virtual void free() { request.reset(); }
void printself(std::ostream & stream, int indent = 0) const {
request->printself(stream, indent);
};
UInt getSource() const { return request->getSource(); }
UInt getDestination() const { return request->getDestination(); }
- bool isFreed() const { return request.get() == nullptr; }
+ bool isFreed() const { return request == nullptr; }
InternalCommunicationRequest & getInternal() { return *request; }
private:
std::shared_ptr<InternalCommunicationRequest> request;
};
/* -------------------------------------------------------------------------- */
class CommunicationStatus {
public:
AKANTU_GET_MACRO(Source, source, Int);
UInt size() const { return size_; }
AKANTU_GET_MACRO(Tag, tag, Int);
AKANTU_SET_MACRO(Source, source, Int);
AKANTU_SET_MACRO(Size, size_, UInt);
AKANTU_SET_MACRO(Tag, tag, Int);
private:
Int source{0};
UInt size_{0};
Int tag{0};
};
/* -------------------------------------------------------------------------- */
/// Datatype to pack pairs for MPI_{MIN,MAX}LOC
template <typename T1, typename T2> struct SCMinMaxLoc {
T1 min_max;
T2 loc;
};
} // namespace akantu
-#endif /* __AKANTU_REAL_STATIC_COMMUNICATOR_HH__ */
+#endif /* AKANTU_REAL_STATIC_COMMUNICATOR_HH_ */
diff --git a/src/synchronizer/communication_tag.hh b/src/synchronizer/communication_tag.hh
index c0c202ed9..caab2255c 100644
--- a/src/synchronizer/communication_tag.hh
+++ b/src/synchronizer/communication_tag.hh
@@ -1,123 +1,126 @@
/**
* @file communication_tag.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 07 2016
* @date last modification: Wed Nov 08 2017
*
* @brief Description of the communication tags
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COMMUNICATION_TAG_HH__
-#define __AKANTU_COMMUNICATION_TAG_HH__
+#ifndef AKANTU_COMMUNICATION_TAG_HH_
+#define AKANTU_COMMUNICATION_TAG_HH_
namespace akantu {
/**
* tag = |__________20_________|___8____|_4_|
* | proc | num mes| ct|
*/
class Tag {
public:
Tag() = default;
Tag(int val) : tag(val) {}
Tag(int val, int hash) : tag(val), hash(hash) {}
operator int() const {
return int(max_tag == 0 ? tag : (uint32_t(tag) % max_tag));
}
/// generates a tag
template <typename CommTag>
static inline Tag genTag(int proc, UInt msg_count, CommTag tag) {
int _tag = ((((proc & 0xFFFFF) << 12) + ((msg_count & 0xFF) << 4) +
((int)tag & 0xF)));
Tag t(_tag);
return t;
}
/// generates a tag and hashes it
template <typename CommTag>
static inline Tag genTag(int proc, UInt msg_count, CommTag tag, int hash) {
Tag t = genTag(proc, msg_count, tag);
t.tag = t.tag ^ hash;
t.hash = hash;
return t;
}
- virtual void printself(std::ostream & stream, int) const {
+ virtual void printself(std::ostream & stream, int /*unused*/) const {
int t = tag;
stream << "TAG(";
- if (hash != 0)
+ if (hash != 0) {
t = t ^ hash;
+ }
stream << (t >> 12) << ":" << (t >> 4 & 0xFF) << ":" << (t & 0xF) << " -> "
<< std::hex << "0x" << int(*this);
- if (hash != 0)
+ if (hash != 0) {
stream << " {hash: 0x" << hash << "}";
- stream << " [0x" << this->max_tag << "]";
+ }
+ stream << " [0x" << max_tag << "]";
stream << ")" << std::dec;
}
enum CommTags : int {
- _SIZES = 1,
- _CONNECTIVITY = 2,
- _DATA = 3,
- _PARTITIONS = 4,
- _NB_NODES = 5,
- _NODES = 6,
- _COORDINATES = 7,
- _NODES_TYPE = 8,
- _MESH_DATA = 9,
- _ELEMENT_GROUP = 10,
- _NODE_GROUP = 11,
- _MODIFY_SCHEME = 12,
- _GATHER_INITIALIZATION = 1,
- _GATHER = 2,
- _SCATTER = 3,
- _SYNCHRONIZE = 15,
- _REDUCE,
- _PERIODIC_SLAVES,
- _PERIODIC_NODES,
+ _sizes = 1,
+ _connectivity = 2,
+ _data = 3,
+ _partitions = 4,
+ _nb_nodes = 5,
+ _nodes = 6,
+ _coordinates = 7,
+ _nodes_type = 8,
+ _mesh_data = 9,
+ _element_group = 10,
+ _node_group = 11,
+ _modify_scheme = 12,
+ _gather_initialization = 1,
+ _gather = 2,
+ _scatter = 3,
+ _synchronize = 15,
+ _reduce,
+ _periodic_slaves,
+ _periodic_nodes,
};
private:
static void setMaxTag(int _max_tag) { max_tag = _max_tag; }
- friend void initialize(const std::string &, int &, char **&);
+ friend void initialize(const std::string & /*input_file*/, int & /*argc*/,
+ char **& /*argv*/);
private:
int tag{0};
int hash{0};
static int max_tag;
};
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream, const Tag & _this) {
_this.printself(stream, 0);
return stream;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_COMMUNICATION_TAG_HH__ */
+#endif /* AKANTU_COMMUNICATION_TAG_HH_ */
diff --git a/src/synchronizer/communications.hh b/src/synchronizer/communications.hh
index 282741798..365eb662c 100644
--- a/src/synchronizer/communications.hh
+++ b/src/synchronizer/communications.hh
@@ -1,276 +1,275 @@
/**
* @file communications.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 07 2016
* @date last modification: Tue Feb 20 2018
*
* @brief Class handling the pending communications and the communications
* schemes
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_descriptor.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COMMUNICATIONS_HH__
-#define __AKANTU_COMMUNICATIONS_HH__
+#ifndef AKANTU_COMMUNICATIONS_HH_
+#define AKANTU_COMMUNICATIONS_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications {
public:
using Scheme = Array<Entity>;
protected:
using CommunicationPerProcs = std::map<UInt, Communication>;
using CommunicationsPerTags =
std::map<SynchronizationTag, CommunicationPerProcs>;
using CommunicationSchemes = std::map<UInt, Scheme>;
using Request = std::map<UInt, std::vector<CommunicationRequest>>;
friend class CommunicationDescriptor<Entity>;
public:
using scheme_iterator = typename CommunicationSchemes::iterator;
using const_scheme_iterator = typename CommunicationSchemes::const_iterator;
/* ------------------------------------------------------------------------ */
class iterator;
class tag_iterator;
/* ------------------------------------------------------------------------ */
public:
CommunicationPerProcs & getCommunications(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
bool hasPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) const;
UInt getPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) const;
/* ------------------------------------------------------------------------ */
iterator begin(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
iterator end(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
iterator waitAny(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
void waitAll(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
void incrementPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
void decrementPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
void freeRequests(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
Scheme & createScheme(UInt proc, const CommunicationSendRecv & sr);
void resetSchemes(const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
void setCommunicationSize(const SynchronizationTag & tag, UInt proc,
UInt size, const CommunicationSendRecv & sr);
public:
explicit Communications(const Communicator & communicator);
- explicit Communications(const Communications & communications);
+ explicit Communications(const Communications & other);
/* ------------------------------------------------------------------------ */
void swapSendRecv();
/* ------------------------------------------------------------------------ */
class IterableCommunicationDesc {
public:
IterableCommunicationDesc(Communications & communications,
SynchronizationTag tag, CommunicationSendRecv sr)
- : communications(communications), tag(std::move(tag)),
- sr(std::move(sr)) {}
+ : communications(communications), tag(tag), sr(sr) {}
auto begin() { return communications.begin(tag, sr); }
auto end() { return communications.end(tag, sr); }
private:
Communications & communications;
SynchronizationTag tag;
CommunicationSendRecv sr;
};
auto iterateRecv(const SynchronizationTag & tag) {
return IterableCommunicationDesc(*this, tag, _recv);
}
auto iterateSend(const SynchronizationTag & tag) {
return IterableCommunicationDesc(*this, tag, _send);
}
/* ------------------------------------------------------------------------ */
// iterator begin_send(const SynchronizationTag & tag);
// iterator end_send(const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
// iterator begin_recv(const SynchronizationTag & tag);
// iterator end_recv(const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
class IterableTags {
public:
explicit IterableTags(Communications & communications)
: communications(communications) {}
decltype(auto) begin() { return communications.begin_tag(); }
decltype(auto) end() { return communications.end_tag(); }
private:
Communications & communications;
};
decltype(auto) iterateTags() { return IterableTags(*this); }
tag_iterator begin_tag();
tag_iterator end_tag();
/* ------------------------------------------------------------------------ */
bool hasCommunication(const SynchronizationTag & tag) const;
void incrementCounter(const SynchronizationTag & tag);
UInt getCounter(const SynchronizationTag & tag) const;
bool hasCommunicationSize(const SynchronizationTag & tag) const;
void invalidateSizes();
/* ------------------------------------------------------------------------ */
bool hasPendingRecv(const SynchronizationTag & tag) const;
bool hasPendingSend(const SynchronizationTag & tag) const;
const auto & getCommunicator() const;
/* ------------------------------------------------------------------------ */
iterator waitAnyRecv(const SynchronizationTag & tag);
iterator waitAnySend(const SynchronizationTag & tag);
void waitAllRecv(const SynchronizationTag & tag);
void waitAllSend(const SynchronizationTag & tag);
void freeSendRequests(const SynchronizationTag & tag);
void freeRecvRequests(const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
class IterableSchemes {
public:
IterableSchemes(Communications & communications, CommunicationSendRecv sr)
- : communications(communications), sr(std::move(sr)) {}
+ : communications(communications), sr(sr) {}
decltype(auto) begin() { return communications.begin_scheme(sr); }
decltype(auto) end() { return communications.end_scheme(sr); }
private:
Communications & communications;
CommunicationSendRecv sr;
};
class ConstIterableSchemes {
public:
ConstIterableSchemes(const Communications & communications,
CommunicationSendRecv sr)
- : communications(communications), sr(std::move(sr)) {}
+ : communications(communications), sr(sr) {}
decltype(auto) begin() const { return communications.begin_scheme(sr); }
decltype(auto) end() const { return communications.end_scheme(sr); }
private:
const Communications & communications;
CommunicationSendRecv sr;
};
decltype(auto) iterateSchemes(const CommunicationSendRecv & sr) {
return IterableSchemes(*this, sr);
}
decltype(auto) iterateSchemes(const CommunicationSendRecv & sr) const {
return ConstIterableSchemes(*this, sr);
}
decltype(auto) iterateSendSchemes() { return IterableSchemes(*this, _send); }
decltype(auto) iterateSendSchemes() const {
return ConstIterableSchemes(*this, _send);
}
decltype(auto) iterateRecvSchemes() { return IterableSchemes(*this, _recv); }
decltype(auto) iterateRecvSchemes() const {
return ConstIterableSchemes(*this, _recv);
}
scheme_iterator begin_scheme(const CommunicationSendRecv & sr);
scheme_iterator end_scheme(const CommunicationSendRecv & sr);
const_scheme_iterator begin_scheme(const CommunicationSendRecv & sr) const;
const_scheme_iterator end_scheme(const CommunicationSendRecv & sr) const;
/* ------------------------------------------------------------------------ */
scheme_iterator begin_send_scheme();
scheme_iterator end_send_scheme();
const_scheme_iterator begin_send_scheme() const;
const_scheme_iterator end_send_scheme() const;
/* ------------------------------------------------------------------------ */
scheme_iterator begin_recv_scheme();
scheme_iterator end_recv_scheme();
const_scheme_iterator begin_recv_scheme() const;
const_scheme_iterator end_recv_scheme() const;
/* ------------------------------------------------------------------------ */
Scheme & createSendScheme(UInt proc);
Scheme & createRecvScheme(UInt proc);
/* ------------------------------------------------------------------------ */
Scheme & getScheme(UInt proc, const CommunicationSendRecv & sr);
const Scheme & getScheme(UInt proc, const CommunicationSendRecv & sr) const;
/* ------------------------------------------------------------------------ */
void resetSchemes();
/* ------------------------------------------------------------------------ */
void setSendCommunicationSize(const SynchronizationTag & tag, UInt proc,
UInt size);
void setRecvCommunicationSize(const SynchronizationTag & tag, UInt proc,
UInt size);
void initializeCommunications(const SynchronizationTag & tag);
protected:
CommunicationSchemes schemes[2];
CommunicationsPerTags communications[2];
std::map<SynchronizationTag, UInt> comm_counter;
std::map<SynchronizationTag, UInt> pending_communications[2];
std::map<SynchronizationTag, bool> comm_size_computed;
const Communicator & communicator;
};
} // namespace akantu
#include "communications_tmpl.hh"
-#endif /* __AKANTU_COMMUNICATIONS_HH__ */
+#endif /* AKANTU_COMMUNICATIONS_HH_ */
diff --git a/src/synchronizer/communications_tmpl.hh b/src/synchronizer/communications_tmpl.hh
index 1d6447403..27c13c5d1 100644
--- a/src/synchronizer/communications_tmpl.hh
+++ b/src/synchronizer/communications_tmpl.hh
@@ -1,550 +1,552 @@
/**
* @file communications_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 07 2016
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of Communications
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communications.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COMMUNICATIONS_TMPL_HH__
-#define __AKANTU_COMMUNICATIONS_TMPL_HH__
+#ifndef AKANTU_COMMUNICATIONS_TMPL_HH_
+#define AKANTU_COMMUNICATIONS_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity>
Communications<Entity>::Communications(const Communicator & communicator)
: communicator(communicator) {}
/* -------------------------------------------------------------------------- */
template <class Entity>
Communications<Entity>::Communications(const Communications & other)
: communicator(other.communicator) {
for (auto sr : iterate_send_recv) {
for (const auto & scheme_pair : other.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & other_scheme = scheme_pair.second;
auto & scheme = this->createScheme(proc, sr);
scheme.copy(other_scheme);
}
}
this->invalidateSizes();
}
/* -------------------------------------------------------------------------- */
template <class Entity> void Communications<Entity>::swapSendRecv() {
std::swap(schemes[_send], schemes[_recv]);
}
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications<Entity>::iterator {
using communication_iterator =
typename std::map<UInt, Communication>::iterator;
public:
iterator() : communications(nullptr) {}
iterator(scheme_iterator scheme_it, communication_iterator comm_it,
Communications<Entity> & communications,
const SynchronizationTag & tag)
: scheme_it(scheme_it), comm_it(comm_it), communications(&communications),
tag(tag) {}
iterator(const iterator & other) = default;
iterator(iterator && other) noexcept = default;
iterator & operator=(const iterator & other) = default;
iterator & operator=(iterator && other) noexcept = default;
iterator & operator++() {
++scheme_it;
++comm_it;
return *this;
}
CommunicationDescriptor<Entity> operator*() {
AKANTU_DEBUG_ASSERT(
scheme_it->first == comm_it->first,
"The two iterators are not in phase, something wrong"
<< " happened, time to take out your favorite debugger ("
<< scheme_it->first << " != " << comm_it->first << ")");
return CommunicationDescriptor<Entity>(comm_it->second, scheme_it->second,
*communications, tag,
scheme_it->first);
}
bool operator==(const iterator & other) const {
return scheme_it == other.scheme_it && comm_it == other.comm_it;
}
bool operator!=(const iterator & other) const {
return scheme_it != other.scheme_it || comm_it != other.comm_it;
}
private:
scheme_iterator scheme_it;
communication_iterator comm_it;
Communications<Entity> * communications;
SynchronizationTag tag;
};
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications<Entity>::tag_iterator {
using internal_iterator = std::map<SynchronizationTag, UInt>::const_iterator;
public:
tag_iterator(const internal_iterator & it) : it(it) {}
tag_iterator & operator++() {
++it;
return *this;
}
SynchronizationTag operator*() { return it->first; }
bool operator==(const tag_iterator & other) const { return it == other.it; }
bool operator!=(const tag_iterator & other) const { return it != other.it; }
private:
internal_iterator it;
};
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::CommunicationPerProcs &
Communications<Entity>::getCommunications(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto comm_it = this->communications[sr].find(tag);
- if (comm_it == this->communications[sr].end())
+ if (comm_it == this->communications[sr].end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No known communications for the tag: " << tag);
+ }
return comm_it->second;
}
/* ---------------------------------------------------------------------- */
template <class Entity>
UInt Communications<Entity>::getPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) const {
const std::map<SynchronizationTag, UInt> & pending =
pending_communications[sr];
auto it = pending.find(tag);
- if (it == pending.end())
+ if (it == pending.end()) {
return 0;
+ }
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
bool Communications<Entity>::hasPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) const {
return this->hasCommunication(tag) && (this->getPending(tag, sr) != 0);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::begin(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
return iterator(this->schemes[sr].begin(), comms.begin(), *this, tag);
}
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::end(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
return iterator(this->schemes[sr].end(), comms.end(), *this, tag);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAny(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
auto it = comms.begin();
auto end = comms.end();
std::vector<CommunicationRequest> requests;
for (; it != end; ++it) {
auto & request = it->second.request();
- if (!request.isFreed())
+ if (!request.isFreed()) {
requests.push_back(request);
+ }
}
- UInt req_id = communicator.waitAny(requests);
+ UInt req_id = Communicator::waitAny(requests);
if (req_id != UInt(-1)) {
auto & request = requests[req_id];
UInt proc = sr == _recv ? request.getSource() : request.getDestination();
return iterator(this->schemes[sr].find(proc), comms.find(proc), *this, tag);
- } else {
- return this->end(tag, sr);
}
+ return this->end(tag, sr);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::waitAll(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
auto it = comms.begin();
auto end = comms.end();
std::vector<CommunicationRequest> requests;
for (; it != end; ++it) {
requests.push_back(it->second.request());
}
- communicator.waitAll(requests);
+ Communicator::waitAll(requests);
}
template <class Entity>
void Communications<Entity>::incrementPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) {
++(pending_communications[sr][tag]);
}
template <class Entity>
void Communications<Entity>::decrementPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) {
--(pending_communications[sr][tag]);
}
template <class Entity>
void Communications<Entity>::freeRequests(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
iterator it = this->begin(tag, sr);
iterator end = this->end(tag, sr);
for (; it != end; ++it) {
(*it).freeRequest();
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createScheme(UInt proc,
const CommunicationSendRecv & sr) {
// scheme_iterator it = schemes[sr].find(proc);
// if (it != schemes[sr].end()) {
// AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
// "Communication scheme("
// << sr
// << ") already created for proc: " <<
// proc);
// }
return schemes[sr][proc];
}
template <class Entity>
void Communications<Entity>::resetSchemes(const CommunicationSendRecv & sr) {
auto it = this->schemes[sr].begin();
auto end = this->schemes[sr].end();
for (; it != end; ++it) {
it->second.resize(0);
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::setCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size,
const CommunicationSendRecv & sr) {
// accessor that fails if it does not exists
comm_size_computed[tag] = true; // TODO: need perhaps to be split based on sr
auto & comms = this->communications[sr];
auto & comms_per_tag = comms.at(tag);
comms_per_tag.at(proc).resize(size);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::initializeCommunications(
const SynchronizationTag & tag) {
for (auto t : send_recv_t{}) {
pending_communications[t].insert(std::make_pair(tag, 0));
auto & comms = this->communications[t];
auto & comms_per_tag =
comms.insert(std::make_pair(tag, CommunicationPerProcs()))
.first->second;
- for (auto pair : this->schemes[t]) {
+ for (const auto & pair : this->schemes[t]) {
comms_per_tag.emplace(std::piecewise_construct,
std::forward_as_tuple(pair.first),
std::forward_as_tuple(t));
}
}
comm_counter.insert(std::make_pair(tag, 0));
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::tag_iterator
Communications<Entity>::begin_tag() {
return tag_iterator(comm_counter.begin());
}
template <class Entity>
typename Communications<Entity>::tag_iterator
Communications<Entity>::end_tag() {
return tag_iterator(comm_counter.end());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_scheme(const CommunicationSendRecv & sr) {
return this->schemes[sr].begin();
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_scheme(const CommunicationSendRecv & sr) {
return this->schemes[sr].end();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_scheme(const CommunicationSendRecv & sr) const {
return this->schemes[sr].begin();
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_scheme(const CommunicationSendRecv & sr) const {
return this->schemes[sr].end();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_send_scheme() {
return this->begin_scheme(_send);
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_send_scheme() {
return this->end_scheme(_send);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_send_scheme() const {
return this->begin_scheme(_send);
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_send_scheme() const {
return this->end_scheme(_send);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_recv_scheme() {
return this->begin_scheme(_recv);
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_recv_scheme() {
return this->end_scheme(_recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_recv_scheme() const {
return this->begin_scheme(_recv);
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_recv_scheme() const {
return this->end_scheme(_recv);
}
/* ------------------------------------------------------------------------ */
template <class Entity>
bool Communications<Entity>::hasCommunication(
const SynchronizationTag & tag) const {
return (communications[_send].find(tag) != communications[_send].end());
}
template <class Entity>
void Communications<Entity>::incrementCounter(const SynchronizationTag & tag) {
auto it = comm_counter.find(tag);
if (it == comm_counter.end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No counter initialized in communications for the tags: " << tag);
}
++(it->second);
}
template <class Entity>
UInt Communications<Entity>::getCounter(const SynchronizationTag & tag) const {
auto it = comm_counter.find(tag);
if (it == comm_counter.end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No counter initialized in communications for the tags: " << tag);
}
return it->second;
}
template <class Entity>
bool Communications<Entity>::hasCommunicationSize(
const SynchronizationTag & tag) const {
auto it = comm_size_computed.find(tag);
if (it == comm_size_computed.end()) {
return false;
}
return it->second;
}
template <class Entity> void Communications<Entity>::invalidateSizes() {
for (auto && pair : comm_size_computed) {
pair.second = false;
}
}
template <class Entity>
bool Communications<Entity>::hasPendingRecv(
const SynchronizationTag & tag) const {
return this->hasPending(tag, _recv);
}
template <class Entity>
bool Communications<Entity>::hasPendingSend(
const SynchronizationTag & tag) const {
return this->hasPending(tag, _send);
}
template <class Entity>
const auto & Communications<Entity>::getCommunicator() const {
return communicator;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAnyRecv(const SynchronizationTag & tag) {
return this->waitAny(tag, _recv);
}
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAnySend(const SynchronizationTag & tag) {
return this->waitAny(tag, _send);
}
template <class Entity>
void Communications<Entity>::waitAllRecv(const SynchronizationTag & tag) {
this->waitAll(tag, _recv);
}
template <class Entity>
void Communications<Entity>::waitAllSend(const SynchronizationTag & tag) {
this->waitAll(tag, _send);
}
template <class Entity>
void Communications<Entity>::freeSendRequests(const SynchronizationTag & tag) {
this->freeRequests(tag, _send);
}
template <class Entity>
void Communications<Entity>::freeRecvRequests(const SynchronizationTag & tag) {
this->freeRequests(tag, _recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createSendScheme(UInt proc) {
return createScheme(proc, _send);
}
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createRecvScheme(UInt proc) {
return createScheme(proc, _recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity> void Communications<Entity>::resetSchemes() {
resetSchemes(_send);
resetSchemes(_recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::getScheme(UInt proc, const CommunicationSendRecv & sr) {
return this->schemes[sr].find(proc)->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
const typename Communications<Entity>::Scheme &
Communications<Entity>::getScheme(UInt proc,
const CommunicationSendRecv & sr) const {
return this->schemes[sr].find(proc)->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::setSendCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size) {
this->setCommunicationSize(tag, proc, size, _send);
}
template <class Entity>
void Communications<Entity>::setRecvCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size) {
this->setCommunicationSize(tag, proc, size, _recv);
}
} // namespace akantu
-#endif /* __AKANTU_COMMUNICATIONS_TMPL_HH__ */
+#endif /* AKANTU_COMMUNICATIONS_TMPL_HH_ */
diff --git a/src/synchronizer/communicator.cc b/src/synchronizer/communicator.cc
index 0dc1fbaa4..9f49130f5 100644
--- a/src/synchronizer/communicator.cc
+++ b/src/synchronizer/communicator.cc
@@ -1,186 +1,190 @@
/**
* @file communicator.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Feb 05 2018
*
* @brief implementation of the common part of the static communicator
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
#if defined(AKANTU_USE_MPI)
int MPICommunicatorData::is_externaly_initialized = 0;
#endif
UInt InternalCommunicationRequest::counter = 0;
/* -------------------------------------------------------------------------- */
InternalCommunicationRequest::InternalCommunicationRequest(UInt source,
UInt dest)
: source(source), destination(dest) {
this->id = counter++;
}
/* -------------------------------------------------------------------------- */
InternalCommunicationRequest::~InternalCommunicationRequest() = default;
/* -------------------------------------------------------------------------- */
void InternalCommunicationRequest::printself(std::ostream & stream,
int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "CommunicationRequest [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + source : " << source << std::endl;
stream << space << " + destination : " << destination << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
Communicator::~Communicator() {
auto * event = new FinalizeCommunicatorEvent(*this);
this->sendEvent(*event);
delete event;
}
/* -------------------------------------------------------------------------- */
Communicator & Communicator::getStaticCommunicator() {
AKANTU_DEBUG_IN();
if (!static_communicator) {
int nb_args = 0;
char ** null = nullptr;
static_communicator =
std::make_unique<Communicator>(nb_args, null, private_member{});
}
AKANTU_DEBUG_OUT();
return *static_communicator;
}
/* -------------------------------------------------------------------------- */
Communicator & Communicator::getStaticCommunicator(int & argc, char **& argv) {
- if (!static_communicator)
+ if (!static_communicator) {
static_communicator =
std::make_unique<Communicator>(argc, argv, private_member{});
+ }
return getStaticCommunicator();
}
} // namespace akantu
#ifdef AKANTU_USE_MPI
#include "communicator_mpi_inline_impl.hh"
#else
#include "communicator_dummy_inline_impl.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Template instantiation */
/* -------------------------------------------------------------------------- */
#define AKANTU_COMM_INSTANTIATE(T) \
template void Communicator::probe<T>(Int sender, Int tag, \
CommunicationStatus & status) const; \
template bool Communicator::asyncProbe<T>( \
Int sender, Int tag, CommunicationStatus & status) const; \
template void Communicator::sendImpl<T>( \
- const T * buffer, Int size, Int receiver, Int tag, \
+ const T * buffer /*NOLINT*/, Int size, Int receiver, Int tag, \
const CommunicationMode & mode) const; \
- template void Communicator::receiveImpl<T>(T * buffer, Int size, Int sender, \
- Int tag) const; \
+ template void Communicator::receiveImpl<T>(T * buffer /*NOLINT*/, Int size, \
+ Int sender, Int tag) const; \
template CommunicationRequest Communicator::asyncSendImpl<T>( \
- const T * buffer, Int size, Int receiver, Int tag, \
+ const T * buffer /*NOLINT*/, Int size, Int receiver, Int tag, \
const CommunicationMode & mode) const; \
template CommunicationRequest Communicator::asyncReceiveImpl<T>( \
- T * buffer, Int size, Int sender, Int tag) const; \
- template void Communicator::allGatherImpl<T>(T * values, int nb_values) \
- const; \
- template void Communicator::allGatherVImpl<T>(T * values, int * nb_values) \
- const; \
- template void Communicator::gatherImpl<T>(T * values, int nb_values, \
- int root) const; \
+ T * buffer /* NOLINT */, Int size, Int sender, Int tag) const; \
+ template void Communicator::allGatherImpl<T>(T * values /*NOLINT*/, \
+ int nb_values) const; \
+ template void Communicator::allGatherVImpl<T>(T * values /*NOLINT*/, \
+ int * nb_values) const; \
+ template void Communicator::gatherImpl<T>(T * values /*NOLINT*/, \
+ int nb_values, int root) const; \
template void Communicator::gatherImpl<T>( \
- T * values, int nb_values, T * gathered, int nb_gathered) const; \
- template void Communicator::gatherVImpl<T>(T * values, int * nb_values, \
- int root) const; \
- template void Communicator::broadcastImpl<T>(T * values, int nb_values, \
- int root) const; \
+ T * values /*NOLINT*/, int nb_values, T * gathered /*NOLINT*/, \
+ int nb_gathered) const; \
+ template void Communicator::gatherVImpl<T>(T * values /*NOLINT*/, \
+ int * nb_values, int root) const; \
+ template void Communicator::broadcastImpl<T>(T * values /*NOLINT*/, \
+ int nb_values, int root) const; \
template void Communicator::allReduceImpl<T>( \
- T * values, int nb_values, SynchronizerOperation op) const; \
- template void Communicator::scanImpl<T>(T * values, T *, int nb_values, \
+ T * values /*NOLINT*/, int nb_values, SynchronizerOperation op) const; \
+ template void Communicator::scanImpl<T>(T * values /*NOLINT*/, \
+ T * /*NOLINT*/, int nb_values, \
SynchronizerOperation op) const; \
template void Communicator::exclusiveScanImpl<T>( \
- T * values, T *, int nb_values, SynchronizerOperation op) const
+ T * values /*NOLINT*/, T * /*NOLINT*/, int nb_values, \
+ SynchronizerOperation op) const
#define MIN_MAX_REAL SCMinMaxLoc<Real, int>
#if !defined(DOXYGEN)
AKANTU_COMM_INSTANTIATE(bool);
AKANTU_COMM_INSTANTIATE(Real);
AKANTU_COMM_INSTANTIATE(UInt);
AKANTU_COMM_INSTANTIATE(Int);
AKANTU_COMM_INSTANTIATE(char);
AKANTU_COMM_INSTANTIATE(NodeFlag);
AKANTU_COMM_INSTANTIATE(MIN_MAX_REAL);
#if AKANTU_INTEGER_SIZE > 4
AKANTU_COMM_INSTANTIATE(int);
#endif
#endif
// template void Communicator::send<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int receiver, Int tag);
// template void Communicator::receive<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int sender, Int tag);
// template CommunicationRequest
// Communicator::asyncSend<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int receiver, Int tag);
// template CommunicationRequest
// Communicator::asyncReceive<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int sender, Int tag);
// template void Communicator::probe<SCMinMaxLoc<Real, int>>(
// Int sender, Int tag, CommunicationStatus & status);
// template void Communicator::allGather<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values);
// template void Communicator::allGatherV<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int * nb_values);
// template void Communicator::gather<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values, int root);
// template void Communicator::gatherV<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int * nb_values, int root);
// template void Communicator::broadcast<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values, int root);
// template void Communicator::allReduce<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values,
// const SynchronizerOperation & op);
} // namespace akantu
diff --git a/src/synchronizer/communicator.hh b/src/synchronizer/communicator.hh
index 97efde51d..d1ff00126 100644
--- a/src/synchronizer/communicator.hh
+++ b/src/synchronizer/communicator.hh
@@ -1,539 +1,559 @@
/**
* @file communicator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 15 2017
*
* @brief Class handling the parallel communications
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_event_handler_manager.hh"
#include "communication_buffer.hh"
#include "communication_request.hh"
#include "communicator_event_handler.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_STATIC_COMMUNICATOR_HH__
-#define __AKANTU_STATIC_COMMUNICATOR_HH__
+#ifndef AKANTU_STATIC_COMMUNICATOR_HH_
+#define AKANTU_STATIC_COMMUNICATOR_HH_
namespace akantu {
namespace debug {
class CommunicationException : public Exception {
public:
CommunicationException()
: Exception("An exception happen during a communication process.") {}
};
} // namespace debug
/// @enum SynchronizerOperation reduce operation that the synchronizer can
/// perform
enum class SynchronizerOperation {
_sum,
_min,
_max,
_prod,
_land,
_band,
_lor,
_bor,
_lxor,
_bxor,
_min_loc,
_max_loc,
_null
};
enum class CommunicationMode { _auto, _synchronous, _ready };
namespace {
int _any_source = -1;
}
} // namespace akantu
namespace akantu {
struct CommunicatorInternalData {
virtual ~CommunicatorInternalData() = default;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class Communicator : public EventHandlerManager<CommunicatorEventHandler> {
struct private_member {};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- Communicator(int & argc, char **& argv, const private_member &);
- Communicator(const private_member & = private_member{});
+ Communicator(int & argc, char **& argv, const private_member & /*m*/);
+ Communicator(const private_member & /*unused*/ = private_member{});
~Communicator() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Point to Point */
/* ------------------------------------------------------------------------ */
template <typename T>
void probe(Int sender, Int tag, CommunicationStatus & status) const;
template <typename T>
bool asyncProbe(Int sender, Int tag, CommunicationStatus & status) const;
/* ------------------------------------------------------------------------ */
template <typename T>
inline void receive(Array<T> & values, Int sender, Int tag) const {
return this->receiveImpl(
values.storage(), values.size() * values.getNbComponent(), sender, tag);
}
template <typename T>
inline void receive(std::vector<T> & values, Int sender, Int tag) const {
return this->receiveImpl(values.data(), values.size(), sender, tag);
}
template <typename Tensor>
inline void
receive(Tensor & values, Int sender, Int tag,
- std::enable_if_t<aka::is_tensor<Tensor>::value> * = nullptr) const {
+ std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
+ nullptr) const {
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
inline void receive(CommunicationBufferTemplated<true> & values, Int sender,
Int tag) const {
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
inline void receive(CommunicationBufferTemplated<false> & values, Int sender,
Int tag) const {
CommunicationStatus status;
this->probe<char>(sender, tag, status);
values.reserve(status.size());
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
template <typename T>
inline void
receive(T & values, Int sender, Int tag,
- std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
+ std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
+ nullptr) const {
return this->receiveImpl(&values, 1, sender, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void
send(const Array<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.storage(),
values.size() * values.getNbComponent(), receiver,
tag, mode);
}
template <typename T>
inline void
send(const std::vector<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.data(), values.size(), receiver, tag, mode);
}
template <typename Tensor>
inline void
send(const Tensor & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
- std::enable_if_t<aka::is_tensor<Tensor>::value> * = nullptr) const {
+ std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
+ nullptr) const {
return this->sendImpl(values.storage(), values.size(), receiver, tag, mode);
}
template <bool is_static>
inline void
send(const CommunicationBufferTemplated<is_static> & values, Int receiver,
Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.storage(), values.size(), receiver, tag, mode);
}
template <typename T>
- inline void
- send(const T & values, Int receiver, Int tag,
- const CommunicationMode & mode = CommunicationMode::_auto,
- std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
+ inline void send(const T & values, Int receiver, Int tag,
+ const CommunicationMode & mode = CommunicationMode::_auto,
+ std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
+ nullptr) const {
return this->sendImpl(&values, 1, receiver, tag, mode);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest
asyncSend(const Array<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.storage(),
values.size() * values.getNbComponent(),
receiver, tag, mode);
}
template <typename T>
inline CommunicationRequest
asyncSend(const std::vector<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.data(), values.size(), receiver, tag,
mode);
}
template <typename Tensor>
inline CommunicationRequest
asyncSend(const Tensor & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
- std::enable_if_t<aka::is_tensor<Tensor>::value> * = nullptr) const {
+ std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
+ nullptr) const {
return this->asyncSendImpl(values.storage(), values.size(), receiver, tag,
mode);
}
template <bool is_static>
inline CommunicationRequest
asyncSend(const CommunicationBufferTemplated<is_static> & values,
Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.storage(), values.size(), receiver, tag,
mode);
}
template <typename T>
inline CommunicationRequest
asyncSend(const T & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
- std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
+ std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
+ nullptr) const {
return this->asyncSendImpl(&values, 1, receiver, tag, mode);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest asyncReceive(Array<T> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(
values.storage(), values.size() * values.getNbComponent(), sender, tag);
}
template <typename T>
inline CommunicationRequest asyncReceive(std::vector<T> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.data(), values.size(), sender, tag);
}
template <typename Tensor,
typename = std::enable_if_t<aka::is_tensor<Tensor>::value>>
inline CommunicationRequest asyncReceive(Tensor & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.storage(), values.size(), sender, tag);
}
template <bool is_static>
inline CommunicationRequest
asyncReceive(CommunicationBufferTemplated<is_static> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.storage(), values.size(), sender, tag);
}
/* ------------------------------------------------------------------------ */
/* Collectives */
/* ------------------------------------------------------------------------ */
template <typename T>
inline void
allReduce(Array<T> & values,
SynchronizerOperation op = SynchronizerOperation::_sum) const {
this->allReduceImpl(values.storage(),
values.size() * values.getNbComponent(), op);
}
template <typename Tensor>
inline void
allReduce(Tensor & values,
SynchronizerOperation op = SynchronizerOperation::_sum,
- std::enable_if_t<aka::is_tensor<Tensor>::value> * = nullptr) const {
+ std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
+ nullptr) const {
this->allReduceImpl(values.storage(), values.size(), op);
}
template <typename T>
inline void
allReduce(T & values, SynchronizerOperation op = SynchronizerOperation::_sum,
- std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
+ std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
+ nullptr) const {
this->allReduceImpl(&values, 1, op);
}
template <typename T>
inline void
scan(Array<T> & values,
SynchronizerOperation op = SynchronizerOperation::_sum) const {
this->scanImpl(values.storage(), values.storage(),
values.size() * values.getNbComponent(), op);
}
template <typename Tensor>
inline void
scan(Tensor & values, SynchronizerOperation op,
- std::enable_if_t<aka::is_tensor<Tensor>::value> * = nullptr) const {
+ std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
+ nullptr) const {
this->scanImpl(values.storage(), values.storage(), values.size(), op);
}
template <typename T>
- inline void
- scan(T & values, SynchronizerOperation op = SynchronizerOperation::_sum,
- std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
+ inline void scan(T & values,
+ SynchronizerOperation op = SynchronizerOperation::_sum,
+ std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
+ nullptr) const {
this->scanImpl(&values, &values, 1, op);
}
template <typename T>
inline void
exclusiveScan(Array<T> & values,
SynchronizerOperation op = SynchronizerOperation::_sum) const {
this->exclusiveScanImpl(values.storage(), values.storage(),
values.size() * values.getNbComponent(), op);
}
template <typename Tensor>
- inline void exclusiveScan(
- Tensor & values, SynchronizerOperation op = SynchronizerOperation::_sum,
- std::enable_if_t<aka::is_tensor<Tensor>::value> * = nullptr) const {
+ inline void
+ exclusiveScan(Tensor & values,
+ SynchronizerOperation op = SynchronizerOperation::_sum,
+ std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
+ nullptr) const {
this->exclusiveScanImpl(values.storage(), values.storage(), values.size(),
op);
}
template <typename T>
- inline void exclusiveScan(
- T & values, SynchronizerOperation op = SynchronizerOperation::_sum,
- std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
+ inline void
+ exclusiveScan(T & values,
+ SynchronizerOperation op = SynchronizerOperation::_sum,
+ std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
+ nullptr) const {
this->exclusiveScanImpl(&values, &values, 1, op);
}
template <typename T>
- inline void exclusiveScan(
- T & values, T & result,
- SynchronizerOperation op = SynchronizerOperation::_sum,
- std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
+ inline void
+ exclusiveScan(T & values, T & result,
+ SynchronizerOperation op = SynchronizerOperation::_sum,
+ std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
+ nullptr) const {
this->exclusiveScanImpl(&values, &result, 1, op);
}
/* ------------------------------------------------------------------------ */
template <typename T> inline void allGather(Array<T> & values) const {
AKANTU_DEBUG_ASSERT(UInt(getNbProc()) == values.size(),
"The array size is not correct");
this->allGatherImpl(values.storage(), values.getNbComponent());
}
template <typename Tensor,
typename = std::enable_if_t<aka::is_tensor<Tensor>::value>>
inline void allGather(Tensor & values) const {
AKANTU_DEBUG_ASSERT(values.size() / getNbProc() > 0,
"The vector size is not correct");
this->allGatherImpl(values.storage(), values.size() / getNbProc());
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void allGatherV(Array<T> & values, const Array<Int> & sizes) const {
this->allGatherVImpl(values.storage(), sizes.storage());
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void reduce(Array<T> & values, SynchronizerOperation op,
int root = 0) const {
this->reduceImpl(values.storage(), values.size() * values.getNbComponent(),
op, root);
}
/* ------------------------------------------------------------------------ */
template <typename Tensor>
inline void
gather(Tensor & values, int root = 0,
- std::enable_if_t<aka::is_tensor<Tensor>::value> * = nullptr) const {
+ std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
+ nullptr) const {
this->gatherImpl(values.storage(), values.getNbComponent(), root);
}
template <typename T>
inline void
gather(T values, int root = 0,
- std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
+ std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
+ nullptr) const {
this->gatherImpl(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
template <typename Tensor, typename T>
inline void
gather(Tensor & values, Array<T> & gathered,
- std::enable_if_t<aka::is_tensor<Tensor>::value> * = nullptr) const {
+ std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
+ nullptr) const {
AKANTU_DEBUG_ASSERT(values.size() == gathered.getNbComponent(),
"The array size is not correct");
gathered.resize(getNbProc());
this->gatherImpl(values.data(), values.size(), gathered.storage(),
gathered.getNbComponent());
}
template <typename T>
inline void
gather(T values, Array<T> & gathered,
- std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
+ std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
+ nullptr) const {
this->gatherImpl(&values, 1, gathered.storage(), 1);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void gatherV(Array<T> & values, const Array<Int> & sizes,
int root = 0) const {
this->gatherVImpl(values.storage(), sizes.storage(), root);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void broadcast(Array<T> & values, int root = 0) const {
this->broadcastImpl(values.storage(),
values.size() * values.getNbComponent(), root);
}
template <typename T>
inline void broadcast(std::vector<T> & values, int root = 0) const {
this->broadcastImpl(values.data(), values.size(), root);
}
inline void broadcast(CommunicationBufferTemplated<true> & buffer,
int root = 0) const {
this->broadcastImpl(buffer.storage(), buffer.size(), root);
}
inline void broadcast(CommunicationBufferTemplated<false> & buffer,
int root = 0) const {
UInt buffer_size = buffer.size();
this->broadcastImpl(&buffer_size, 1, root);
- if (whoAmI() != root)
+ if (whoAmI() != root) {
buffer.reserve(buffer_size);
+ }
- if (buffer_size == 0)
+ if (buffer_size == 0) {
return;
+ }
this->broadcastImpl(buffer.storage(), buffer.size(), root);
}
template <typename T> inline void broadcast(T & values, int root = 0) const {
this->broadcastImpl(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
void barrier() const;
CommunicationRequest asyncBarrier() const;
/* ------------------------------------------------------------------------ */
/* Request handling */
/* ------------------------------------------------------------------------ */
- bool test(CommunicationRequest & request) const;
- bool testAll(std::vector<CommunicationRequest> & request) const;
- void wait(CommunicationRequest & request) const;
- void waitAll(std::vector<CommunicationRequest> & requests) const;
- UInt waitAny(std::vector<CommunicationRequest> & requests) const;
- inline void freeCommunicationRequest(CommunicationRequest & request) const;
- inline void
- freeCommunicationRequest(std::vector<CommunicationRequest> & requests) const;
+ static bool test(CommunicationRequest & request);
+ static bool testAll(std::vector<CommunicationRequest> & request);
+ static void wait(CommunicationRequest & request);
+ static void waitAll(std::vector<CommunicationRequest> & requests);
+ static UInt waitAny(std::vector<CommunicationRequest> & requests);
+ static inline void freeCommunicationRequest(CommunicationRequest & request);
+ static inline void
+ freeCommunicationRequest(std::vector<CommunicationRequest> & requests);
template <typename T, typename MsgProcessor>
inline void
receiveAnyNumber(std::vector<CommunicationRequest> & send_requests,
MsgProcessor && processor, Int tag) const;
protected:
template <typename T>
void
sendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const;
template <typename T>
void receiveImpl(T * buffer, Int size, Int sender, Int tag) const;
template <typename T>
CommunicationRequest asyncSendImpl(
const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const;
template <typename T>
CommunicationRequest asyncReceiveImpl(T * buffer, Int size, Int sender,
Int tag) const;
template <typename T>
void allReduceImpl(T * values, int nb_values, SynchronizerOperation op) const;
template <typename T>
void scanImpl(T * values, T * results, int nb_values,
SynchronizerOperation op) const;
template <typename T>
void exclusiveScanImpl(T * values, T * results, int nb_values,
SynchronizerOperation op) const;
template <typename T> void allGatherImpl(T * values, int nb_values) const;
template <typename T> void allGatherVImpl(T * values, int * nb_values) const;
template <typename T>
void reduceImpl(T * values, int nb_values, SynchronizerOperation op,
int root = 0) const;
template <typename T>
void gatherImpl(T * values, int nb_values, int root = 0) const;
template <typename T>
void gatherImpl(T * values, int nb_values, T * gathered,
int nb_gathered = 0) const;
template <typename T>
void gatherVImpl(T * values, int * nb_values, int root = 0) const;
template <typename T>
void broadcastImpl(T * values, int nb_values, int root = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
Int getNbProc() const;
Int whoAmI() const;
static Communicator & getStaticCommunicator();
static Communicator & getStaticCommunicator(int & argc, char **& argv);
int getMaxTag() const;
int getMinTag() const;
AKANTU_GET_MACRO(CommunicatorData, (*communicator_data), decltype(auto));
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
static std::unique_ptr<Communicator> static_communicator;
protected:
std::unique_ptr<CommunicatorInternalData> communicator_data;
};
inline std::ostream & operator<<(std::ostream & stream,
const CommunicationRequest & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "communicator_inline_impl.hh"
-#endif /* __AKANTU_STATIC_COMMUNICATOR_HH__ */
+#endif /* AKANTU_STATIC_COMMUNICATOR_HH_ */
diff --git a/src/synchronizer/communicator_event_handler.hh b/src/synchronizer/communicator_event_handler.hh
index 38182707f..f4bfffc81 100644
--- a/src/synchronizer/communicator_event_handler.hh
+++ b/src/synchronizer/communicator_event_handler.hh
@@ -1,60 +1,60 @@
/**
* @file communicator_event_handler.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 15 2017
*
* @brief Event handler of the communicator
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_COMMUNICATOR_EVENT_HANDLER_HH__
-#define __AKANTU_COMMUNICATOR_EVENT_HANDLER_HH__
+#ifndef AKANTU_COMMUNICATOR_EVENT_HANDLER_HH_
+#define AKANTU_COMMUNICATOR_EVENT_HANDLER_HH_
namespace akantu {
class Communicator;
struct FinalizeCommunicatorEvent {
explicit FinalizeCommunicatorEvent(const Communicator & comm)
: communicator(comm) {}
const Communicator & communicator;
};
class CommunicatorEventHandler {
public:
virtual ~CommunicatorEventHandler() = default;
virtual void onCommunicatorFinalize() = 0;
private:
- inline void sendEvent(const FinalizeCommunicatorEvent &) {
+ inline void sendEvent(const FinalizeCommunicatorEvent & /*unused*/) {
this->onCommunicatorFinalize();
}
template <class EventHandler> friend class EventHandlerManager;
};
} // namespace akantu
-#endif /* __AKANTU_COMMUNICATOR_EVENT_HANDLER_HH__ */
+#endif /* AKANTU_COMMUNICATOR_EVENT_HANDLER_HH_ */
diff --git a/src/synchronizer/communicator_inline_impl.hh b/src/synchronizer/communicator_inline_impl.hh
index de301f549..ae6ced78b 100644
--- a/src/synchronizer/communicator_inline_impl.hh
+++ b/src/synchronizer/communicator_inline_impl.hh
@@ -1,95 +1,96 @@
/**
* @file communicator_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 02 2016
* @date last modification: Tue Nov 07 2017
*
* @brief implementation of inline functions
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH__
-#define __AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH__
+#ifndef AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH_
+#define AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
-inline void
-Communicator::freeCommunicationRequest(CommunicationRequest & request) const {
+ inline void
+Communicator::freeCommunicationRequest(CommunicationRequest & request) {
request.free();
}
/* -------------------------------------------------------------------------- */
-inline void Communicator::freeCommunicationRequest(
- std::vector<CommunicationRequest> & requests) const {
+ inline void Communicator::freeCommunicationRequest(
+ std::vector<CommunicationRequest> & requests) {
std::vector<CommunicationRequest>::iterator it;
for (it = requests.begin(); it != requests.end(); ++it) {
it->free();
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename MsgProcessor>
inline void Communicator::receiveAnyNumber(
std::vector<CommunicationRequest> & send_requests,
MsgProcessor && processor, Int tag) const {
CommunicationRequest barrier_request;
- bool got_all = false, are_send_finished = false;
+ bool got_all{false};
+ bool are_send_finished{false};
AKANTU_DEBUG_INFO("Sending " << send_requests.size()
<< " messages and checking for receives TAG["
<< tag << "]");
while (not got_all) {
bool are_receives_ready = true;
while (are_receives_ready) {
CommunicationStatus status;
are_receives_ready = asyncProbe<T>(_any_source, tag, status);
if (are_receives_ready) {
AKANTU_DEBUG_INFO("Receiving message from " << status.getSource());
Array<T> receive_buffer(status.size(), 1);
receive(receive_buffer, status.getSource(), tag);
std::forward<MsgProcessor>(processor)(status.getSource(),
receive_buffer);
}
}
if (not are_send_finished) {
are_send_finished = testAll(send_requests);
if (are_send_finished) {
AKANTU_DEBUG_INFO("All messages send, checking for more receives");
barrier_request = asyncBarrier();
}
}
if (are_send_finished) {
got_all = test(barrier_request);
}
}
AKANTU_DEBUG_INFO("Finished receiving");
}
} // namespace akantu
-#endif /* __AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH__ */
+#endif /* AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH_ */
diff --git a/src/synchronizer/communicator_mpi_inline_impl.hh b/src/synchronizer/communicator_mpi_inline_impl.hh
index 66ec4674a..5ecd98144 100644
--- a/src/synchronizer/communicator_mpi_inline_impl.hh
+++ b/src/synchronizer/communicator_mpi_inline_impl.hh
@@ -1,500 +1,509 @@
/**
* @file communicator_mpi_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 07 2017
* @date last modification: Mon Dec 18 2017
*
* @brief StaticCommunicatorMPI implementation
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "mpi_communicator_data.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
#include <type_traits>
#include <unordered_map>
#include <vector>
/* -------------------------------------------------------------------------- */
#include <mpi.h>
/* -------------------------------------------------------------------------- */
#if (defined(__GNUC__) || defined(__GNUG__))
#if AKA_GCC_VERSION < 60000
namespace std {
template <> struct hash<akantu::SynchronizerOperation> {
using argument_type = akantu::SynchronizerOperation;
size_t operator()(const argument_type & e) const noexcept {
auto ue = underlying_type_t<argument_type>(e);
return uh(ue);
}
private:
const hash<underlying_type_t<argument_type>> uh{};
};
} // namespace std
#endif
#endif
namespace akantu {
class CommunicationRequestMPI : public InternalCommunicationRequest {
public:
CommunicationRequestMPI(UInt source, UInt dest)
: InternalCommunicationRequest(source, dest),
request(std::make_unique<MPI_Request>()) {}
MPI_Request & getMPIRequest() { return *request; };
private:
std::unique_ptr<MPI_Request> request;
};
namespace {
template <typename T> inline MPI_Datatype getMPIDatatype();
MPI_Op getMPISynchronizerOperation(SynchronizerOperation op) {
std::unordered_map<SynchronizerOperation, MPI_Op> _operations{
{SynchronizerOperation::_sum, MPI_SUM},
{SynchronizerOperation::_min, MPI_MIN},
{SynchronizerOperation::_max, MPI_MAX},
{SynchronizerOperation::_prod, MPI_PROD},
{SynchronizerOperation::_land, MPI_LAND},
{SynchronizerOperation::_band, MPI_BAND},
{SynchronizerOperation::_lor, MPI_LOR},
{SynchronizerOperation::_bor, MPI_BOR},
{SynchronizerOperation::_lxor, MPI_LXOR},
{SynchronizerOperation::_bxor, MPI_BXOR},
{SynchronizerOperation::_min_loc, MPI_MINLOC},
{SynchronizerOperation::_max_loc, MPI_MAXLOC},
{SynchronizerOperation::_null, MPI_OP_NULL}};
return _operations[op];
}
template <typename T> MPI_Datatype inline getMPIDatatype() {
return MPI_DATATYPE_NULL;
}
#define SPECIALIZE_MPI_DATATYPE(type, mpi_type) \
template <> MPI_Datatype inline getMPIDatatype<type>() { return mpi_type; }
#define COMMA ,
SPECIALIZE_MPI_DATATYPE(char, MPI_CHAR)
SPECIALIZE_MPI_DATATYPE(std::uint8_t, MPI_UINT8_T)
SPECIALIZE_MPI_DATATYPE(float, MPI_FLOAT)
SPECIALIZE_MPI_DATATYPE(double, MPI_DOUBLE)
SPECIALIZE_MPI_DATATYPE(long double, MPI_LONG_DOUBLE)
SPECIALIZE_MPI_DATATYPE(signed int, MPI_INT)
SPECIALIZE_MPI_DATATYPE(unsigned int, MPI_UNSIGNED)
SPECIALIZE_MPI_DATATYPE(signed long int, MPI_LONG)
SPECIALIZE_MPI_DATATYPE(unsigned long int, MPI_UNSIGNED_LONG)
SPECIALIZE_MPI_DATATYPE(signed long long int, MPI_LONG_LONG)
SPECIALIZE_MPI_DATATYPE(unsigned long long int, MPI_UNSIGNED_LONG_LONG)
SPECIALIZE_MPI_DATATYPE(SCMinMaxLoc<double COMMA int>, MPI_DOUBLE_INT)
SPECIALIZE_MPI_DATATYPE(SCMinMaxLoc<float COMMA int>, MPI_FLOAT_INT)
SPECIALIZE_MPI_DATATYPE(bool, MPI_CXX_BOOL)
template <> MPI_Datatype inline getMPIDatatype<NodeFlag>() {
return getMPIDatatype<std::underlying_type_t<NodeFlag>>();
}
inline int getMPISource(int src) {
- if (src == _any_source)
+ if (src == _any_source) {
return MPI_ANY_SOURCE;
+ }
return src;
}
decltype(auto) convertRequests(std::vector<CommunicationRequest> & requests) {
std::vector<MPI_Request> mpi_requests(requests.size());
for (auto && request_pair : zip(requests, mpi_requests)) {
auto && req = std::get<0>(request_pair);
auto && mpi_req = std::get<1>(request_pair);
mpi_req = aka::as_type<CommunicationRequestMPI>(req.getInternal())
.getMPIRequest();
}
return mpi_requests;
}
} // namespace
// this is ugly but shorten the code a lot
#define MPIDATA \
(*reinterpret_cast<MPICommunicatorData *>(communicator_data.get()))
/* -------------------------------------------------------------------------- */
/* Implementation */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
Communicator::Communicator(int & /*argc*/, char **& /*argv*/,
const private_member & m)
: Communicator(m) {}
/* -------------------------------------------------------------------------- */
-Communicator::Communicator(const private_member &)
+Communicator::Communicator(const private_member & /*unused*/)
: communicator_data(std::make_unique<MPICommunicatorData>()) {
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::sendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
switch (mode) {
case CommunicationMode::_auto:
MPI_Send(buffer, size, type, receiver, tag, communicator);
break;
case CommunicationMode::_synchronous:
MPI_Ssend(buffer, size, type, receiver, tag, communicator);
break;
case CommunicationMode::_ready:
MPI_Rsend(buffer, size, type, receiver, tag, communicator);
break;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::receiveImpl(T * buffer, Int size, Int sender,
Int tag) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status status;
MPI_Datatype type = getMPIDatatype<T>();
MPI_Recv(buffer, size, type, getMPISource(sender), tag, communicator,
&status);
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest
Communicator::asyncSendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
auto * request = new CommunicationRequestMPI(whoAmI(), receiver);
MPI_Request & req = request->getMPIRequest();
MPI_Datatype type = getMPIDatatype<T>();
switch (mode) {
case CommunicationMode::_auto:
MPI_Isend(buffer, size, type, receiver, tag, communicator, &req);
break;
case CommunicationMode::_synchronous:
MPI_Issend(buffer, size, type, receiver, tag, communicator, &req);
break;
case CommunicationMode::_ready:
MPI_Irsend(buffer, size, type, receiver, tag, communicator, &req);
break;
}
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest Communicator::asyncReceiveImpl(T * buffer, Int size,
Int sender, Int tag) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
auto * request = new CommunicationRequestMPI(sender, whoAmI());
MPI_Datatype type = getMPIDatatype<T>();
MPI_Request & req = request->getMPIRequest();
MPI_Irecv(buffer, size, type, getMPISource(sender), tag, communicator, &req);
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::probe(Int sender, Int tag,
CommunicationStatus & status) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status mpi_status;
MPI_Probe(getMPISource(sender), tag, communicator, &mpi_status);
MPI_Datatype type = getMPIDatatype<T>();
int count;
MPI_Get_count(&mpi_status, type, &count);
status.setSource(mpi_status.MPI_SOURCE);
status.setTag(mpi_status.MPI_TAG);
status.setSize(count);
}
/* -------------------------------------------------------------------------- */
template <typename T>
bool Communicator::asyncProbe(Int sender, Int tag,
CommunicationStatus & status) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status mpi_status;
int test;
MPI_Iprobe(getMPISource(sender), tag, communicator, &test, &mpi_status);
- if (not test)
+ if (not test) {
return false;
+ }
MPI_Datatype type = getMPIDatatype<T>();
int count;
MPI_Get_count(&mpi_status, type, &count);
status.setSource(mpi_status.MPI_SOURCE);
status.setTag(mpi_status.MPI_TAG);
status.setSize(count);
return true;
}
/* -------------------------------------------------------------------------- */
-bool Communicator::test(CommunicationRequest & request) const {
+bool Communicator::test(CommunicationRequest & request) {
MPI_Status status;
int flag;
auto & req_mpi = aka::as_type<CommunicationRequestMPI>(request.getInternal());
MPI_Request & req = req_mpi.getMPIRequest();
MPI_Test(&req, &flag, &status);
- return flag;
+ return flag != 0;
}
/* -------------------------------------------------------------------------- */
-bool Communicator::testAll(std::vector<CommunicationRequest> & requests) const {
+bool Communicator::testAll(std::vector<CommunicationRequest> & requests) {
// int are_finished;
// auto && mpi_requests = convertRequests(requests);
// MPI_Testall(mpi_requests.size(), mpi_requests.data(), &are_finished,
// MPI_STATUSES_IGNORE);
// return are_finished;
for (auto & request : requests) {
- if (not test(request))
+ if (not test(request)) {
return false;
+ }
}
return true;
}
/* -------------------------------------------------------------------------- */
-void Communicator::wait(CommunicationRequest & request) const {
+void Communicator::wait(CommunicationRequest & request) {
MPI_Status status;
auto & req_mpi = aka::as_type<CommunicationRequestMPI>(request.getInternal());
MPI_Request & req = req_mpi.getMPIRequest();
MPI_Wait(&req, &status);
}
/* -------------------------------------------------------------------------- */
-void Communicator::waitAll(std::vector<CommunicationRequest> & requests) const {
+void Communicator::waitAll(std::vector<CommunicationRequest> & requests) {
auto && mpi_requests = convertRequests(requests);
MPI_Waitall(mpi_requests.size(), mpi_requests.data(), MPI_STATUSES_IGNORE);
}
/* -------------------------------------------------------------------------- */
-UInt Communicator::waitAny(std::vector<CommunicationRequest> & requests) const {
+UInt Communicator::waitAny(std::vector<CommunicationRequest> & requests) {
auto && mpi_requests = convertRequests(requests);
int pos;
MPI_Waitany(mpi_requests.size(), mpi_requests.data(), &pos,
MPI_STATUSES_IGNORE);
if (pos != MPI_UNDEFINED) {
return pos;
- } else {
- return UInt(-1);
}
+ return UInt(-1);
}
/* -------------------------------------------------------------------------- */
void Communicator::barrier() const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Barrier(communicator);
}
/* -------------------------------------------------------------------------- */
CommunicationRequest Communicator::asyncBarrier() const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
auto * request = new CommunicationRequestMPI(0, 0);
MPI_Request & req = request->getMPIRequest();
MPI_Ibarrier(communicator, &req);
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::reduceImpl(T * values, int nb_values,
SynchronizerOperation op, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Reduce(MPI_IN_PLACE, values, nb_values, type,
getMPISynchronizerOperation(op), root, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allReduceImpl(T * values, int nb_values,
SynchronizerOperation op) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allreduce(MPI_IN_PLACE, values, nb_values, type,
getMPISynchronizerOperation(op), communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::scanImpl(T * values, T * result, int nb_values,
SynchronizerOperation op) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
if (values == result) {
values = reinterpret_cast<T *>(MPI_IN_PLACE);
}
MPI_Scan(values, result, nb_values, type, getMPISynchronizerOperation(op),
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::exclusiveScanImpl(T * values, T * result, int nb_values,
SynchronizerOperation op) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
if (values == result) {
values = reinterpret_cast<T *>(MPI_IN_PLACE);
}
MPI_Exscan(values, result, nb_values, type, getMPISynchronizerOperation(op),
communicator);
if (whoAmI() == 0) {
result[0] = T();
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allGatherImpl(T * values, int nb_values) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allgather(MPI_IN_PLACE, nb_values, type, values, nb_values, type,
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allGatherVImpl(T * values, int * nb_values) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
std::vector<int> displs(getNbProc());
displs[0] = 0;
for (int i = 1; i < getNbProc(); ++i) {
displs[i] = displs[i - 1] + nb_values[i - 1];
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allgatherv(MPI_IN_PLACE, *nb_values, type, values, nb_values,
displs.data(), type, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
- T *send_buf = nullptr, *recv_buf = nullptr;
+ T * send_buf = nullptr;
+ T * recv_buf = nullptr;
if (whoAmI() == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
} else {
send_buf = values;
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_values, type, root,
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, T * gathered,
int nb_gathered) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
T * send_buf = values;
T * recv_buf = gathered;
- if (nb_gathered == 0)
+ if (nb_gathered == 0) {
nb_gathered = nb_values;
+ }
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_gathered, type,
whoAmI(), communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherVImpl(T * values, int * nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
int * displs = nullptr;
auto psize = getNbProc();
auto prank = whoAmI();
if (prank == root) {
displs = new int[psize];
displs[0] = 0;
for (int i = 1; i < psize; ++i) {
displs[i] = displs[i - 1] + nb_values[i - 1];
}
}
- T *send_buf = nullptr, *recv_buf = nullptr;
+ T * send_buf = nullptr;
+ T * recv_buf = nullptr;
if (prank == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
- } else
+ } else {
send_buf = values;
+ }
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gatherv(send_buf, *nb_values, type, recv_buf, nb_values, displs, type,
root, communicator);
if (prank == root) {
delete[] displs;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::broadcastImpl(T * values, int nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Bcast(values, nb_values, type, root, communicator);
}
/* -------------------------------------------------------------------------- */
int Communicator::getMaxTag() const { return MPIDATA.getMaxTag(); }
-int Communicator::getMinTag() const { return 0; }
-
+int Communicator::
+ getMinTag() // NOLINT(readability-convert-member-functions-to-static)
+ const {
+ return 0;
+}
/* -------------------------------------------------------------------------- */
Int Communicator::getNbProc() const { return MPIDATA.size(); }
Int Communicator::whoAmI() const { return MPIDATA.rank(); }
} // namespace akantu
diff --git a/src/synchronizer/data_accessor.cc b/src/synchronizer/data_accessor.cc
index 0a1b9bda5..75f6e98de 100644
--- a/src/synchronizer/data_accessor.cc
+++ b/src/synchronizer/data_accessor.cc
@@ -1,153 +1,156 @@
/**
* @file data_accessor.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief data accessors constructor functions
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "fe_engine.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void DataAccessor<Element>::packUnpackNodalDataHelper(
Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
UInt nb_component = data.getNbComponent();
UInt nb_nodes_per_element = 0;
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt * conn = nullptr;
- for (auto & el : elements) {
+ for (const auto & el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
conn = mesh.getConnectivity(el.type, el.ghost_type).storage();
nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
}
UInt el_offset = el.element * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt offset_conn = conn[el_offset + n];
Vector<T> data_vect(data.storage() + offset_conn * nb_component,
nb_component);
- if (pack_helper)
+ if (pack_helper) {
buffer << data_vect;
- else
+ } else {
buffer >> data_vect;
+ }
}
}
}
/* ------------------------------------------------------------------------ */
template <typename T, bool pack_helper>
void DataAccessor<Element>::packUnpackElementalDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & element, bool per_quadrature_point_data,
const FEEngine & fem) {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt nb_quad_per_elem = 0;
UInt nb_component = 0;
Array<T> * vect = nullptr;
- for (auto & el : element) {
+ for (const auto & el : element) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect = &data_to_pack(el.type, el.ghost_type);
nb_quad_per_elem =
per_quadrature_point_data
? fem.getNbIntegrationPoints(el.type, el.ghost_type)
: 1;
nb_component = vect->getNbComponent();
}
Vector<T> data(vect->storage() +
el.element * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem);
- if (pack_helper)
+ if (pack_helper) {
buffer << data;
- else
+ } else {
buffer >> data;
+ }
}
}
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void DataAccessor<UInt>::packUnpackDOFDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
T * data_ptr = data.storage();
for (const auto & dof : dofs) {
- if (pack_helper)
+ if (pack_helper) {
buffer << data_ptr[dof];
- else
+ } else {
buffer >> data_ptr[dof];
+ }
}
}
/* -------------------------------------------------------------------------- */
#define DECLARE_HELPERS(T) \
template void DataAccessor<Element>::packUnpackNodalDataHelper<T, false>( \
Array<T> & data, CommunicationBuffer & buffer, \
const Array<Element> & elements, const Mesh & mesh); \
template void DataAccessor<Element>::packUnpackNodalDataHelper<T, true>( \
Array<T> & data, CommunicationBuffer & buffer, \
const Array<Element> & elements, const Mesh & mesh); \
template void \
DataAccessor<Element>::packUnpackElementalDataHelper<T, false>( \
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer, \
const Array<Element> & element, bool per_quadrature_point_data, \
const FEEngine & fem); \
template void DataAccessor<Element>::packUnpackElementalDataHelper<T, true>( \
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer, \
const Array<Element> & element, bool per_quadrature_point_data, \
const FEEngine & fem); \
template void DataAccessor<UInt>::packUnpackDOFDataHelper<T, true>( \
Array<T> & data, CommunicationBuffer & buffer, \
const Array<UInt> & dofs); \
template void DataAccessor<UInt>::packUnpackDOFDataHelper<T, false>( \
Array<T> & data, CommunicationBuffer & buffer, const Array<UInt> & dofs)
/* -------------------------------------------------------------------------- */
DECLARE_HELPERS(Real);
DECLARE_HELPERS(UInt);
DECLARE_HELPERS(bool);
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/data_accessor.hh b/src/synchronizer/data_accessor.hh
index 7a243b1be..21e76cbdc 100644
--- a/src/synchronizer/data_accessor.hh
+++ b/src/synchronizer/data_accessor.hh
@@ -1,277 +1,280 @@
/**
* @file data_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Sun Feb 04 2018
*
* @brief Interface of accessors for pack_unpack system
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "communication_buffer.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DATA_ACCESSOR_HH__
-#define __AKANTU_DATA_ACCESSOR_HH__
+#ifndef AKANTU_DATA_ACCESSOR_HH_
+#define AKANTU_DATA_ACCESSOR_HH_
namespace akantu {
class FEEngine;
} // namespace akantu
namespace akantu {
class DataAccessorBase {
public:
DataAccessorBase() = default;
virtual ~DataAccessorBase() = default;
};
template <class T> class DataAccessor : public virtual DataAccessorBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DataAccessor() = default;
~DataAccessor() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief get the number of data to exchange for a given array of T
* (elements or dofs) and a given akantu::SynchronizationTag
*/
virtual UInt getNbData(const Array<T> & elements,
const SynchronizationTag & tag) const = 0;
/**
* @brief pack the data for a given array of T (elements or dofs) and a given
* akantu::SynchronizationTag
*/
virtual void packData(CommunicationBuffer & buffer, const Array<T> & element,
const SynchronizationTag & tag) const = 0;
/**
* @brief unpack the data for a given array of T (elements or dofs) and a
* given akantu::SynchronizationTag
*/
virtual void unpackData(CommunicationBuffer & buffer,
const Array<T> & element,
const SynchronizationTag & tag) = 0;
};
/* -------------------------------------------------------------------------- */
/* Specialization */
/* -------------------------------------------------------------------------- */
template <> class DataAccessor<Element> : public virtual DataAccessorBase {
public:
DataAccessor() = default;
~DataAccessor() override = default;
virtual UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const = 0;
virtual void packData(CommunicationBuffer & buffer,
const Array<Element> & element,
const SynchronizationTag & tag) const = 0;
virtual void unpackData(CommunicationBuffer & buffer,
const Array<Element> & element,
const SynchronizationTag & tag) = 0;
/* ------------------------------------------------------------------------ */
public:
template <typename T, bool pack_helper>
static void
packUnpackNodalDataHelper(Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh);
/* ------------------------------------------------------------------------ */
template <typename T, bool pack_helper>
static void packUnpackElementalDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & element, bool per_quadrature_point_data,
const FEEngine & fem);
/* ------------------------------------------------------------------------ */
template <typename T>
static void
packNodalDataHelper(const Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
packUnpackNodalDataHelper<T, true>(const_cast<Array<T> &>(data), buffer,
elements, mesh);
}
template <typename T>
static inline void
unpackNodalDataHelper(Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
packUnpackNodalDataHelper<T, false>(data, buffer, elements, mesh);
}
/* ------------------------------------------------------------------------ */
template <typename T>
static inline void
packElementalDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point, const FEEngine & fem) {
packUnpackElementalDataHelper<T, true>(
const_cast<ElementTypeMapArray<T> &>(data_to_pack), buffer, elements,
per_quadrature_point, fem);
}
template <typename T>
static inline void
unpackElementalDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point, const FEEngine & fem) {
packUnpackElementalDataHelper<T, false>(data_to_unpack, buffer, elements,
per_quadrature_point, fem);
}
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <> class DataAccessor<UInt> : public virtual DataAccessorBase {
public:
DataAccessor() = default;
~DataAccessor() override = default;
virtual UInt getNbData(const Array<UInt> & elements,
const SynchronizationTag & tag) const = 0;
virtual void packData(CommunicationBuffer & buffer,
const Array<UInt> & element,
const SynchronizationTag & tag) const = 0;
virtual void unpackData(CommunicationBuffer & buffer,
const Array<UInt> & element,
const SynchronizationTag & tag) = 0;
/* ------------------------------------------------------------------------ */
public:
template <typename T, bool pack_helper>
static void packUnpackDOFDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<UInt> & dofs);
template <typename T>
static inline void packDOFDataHelper(const Array<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
packUnpackDOFDataHelper<T, true>(const_cast<Array<T> &>(data_to_pack),
buffer, dofs);
}
template <typename T>
static inline void unpackDOFDataHelper(Array<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
packUnpackDOFDataHelper<T, false>(data_to_unpack, buffer, dofs);
}
};
/* -------------------------------------------------------------------------- */
template <typename T> class AddOperation {
public:
inline T operator()(T & a, T & b) { return a + b; };
};
template <typename T> class IdentityOperation {
public:
- inline T & operator()(T &, T & b) { return b; };
+ inline T & operator()(T & /*unused*/, T & b) { return b; };
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <class Entity, template <class> class Op, class T>
class ReduceDataAccessor : public virtual DataAccessor<Entity> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ReduceDataAccessor(Array<T> & data, const SynchronizationTag & tag)
: data(data), tag(tag) {}
~ReduceDataAccessor() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<Entity> & entities,
const SynchronizationTag & tag) const override {
- if (tag != this->tag)
+ if (tag != this->tag) {
return 0;
+ }
Vector<T> tmp(data.getNbComponent());
return entities.size() * CommunicationBuffer::sizeInBuffer(tmp);
}
/* ------------------------------------------------------------------------ */
void packData(CommunicationBuffer & buffer, const Array<Entity> & entities,
const SynchronizationTag & tag) const override {
- if (tag != this->tag)
+ if (tag != this->tag) {
return;
+ }
auto data_it = data.begin(data.getNbComponent());
for (auto el : entities) {
buffer << Vector<T>(data_it[el]);
}
}
/* ------------------------------------------------------------------------ */
void unpackData(CommunicationBuffer & buffer, const Array<Entity> & entities,
const SynchronizationTag & tag) override {
- if (tag != this->tag)
+ if (tag != this->tag) {
return;
+ }
auto data_it = data.begin(data.getNbComponent());
for (auto el : entities) {
Vector<T> unpacked(data.getNbComponent());
Vector<T> vect(data_it[el]);
buffer >> unpacked;
vect = oper(vect, unpacked);
}
}
protected:
/// data to (un)pack
Array<T> & data;
/// Tag to consider
SynchronizationTag tag;
/// reduction operator
Op<Vector<T>> oper;
};
/* -------------------------------------------------------------------------- */
template <class T>
using SimpleUIntDataAccessor = ReduceDataAccessor<UInt, IdentityOperation, T>;
} // namespace akantu
-#endif /* __AKANTU_DATA_ACCESSOR_HH__ */
+#endif /* AKANTU_DATA_ACCESSOR_HH_ */
diff --git a/src/synchronizer/dof_synchronizer.cc b/src/synchronizer/dof_synchronizer.cc
index b76da0414..9221bd6f6 100644
--- a/src/synchronizer/dof_synchronizer.cc
+++ b/src/synchronizer/dof_synchronizer.cc
@@ -1,230 +1,230 @@
/**
* @file dof_synchronizer.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Tue Feb 06 2018
*
* @brief DOF synchronizing object implementation
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_synchronizer.hh"
#include "aka_iterators.hh"
#include "dof_manager_default.hh"
#include "mesh.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* A DOFSynchronizer needs a mesh and the number of degrees of freedom
* per node to be created. In the constructor computes the local and global dof
* number for each dof. The member
* proc_informations (std vector) is resized with the number of mpi
* processes. Each entry in the vector is a PerProcInformations object
* that contains the interactions of the current mpi process (prank) with the
* mpi process corresponding to the position of that entry. Every
* ProcInformations object contains one array with the dofs that have
* to be sent to prank and a second one with dofs that willl be received form
* prank.
* This information is needed for the asychronous communications. The
* constructor sets up this information.
*/
DOFSynchronizer::DOFSynchronizer(DOFManagerDefault & dof_manager, const ID & id,
MemoryID memory_id)
: SynchronizerImpl<UInt>(dof_manager.getCommunicator(), id, memory_id),
dof_manager(dof_manager) {
std::vector<ID> dof_ids = dof_manager.getDOFIDs();
// Transfers nodes to global equation numbers in new schemes
for (const ID & dof_id : dof_ids) {
registerDOFs(dof_id);
}
}
/* -------------------------------------------------------------------------- */
DOFSynchronizer::~DOFSynchronizer() = default;
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::registerDOFs(const ID & dof_id) {
if (this->nb_proc == 1) {
return;
}
if (dof_manager.getSupportType(dof_id) != _dst_nodal) {
return;
}
const auto & equation_numbers = dof_manager.getLocalEquationsNumbers(dof_id);
const auto & associated_nodes = dof_manager.getDOFsAssociatedNodes(dof_id);
const auto & node_synchronizer = dof_manager.getMesh().getNodeSynchronizer();
const auto & node_communications = node_synchronizer.getCommunications();
auto transcode_node_to_global_dof_scheme =
[this, &associated_nodes, &equation_numbers](
auto && it, auto && end, const CommunicationSendRecv & sr) -> void {
for (; it != end; ++it) {
auto & scheme = communications.createScheme(it->first, sr);
const auto & node_scheme = it->second;
for (auto & node : node_scheme) {
auto an_begin = associated_nodes.begin();
auto an_it = an_begin;
auto an_end = associated_nodes.end();
std::vector<UInt> global_dofs_per_node;
while ((an_it = std::find(an_it, an_end, node)) != an_end) {
UInt pos = an_it - an_begin;
UInt local_eq_num = equation_numbers(pos);
UInt global_eq_num =
dof_manager.localToGlobalEquationNumber(local_eq_num);
global_dofs_per_node.push_back(global_eq_num);
++an_it;
}
std::sort(global_dofs_per_node.begin(), global_dofs_per_node.end());
std::transform(global_dofs_per_node.begin(), global_dofs_per_node.end(),
global_dofs_per_node.begin(), [this](UInt g) -> UInt {
UInt l = dof_manager.globalToLocalEquationNumber(g);
return l;
});
for (auto & leqnum : global_dofs_per_node) {
scheme.push_back(leqnum);
}
}
}
};
for (auto sr : send_recv_t{}) {
auto ncs_it = node_communications.begin_scheme(sr);
auto ncs_end = node_communications.end_scheme(sr);
transcode_node_to_global_dof_scheme(ncs_it, ncs_end, sr);
}
entities_changed = true;
}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::fillEntityToSend(Array<UInt> & dofs_to_send) {
UInt nb_dofs = dof_manager.getLocalSystemSize();
- this->entities_from_root.clear();
+ this->entities_from_root.zero();
dofs_to_send.resize(0);
for (UInt d : arange(nb_dofs)) {
if (not dof_manager.isLocalOrMasterDOF(d)) {
continue;
}
entities_from_root.push_back(d);
}
for (auto d : entities_from_root) {
UInt global_dof = dof_manager.localToGlobalEquationNumber(d);
dofs_to_send.push_back(global_dof);
}
}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::onNodesAdded(const Array<UInt> & /*nodes_list*/) {
auto dof_ids = dof_manager.getDOFIDs();
for (auto sr : iterate_send_recv) {
for (auto && data : communications.iterateSchemes(sr)) {
auto & scheme = data.second;
scheme.resize(0);
}
}
for (auto & dof_id : dof_ids) {
registerDOFs(dof_id);
}
// const auto & node_synchronizer =
// dof_manager.getMesh().getNodeSynchronizer(); const auto &
// node_communications = node_synchronizer.getCommunications();
// std::map<UInt, std::vector<UInt>> nodes_per_proc[2];
// for (auto sr : iterate_send_recv) {
// for (auto && data : node_communications.iterateSchemes(sr)) {
// auto proc = data.first;
// const auto & scheme = data.second;
// for (auto node : scheme) {
// nodes_per_proc[sr][proc].push_back(node);
// }
// }
// }
// std::map<UInt, std::vector<UInt>> dofs_per_proc[2];
// for (auto & dof_id : dof_ids) {
// const auto & associated_nodes =
// dof_manager.getDOFsAssociatedNodes(dof_id); const auto &
// local_equation_numbers =
// dof_manager.getEquationsNumbers(dof_id);
// for (auto tuple : zip(associated_nodes, local_equation_numbers)) {
// UInt assoc_node;
// UInt local_eq_num;
// std::tie(assoc_node, local_eq_num) = tuple;
// for (auto sr_it = send_recv_t::begin(); sr_it != send_recv_t::end();
// ++sr_it) {
// for (auto & pair : nodes_per_proc[*sr_it]) {
// if (std::find(pair.second.end(), pair.second.end(), assoc_node) !=
// pair.second.end()) {
// dofs_per_proc[*sr_it][pair.first].push_back(local_eq_num);
// }
// }
// }
// }
// }
// for (auto sr_it = send_recv_t::begin(); sr_it != send_recv_t::end();
// ++sr_it) {
// for (auto & pair : dofs_per_proc[*sr_it]) {
// std::sort(pair.second.begin(), pair.second.end(),
// [this](UInt la, UInt lb) -> bool {
// UInt ga = dof_manager.localToGlobalEquationNumber(la);
// UInt gb = dof_manager.localToGlobalEquationNumber(lb);
// return ga < gb;
// });
// auto & scheme = communications.getScheme(pair.first, *sr_it);
// scheme.resize(0);
// for (auto leq : pair.second) {
// scheme.push_back(leq);
// }
// }
// }
this->entities_changed = true;
}
} // namespace akantu
diff --git a/src/synchronizer/dof_synchronizer.hh b/src/synchronizer/dof_synchronizer.hh
index c9c55045c..d053f4e3c 100644
--- a/src/synchronizer/dof_synchronizer.hh
+++ b/src/synchronizer/dof_synchronizer.hh
@@ -1,83 +1,83 @@
/**
* @file dof_synchronizer.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Tue Feb 20 2018
*
* @brief Synchronize Array of DOFs
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Mesh;
class DOFManagerDefault;
} // namespace akantu
-#ifndef __AKANTU_DOF_SYNCHRONIZER_HH__
-#define __AKANTU_DOF_SYNCHRONIZER_HH__
+#ifndef AKANTU_DOF_SYNCHRONIZER_HH_
+#define AKANTU_DOF_SYNCHRONIZER_HH_
namespace akantu {
class DOFSynchronizer : public SynchronizerImpl<UInt> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFSynchronizer(DOFManagerDefault & dof_manager,
const ID & id = "dof_synchronizer", MemoryID memory_id = 0);
~DOFSynchronizer() override;
virtual void registerDOFs(const ID & dof_id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void onNodesAdded(const Array<UInt> & nodes);
protected:
Int getRank(const UInt & /*node*/) const final { AKANTU_TO_IMPLEMENT(); }
/// list the entities to send to root process
void fillEntityToSend(Array<UInt> & dofs_to_send) override;
inline UInt canScatterSize() override;
inline UInt gatheredSize() override;
inline UInt localToGlobalEntity(const UInt & local) override;
private:
/// information on the dofs
DOFManagerDefault & dof_manager;
};
} // namespace akantu
#include "dof_synchronizer_inline_impl.hh"
-#endif /* __AKANTU_DOF_SYNCHRONIZER_HH__ */
+#endif /* AKANTU_DOF_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/dof_synchronizer_inline_impl.hh b/src/synchronizer/dof_synchronizer_inline_impl.hh
index 795bb14d8..423549412 100644
--- a/src/synchronizer/dof_synchronizer_inline_impl.hh
+++ b/src/synchronizer/dof_synchronizer_inline_impl.hh
@@ -1,60 +1,60 @@
/**
* @file dof_synchronizer_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Wed Nov 08 2017
*
* @brief DOFSynchronizer inline implementation
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
#include "data_accessor.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_HH__
-#define __AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_HH__
+#ifndef AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_HH_
+#define AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt DOFSynchronizer::canScatterSize() {
return dof_manager.getLocalSystemSize();
}
/* -------------------------------------------------------------------------- */
inline UInt DOFSynchronizer::gatheredSize() {
return dof_manager.getSystemSize();
}
inline UInt DOFSynchronizer::localToGlobalEntity(const UInt & local) {
return dof_manager.localToGlobalEquationNumber(local);
}
} // namespace akantu
-#endif /* __AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_HH__ */
+#endif /* AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_HH_ */
diff --git a/src/synchronizer/element_info_per_processor.cc b/src/synchronizer/element_info_per_processor.cc
index 2e644e466..69877a1d8 100644
--- a/src/synchronizer/element_info_per_processor.cc
+++ b/src/synchronizer/element_info_per_processor.cc
@@ -1,123 +1,125 @@
/**
* @file element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
* @date last modification: Tue Nov 07 2017
*
* @brief Helper class to distribute a mesh
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_info_per_processor.hh"
#include "communicator.hh"
#include "element_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ElementInfoPerProc::ElementInfoPerProc(ElementSynchronizer & synchronizer,
UInt message_cnt, UInt root,
ElementType type)
: MeshAccessor(synchronizer.getMesh()), synchronizer(synchronizer),
rank(synchronizer.getCommunicator().whoAmI()),
nb_proc(synchronizer.getCommunicator().getNbProc()), root(root),
type(type), message_count(message_cnt), mesh(synchronizer.getMesh()),
comm(synchronizer.getCommunicator()) {}
/* -------------------------------------------------------------------------- */
bool ElementInfoPerProc::synchronize() {
auto need_synchronize = needSynchronize();
if (need_synchronize) {
synchronizeConnectivities();
synchronizePartitions();
synchronizeTags();
synchronizeGroups();
}
return need_synchronize;
}
/* -------------------------------------------------------------------------- */
void ElementInfoPerProc::fillCommunicationScheme(
const Array<UInt> & partition) {
AKANTU_DEBUG_IN();
Element element;
element.type = this->type;
auto & communications = this->synchronizer.getCommunications();
auto part = partition.begin();
std::map<UInt, Array<Element>> send_array_per_proc;
for (UInt lel = 0; lel < nb_local_element; ++lel) {
UInt nb_send = *part;
++part;
element.element = lel;
element.ghost_type = _not_ghost;
for (UInt p = 0; p < nb_send; ++p, ++part) {
UInt proc = *part;
AKANTU_DEBUG(dblAccessory,
"Must send : " << element << " to proc " << proc);
send_array_per_proc[proc].push_back(element);
}
}
for (auto & send_schemes : send_array_per_proc) {
- if (send_schemes.second.size() == 0)
+ if (send_schemes.second.empty()) {
continue;
+ }
auto & scheme = communications.createSendScheme(send_schemes.first);
scheme.append(send_schemes.second);
}
std::map<UInt, Array<Element>> recv_array_per_proc;
for (UInt gel = 0; gel < nb_ghost_element; ++gel, ++part) {
UInt proc = *part;
element.element = gel;
element.ghost_type = _ghost;
AKANTU_DEBUG(dblAccessory,
"Must recv : " << element << " from proc " << proc);
recv_array_per_proc[proc].push_back(element);
}
for (auto & recv_schemes : recv_array_per_proc) {
- if (recv_schemes.second.size() == 0)
+ if (recv_schemes.second.empty()) {
continue;
+ }
auto & scheme = communications.createRecvScheme(recv_schemes.first);
scheme.append(recv_schemes.second);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/element_info_per_processor.hh b/src/synchronizer/element_info_per_processor.hh
index 813bf85fe..fd3d677ac 100644
--- a/src/synchronizer/element_info_per_processor.hh
+++ b/src/synchronizer/element_info_per_processor.hh
@@ -1,150 +1,150 @@
/**
* @file element_info_per_processor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
* @date last modification: Tue Nov 07 2017
*
* @brief Helper classes to create the distributed synchronizer and distribute
* a mesh
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "communication_buffer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH__
-#define __AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH__
+#ifndef AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH_
+#define AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH_
namespace akantu {
class ElementSynchronizer;
class Communicator;
class MeshPartition;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementInfoPerProc : protected MeshAccessor {
public:
ElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root, ElementType type);
bool synchronize();
protected:
virtual void synchronizeConnectivities() = 0;
virtual void synchronizePartitions() = 0;
virtual void synchronizeTags() = 0;
virtual void synchronizeGroups() = 0;
virtual bool needSynchronize() = 0;
protected:
void fillCommunicationScheme(const Array<UInt> & partition);
template <class CommunicationBuffer>
void fillElementGroupsFromBuffer(CommunicationBuffer & buffer);
template <typename T, typename BufferType>
void fillMeshDataTemplated(BufferType & buffer, const std::string & tag_name,
UInt nb_component);
template <typename BufferType>
void fillMeshData(BufferType & buffer, const std::string & tag_name,
const MeshDataTypeCode & type_code, UInt nb_component);
protected:
ElementSynchronizer & synchronizer;
UInt rank{0};
UInt nb_proc{1};
UInt root{0};
ElementType type{_not_defined};
UInt nb_tags{0};
UInt nb_nodes_per_element{0};
UInt nb_element{0};
UInt nb_local_element{0};
UInt nb_ghost_element{0};
UInt message_count{0};
Mesh & mesh;
const Communicator & comm;
};
/* -------------------------------------------------------------------------- */
class MasterElementInfoPerProc : public ElementInfoPerProc {
public:
MasterElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root, ElementType type,
const MeshPartition & partition);
protected:
void synchronizeConnectivities() override;
void synchronizePartitions() override;
void synchronizeTags() override;
void synchronizeGroups() override;
bool needSynchronize() override { return type != _not_defined; }
protected:
template <typename T>
void fillTagBufferTemplated(std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name);
void fillTagBuffer(std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name);
private:
const MeshPartition & partition;
Vector<UInt> all_nb_local_element;
Vector<UInt> all_nb_ghost_element;
Vector<UInt> all_nb_element_to_send;
};
/* -------------------------------------------------------------------------- */
class SlaveElementInfoPerProc : public ElementInfoPerProc {
public:
SlaveElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root);
protected:
void synchronizeConnectivities() override;
void synchronizePartitions() override;
void synchronizeTags() override;
void synchronizeGroups() override;
bool needSynchronize() override;
private:
UInt nb_element_to_receive{0};
};
} // namespace akantu
#include "element_info_per_processor_tmpl.hh"
-#endif /* __AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH__ */
+#endif /* AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH_ */
diff --git a/src/synchronizer/element_info_per_processor_tmpl.hh b/src/synchronizer/element_info_per_processor_tmpl.hh
index 27d15e909..080a71fb7 100644
--- a/src/synchronizer/element_info_per_processor_tmpl.hh
+++ b/src/synchronizer/element_info_per_processor_tmpl.hh
@@ -1,146 +1,146 @@
/**
* @file element_info_per_processor_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
* @date last modification: Tue Feb 20 2018
*
* @brief Helper classes to create the distributed synchronizer and distribute
* a mesh
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "element_info_per_processor.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH__
-#define __AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH__
+#ifndef AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH_
+#define AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, typename BufferType>
void ElementInfoPerProc::fillMeshDataTemplated(BufferType & buffer,
const std::string & tag_name,
UInt nb_component) {
AKANTU_DEBUG_ASSERT(this->mesh.getNbElement(this->type) == nb_local_element,
"Did not got enought informations for the tag "
<< tag_name << " and the element type " << this->type
<< ":"
<< "_not_ghost."
<< " Got " << nb_local_element << " values, expected "
<< mesh.getNbElement(this->type));
mesh.getElementalData<T>(tag_name);
Array<T> & data = mesh.getElementalDataArrayAlloc<T>(
tag_name, this->type, _not_ghost, nb_component);
data.resize(nb_local_element);
/// unpacking the data, element by element
for (UInt i(0); i < nb_local_element; ++i) {
for (UInt j(0); j < nb_component; ++j) {
buffer >> data(i, j);
}
}
AKANTU_DEBUG_ASSERT(mesh.getNbElement(this->type, _ghost) == nb_ghost_element,
"Did not got enought informations for the tag "
<< tag_name << " and the element type " << this->type
<< ":"
<< "_ghost."
<< " Got " << nb_ghost_element << " values, expected "
<< mesh.getNbElement(this->type, _ghost));
Array<T> & data_ghost = mesh.getElementalDataArrayAlloc<T>(
tag_name, this->type, _ghost, nb_component);
data_ghost.resize(nb_ghost_element);
/// unpacking the ghost data, element by element
for (UInt j(0); j < nb_ghost_element; ++j) {
for (UInt k(0); k < nb_component; ++k) {
buffer >> data_ghost(j, k);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename BufferType>
void ElementInfoPerProc::fillMeshData(BufferType & buffer,
const std::string & tag_name,
const MeshDataTypeCode & type_code,
UInt nb_component) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
fillMeshDataTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(buffer, tag_name, \
nb_component); \
break; \
}
switch (type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not determine the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
template <class CommunicationBuffer>
void ElementInfoPerProc::fillElementGroupsFromBuffer(
CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
Element el;
el.type = type;
for (auto ghost_type : ghost_types) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
el.ghost_type = ghost_type;
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
std::vector<std::string> element_to_group;
buffer >> element_to_group;
AKANTU_DEBUG_ASSERT(e < mesh.getNbElement(type, ghost_type),
"The mesh does not have the element " << e);
for (auto && element : element_to_group) {
mesh.getElementGroup(element).add(el, false, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH__ */
+#endif /* AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH_ */
diff --git a/src/synchronizer/element_synchronizer.cc b/src/synchronizer/element_synchronizer.cc
index 7a073c4a8..80db73a6a 100644
--- a/src/synchronizer/element_synchronizer.cc
+++ b/src/synchronizer/element_synchronizer.cc
@@ -1,289 +1,294 @@
/**
* @file element_synchronizer.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Tue Feb 20 2018
*
* @brief implementation of a communicator using a static_communicator for
* real
* send/receive
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
#if defined(AKANTU_MODULE)
#define AKANTU_MODULE_SAVE_ AKANTU_MODULE
#undef AKANTU_MODULE
#endif
#define AKANTU_MODULE element_synchronizer
/* -------------------------------------------------------------------------- */
ElementSynchronizer::ElementSynchronizer(Mesh & mesh, const ID & id,
MemoryID memory_id,
bool register_to_event_manager,
EventHandlerPriority event_priority)
: SynchronizerImpl<Element>(mesh.getCommunicator(), id, memory_id),
mesh(mesh), element_to_prank("element_to_prank", id, memory_id) {
AKANTU_DEBUG_IN();
- if (register_to_event_manager)
+ if (register_to_event_manager) {
this->mesh.registerEventHandler(*this, event_priority);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementSynchronizer::ElementSynchronizer(const ElementSynchronizer & other,
const ID & id,
bool register_to_event_manager,
EventHandlerPriority event_priority)
: SynchronizerImpl<Element>(other, id), mesh(other.mesh),
element_to_prank("element_to_prank", id, other.memory_id) {
AKANTU_DEBUG_IN();
element_to_prank.copy(other.element_to_prank);
- if (register_to_event_manager)
+ if (register_to_event_manager) {
this->mesh.registerEventHandler(*this, event_priority);
+ }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementSynchronizer::~ElementSynchronizer() = default;
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::substituteElements(
const std::map<Element, Element> & old_to_new_elements) {
auto found_element_end = old_to_new_elements.end();
// substitute old elements with new ones
for (auto && sr : iterate_send_recv) {
for (auto && scheme_pair : communications.iterateSchemes(sr)) {
auto & list = scheme_pair.second;
for (auto & el : list) {
auto found_element_it = old_to_new_elements.find(el);
- if (found_element_it != found_element_end)
+ if (found_element_it != found_element_end) {
el = found_element_it->second;
+ }
}
}
}
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::onElementsChanged(
const Array<Element> & old_elements_list,
- const Array<Element> & new_elements_list, const ElementTypeMapArray<UInt> &,
- const ChangedElementsEvent &) {
+ const Array<Element> & new_elements_list,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const ChangedElementsEvent & /*unused*/) {
// create a map to link old elements to new ones
std::map<Element, Element> old_to_new_elements;
for (UInt el = 0; el < old_elements_list.size(); ++el) {
AKANTU_DEBUG_ASSERT(old_to_new_elements.find(old_elements_list(el)) ==
old_to_new_elements.end(),
"The same element cannot appear twice in the list");
old_to_new_elements[old_elements_list(el)] = new_elements_list(el);
}
substituteElements(old_to_new_elements);
communications.invalidateSizes();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::onElementsRemoved(
const Array<Element> & element_to_remove,
const ElementTypeMapArray<UInt> & new_numbering,
- const RemovedElementsEvent &) {
+ const RemovedElementsEvent & /*unused*/) {
AKANTU_DEBUG_IN();
this->filterScheme([&](auto && element) {
return std::find(element_to_remove.begin(), element_to_remove.end(),
element) == element_to_remove.end();
});
this->renumberElements(new_numbering);
communications.invalidateSizes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::buildElementToPrank() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
element_to_prank.initialize(mesh, _spatial_dimension = spatial_dimension,
_element_kind = _ek_not_defined,
_with_nb_element = true, _default_value = rank);
/// assign prank to all ghost elements
for (auto && scheme : communications.iterateSchemes(_recv)) {
auto & recv = scheme.second;
auto proc = scheme.first;
for (auto & element : recv) {
element_to_prank(element) = proc;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Int ElementSynchronizer::getRank(const Element & element) const {
if (not element_to_prank.exists(element.type, element.ghost_type)) {
// Nicolas: Ok This is nasty I know....
const_cast<ElementSynchronizer *>(this)->buildElementToPrank();
}
return element_to_prank(element);
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::renumberElements(
const ElementTypeMapArray<UInt> & new_numbering) {
for (auto && sr : iterate_send_recv) {
for (auto && scheme_pair : communications.iterateSchemes(sr)) {
auto & list = scheme_pair.second;
for (auto && el : list) {
- if (new_numbering.exists(el.type, el.ghost_type))
+ if (new_numbering.exists(el.type, el.ghost_type)) {
el.element = new_numbering(el);
+ }
}
}
}
}
/* -------------------------------------------------------------------------- */
UInt ElementSynchronizer::sanityCheckDataSize(const Array<Element> & elements,
const SynchronizationTag & tag,
bool from_comm_desc) const {
UInt size = SynchronizerImpl<Element>::sanityCheckDataSize(elements, tag,
from_comm_desc);
// global connectivities;
size += mesh.getNbNodesPerElementList(elements) * sizeof(UInt);
// barycenters
size += (elements.size() * mesh.getSpatialDimension() * sizeof(Real));
return size;
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::packSanityCheckData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & /*tag*/) const {
for (auto && element : elements) {
Vector<Real> barycenter(mesh.getSpatialDimension());
mesh.getBarycenter(element, barycenter);
buffer << barycenter;
const auto & conns = mesh.getConnectivity(element.type, element.ghost_type);
for (auto n : arange(conns.getNbComponent())) {
buffer << mesh.getNodeGlobalId(conns(element.element, n));
}
}
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::unpackSanityCheckData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag,
UInt proc, UInt rank) const {
auto spatial_dimension = mesh.getSpatialDimension();
std::set<SynchronizationTag> skip_conn_tags{
SynchronizationTag::_smmc_facets_conn,
SynchronizationTag::_giu_global_conn};
bool is_skip_tag_conn = skip_conn_tags.find(tag) != skip_conn_tags.end();
for (auto && element : elements) {
Vector<Real> barycenter_loc(spatial_dimension);
mesh.getBarycenter(element, barycenter_loc);
Vector<Real> barycenter(spatial_dimension);
buffer >> barycenter;
auto dist = barycenter_loc.distance(barycenter);
if (not Math::are_float_equal(dist, 0.)) {
AKANTU_EXCEPTION("Unpacking an unknown value for the element "
<< element << "(barycenter " << barycenter_loc
<< " != buffer " << barycenter << ") [" << dist
<< "] - tag: " << tag << " comm from " << proc << " to "
<< rank);
}
const auto & conns = mesh.getConnectivity(element.type, element.ghost_type);
Vector<UInt> global_conn(conns.getNbComponent());
Vector<UInt> local_global_conn(conns.getNbComponent());
auto is_same = true;
for (auto n : arange(global_conn.size())) {
buffer >> global_conn(n);
auto node = conns(element.element, n);
local_global_conn(n) = mesh.getNodeGlobalId(node);
is_same &= is_skip_tag_conn or mesh.isPureGhostNode(node) or
(local_global_conn(n) == global_conn(n));
}
if (not is_same) {
AKANTU_DEBUG_WARNING(
"The connectivity of the element "
<< element << " " << local_global_conn
<< " does not match the connectivity of the equivalent "
"element on proc "
<< proc << " " << global_conn << " in communication with tag "
<< tag);
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#if defined(AKANTU_MODULE_SAVE_)
#undef AKANTU_MODULE
#define AKANTU_MODULE AKANTU_MODULE_SAVE_
#undef AKANTU_MODULE_SAVE_
#endif
diff --git a/src/synchronizer/element_synchronizer.hh b/src/synchronizer/element_synchronizer.hh
index a032941c7..c50325b89 100644
--- a/src/synchronizer/element_synchronizer.hh
+++ b/src/synchronizer/element_synchronizer.hh
@@ -1,201 +1,201 @@
/**
* @file element_synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Main element synchronizer
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_ELEMENT_SYNCHRONIZER_HH__
-#define __AKANTU_ELEMENT_SYNCHRONIZER_HH__
+#ifndef AKANTU_ELEMENT_SYNCHRONIZER_HH_
+#define AKANTU_ELEMENT_SYNCHRONIZER_HH_
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "mesh_partition.hh"
#include "synchronizer_impl.hh"
namespace akantu {
class Mesh;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer : public SynchronizerImpl<Element>,
public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementSynchronizer(Mesh & mesh, const ID & id = "element_synchronizer",
MemoryID memory_id = 0,
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
ElementSynchronizer(const ElementSynchronizer & other,
const ID & id = "element_synchronizer_copy",
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
public:
~ElementSynchronizer() override;
friend class ElementInfoPerProc;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/// mesh event handler onElementsChanged
void onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) override;
/// mesh event handler onRemovedElement
- void onElementsRemoved(const Array<Element> & element_list,
+ void onElementsRemoved(const Array<Element> & element_to_remove,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
protected:
/// remove elements from the synchronizer without renumbering them
void removeElements(const Array<Element> & element_to_remove);
/// renumber the elements in the synchronizer
void renumberElements(const ElementTypeMapArray<UInt> & new_numbering);
/// build processor to element correspondence
void buildElementToPrank();
protected:
/// fill the nodes type vector
void fillNodesType(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
- const std::string & tag_name, const ElementType & el_type,
+ const std::string & tag_name, ElementType el_type,
const Array<UInt> & partition_num);
template <typename T>
void fillTagBufferTemplated(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name,
- const ElementType & el_type,
+ ElementType el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition);
void fillTagBuffer(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
- const std::string & tag_name, const ElementType & el_type,
+ const std::string & tag_name, ElementType el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition);
/// function that handels the MeshData to be split (root side)
static void synchronizeTagsSend(ElementSynchronizer & communicator, UInt root,
Mesh & mesh, UInt nb_tags,
- const ElementType & type,
+ ElementType type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_local_element, UInt nb_ghost_element);
/// function that handles the MeshData to be split (other nodes)
static void synchronizeTagsRecv(ElementSynchronizer & communicator, UInt root,
Mesh & mesh, UInt nb_tags,
- const ElementType & type,
+ ElementType type,
UInt nb_local_element, UInt nb_ghost_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(ElementSynchronizer & communicator,
UInt root, Mesh & mesh,
- const ElementType & type,
+ ElementType type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(ElementSynchronizer & communicator,
UInt root, Mesh & mesh,
- const ElementType & type);
+ ElementType type);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsMaster(ElementSynchronizer & communicator,
UInt root, Mesh & mesh);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsSlaves(ElementSynchronizer & communicator,
UInt root, Mesh & mesh);
template <class CommunicationBuffer>
static void fillNodeGroupsFromBuffer(ElementSynchronizer & communicator,
Mesh & mesh,
CommunicationBuffer & buffer);
/// substitute elements in the send and recv arrays
void
substituteElements(const std::map<Element, Element> & old_to_new_elements);
/* ------------------------------------------------------------------------ */
/* Sanity checks */
/* ------------------------------------------------------------------------ */
UInt sanityCheckDataSize(const Array<Element> & elements,
const SynchronizationTag & tag,
bool from_comm_desc = true) const override;
void packSanityCheckData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) const override;
void unpackSanityCheckData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/, UInt /*proc*/,
UInt /*rank*/) const override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Mesh, mesh, Mesh &);
AKANTU_GET_MACRO(ElementToRank, element_to_prank,
const ElementTypeMapArray<Int> &);
Int getRank(const Element & element) const final;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// reference to the underlying mesh
Mesh & mesh;
friend class FacetSynchronizer;
ElementTypeMapArray<Int> element_to_prank;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
-#endif /* __AKANTU_ELEMENT_SYNCHRONIZER_HH__ */
+#endif /* AKANTU_ELEMENT_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/facet_synchronizer.cc b/src/synchronizer/facet_synchronizer.cc
index 254283a27..d5fc90ddc 100644
--- a/src/synchronizer/facet_synchronizer.cc
+++ b/src/synchronizer/facet_synchronizer.cc
@@ -1,219 +1,226 @@
/**
* @file facet_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 05 2014
* @date last modification: Fri Jan 26 2018
*
* @brief Facet synchronizer for parallel simulations with cohesive elments
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "facet_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_MODULE)
#define AKANTU_MODULE_SAVE_ AKANTU_MODULE
#undef AKANTU_MODULE
#endif
#define AKANTU_MODULE facet_synchronizer
namespace akantu {
/* -------------------------------------------------------------------------- */
FacetSynchronizer::FacetSynchronizer(
Mesh & mesh, const ElementSynchronizer & element_synchronizer,
const ID & id, MemoryID memory_id)
: ElementSynchronizer(mesh, id, memory_id) {
auto spatial_dimension = mesh.getSpatialDimension();
element_to_prank.initialize(mesh, _spatial_dimension = spatial_dimension - 1,
_ghost_type = _ghost, _with_nb_element = true,
_default_value = rank);
// Build element to prank
for (auto && scheme_pair :
element_synchronizer.communications.iterateSchemes(_recv)) {
auto proc = std::get<0>(scheme_pair);
const auto & scheme = std::get<1>(scheme_pair);
for (auto && elem : scheme) {
const auto & facet_to_element =
mesh.getSubelementToElement(elem.type, elem.ghost_type);
Vector<Element> facets = facet_to_element.begin(
facet_to_element.getNbComponent())[elem.element];
for (UInt f = 0; f < facets.size(); ++f) {
const auto & facet = facets(f);
- if (facet == ElementNull)
+ if (facet == ElementNull) {
continue;
+ }
- if (facet.ghost_type == _not_ghost)
+ if (facet.ghost_type == _not_ghost) {
continue;
+ }
auto & facet_rank = element_to_prank(facet);
- if ((proc < UInt(facet_rank)) || (UInt(facet_rank) == rank))
+ if ((proc < UInt(facet_rank)) || (UInt(facet_rank) == rank)) {
facet_rank = proc;
+ }
}
}
}
ElementTypeMapArray<UInt> facet_global_connectivities(
"facet_global_connectivities", id, memory_id);
facet_global_connectivities.initialize(
mesh, _spatial_dimension = spatial_dimension - 1, _with_nb_element = true,
_with_nb_nodes_per_element = true);
mesh.getGlobalConnectivity(facet_global_connectivities);
// \TODO perhaps a global element numbering might be useful here...
for (auto type : facet_global_connectivities.elementTypes(_spatial_dimension =
_all_dimensions,
_element_kind = _ek_not_defined, _ghost_type = _not_ghost)) {
auto & conn = facet_global_connectivities(type, _not_ghost);
auto conn_view = make_view(conn, conn.getNbComponent());
std::for_each(conn_view.begin(), conn_view.end(), [&](auto & conn) {
std::sort(conn.storage(), conn.storage() + conn.size());
});
}
/// init facet check tracking
ElementTypeMapArray<bool> facet_checked("facet_checked", id, memory_id);
std::map<UInt, ElementTypeMapArray<UInt>> recv_connectivities;
/// Generate the recv scheme and connnectivities to send to the other
/// processors
for (auto && scheme_pair :
element_synchronizer.communications.iterateSchemes(_recv)) {
facet_checked.initialize(mesh, _spatial_dimension = spatial_dimension - 1,
_ghost_type = _ghost, _with_nb_element = true,
_default_value = false);
auto proc = scheme_pair.first;
const auto & elements = scheme_pair.second;
auto & facet_scheme = communications.createScheme(proc, _recv);
// this creates empty arrays...
auto & connectivities_for_proc = recv_connectivities[proc];
connectivities_for_proc.setID(
id + ":connectivities_for_proc:" + std::to_string(proc));
connectivities_for_proc.initialize(
mesh, _spatial_dimension = spatial_dimension - 1,
_with_nb_nodes_per_element = true, _ghost_type = _ghost);
// for every element in the element synchronizer communication scheme,
// check the facets to see if they should be communicated and create a
// connectivity array to match with the one other processors might send
for (auto && element : elements) {
const auto & facet_to_element =
mesh.getSubelementToElement(element.type, element.ghost_type);
Vector<Element> facets = facet_to_element.begin(
facet_to_element.getNbComponent())[element.element];
for (UInt f = 0; f < facets.size(); ++f) {
auto & facet = facets(f);
// exclude no valid facets
- if (facet == ElementNull)
+ if (facet == ElementNull) {
continue;
+ }
// exclude _ghost facet from send scheme and _not_ghost from receive
- if (facet.ghost_type != _ghost)
+ if (facet.ghost_type != _ghost) {
continue;
+ }
// exclude facet from other processors then the one of current
// interest in case of receive scheme
- if (UInt(element_to_prank(facet)) != proc)
+ if (UInt(element_to_prank(facet)) != proc) {
continue;
+ }
auto & checked = facet_checked(facet);
// skip already checked facets
- if (checked)
+ if (checked) {
continue;
+ }
checked = true;
facet_scheme.push_back(facet);
auto & global_conn =
facet_global_connectivities(facet.type, facet.ghost_type);
Vector<UInt> conn =
global_conn.begin(global_conn.getNbComponent())[facet.element];
std::sort(conn.storage(), conn.storage() + conn.size());
connectivities_for_proc(facet.type, facet.ghost_type).push_back(conn);
}
}
}
std::vector<CommunicationRequest> send_requests;
/// do every communication by element type
for (auto && type : mesh.elementTypes(spatial_dimension - 1)) {
for (auto && pair : recv_connectivities) {
auto proc = std::get<0>(pair);
const auto & connectivities_for_proc = std::get<1>(pair);
auto && tag = Tag::genTag(proc, type, 1337);
send_requests.push_back(
communicator.asyncSend(connectivities_for_proc(type, _ghost), proc,
tag, CommunicationMode::_synchronous));
}
auto nb_nodes_per_facet = Mesh::getNbNodesPerElement(type);
communicator.receiveAnyNumber<UInt>(
send_requests,
[&](auto && proc, auto && message) {
auto & local_connectivities =
facet_global_connectivities(type, _not_ghost);
auto & send_scheme = communications.createScheme(proc, _send);
auto conn_view = make_view(local_connectivities, nb_nodes_per_facet);
auto conn_begin = conn_view.begin();
auto conn_end = conn_view.end();
for (const auto & c_to_match :
make_view(message, nb_nodes_per_facet)) {
auto it = std::find(conn_begin, conn_end, c_to_match);
if (it != conn_end) {
auto facet = Element{type, UInt(it - conn_begin), _not_ghost};
send_scheme.push_back(facet);
} else {
AKANTU_EXCEPTION("No local facet found to send to proc "
<< proc << " corresponding to " << c_to_match);
}
}
},
Tag::genTag(rank, type, 1337));
}
}
} // namespace akantu
#if defined(AKANTU_MODULE_SAVE_)
#undef AKANTU_MODULE
#define AKANTU_MODULE AKANTU_MODULE_SAVE_
#undef AKANTU_MODULE_SAVE_
#endif
diff --git a/src/synchronizer/facet_synchronizer.hh b/src/synchronizer/facet_synchronizer.hh
index 619b884fe..23de4e1bb 100644
--- a/src/synchronizer/facet_synchronizer.hh
+++ b/src/synchronizer/facet_synchronizer.hh
@@ -1,96 +1,96 @@
/**
* @file facet_synchronizer.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief Facet synchronizer for parallel simulations with cohesive elments
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "fe_engine.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_FACET_SYNCHRONIZER_HH__
-#define __AKANTU_FACET_SYNCHRONIZER_HH__
+#ifndef AKANTU_FACET_SYNCHRONIZER_HH_
+#define AKANTU_FACET_SYNCHRONIZER_HH_
namespace akantu {
class FacetSynchronizer : public ElementSynchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FacetSynchronizer(Mesh & mesh,
const ElementSynchronizer & element_synchronizer,
const ID & id = "facet_synchronizer",
MemoryID memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// update distributed synchronizer after elements' insertion
void
updateDistributedSynchronizer(ElementSynchronizer & distributed_synchronizer,
DataAccessor<Element> & data_accessor,
const Mesh & mesh_cohesive);
protected:
/// update elements list based on facets list
void updateElementList(Array<Element> * elements,
const Array<Element> * facets,
const Mesh & mesh_cohesive);
/// setup facet synchronization
void
setupFacetSynchronization(ElementSynchronizer & distributed_synchronizer);
/// build send facet arrays
void buildSendElementList(
const Array<ElementTypeMapArray<UInt> *> & send_connectivity,
const Array<ElementTypeMapArray<UInt> *> & recv_connectivity,
const Array<ElementTypeMapArray<UInt> *> & temp_send_element);
/// build recv facet arrays
void buildRecvElementList(
const Array<ElementTypeMapArray<UInt> *> & temp_recv_element);
/// get facets' global connectivity for a list of elements
template <GhostType ghost_facets>
inline void getFacetGlobalConnectivity(
const ElementSynchronizer & distributed_synchronizer,
const ElementTypeMapArray<UInt> & rank_to_facet,
const Array<Element> * elements,
Array<ElementTypeMapArray<UInt> *> & connectivity,
Array<ElementTypeMapArray<UInt> *> & facets);
/// initialize ElementTypeMap containing correspondance between
/// facets and processors
void initRankToFacet(ElementTypeMapArray<UInt> & rank_to_facet);
/// find which processor a facet is assigned to
void buildRankToFacet(ElementTypeMapArray<UInt> & rank_to_facet,
const Array<Element> * elements);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
ElementTypeMapArray<UInt> facet_to_rank;
};
} // namespace akantu
#include "facet_synchronizer_inline_impl.hh"
-#endif /* __AKANTU_FACET_SYNCHRONIZER_HH__ */
+#endif /* AKANTU_FACET_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/facet_synchronizer_inline_impl.hh b/src/synchronizer/facet_synchronizer_inline_impl.hh
index 2f960718e..977db56cf 100644
--- a/src/synchronizer/facet_synchronizer_inline_impl.hh
+++ b/src/synchronizer/facet_synchronizer_inline_impl.hh
@@ -1,142 +1,30 @@
/**
* @file facet_synchronizer_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 05 2014
* @date last modification: Tue Nov 07 2017
*
* @brief facet synchronizer inline implementation
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-/* -------------------------------------------------------------------------- */
-// template<GhostType ghost_facets>
-// inline void FacetSynchronizer::getFacetGlobalConnectivity(const
-// DistributedSynchronizer & distributed_synchronizer,
-// const
-// ElementTypeMapArray<UInt>
-// & rank_to_facet,
-// const Array<Element> *
-// elements,
-// Array<ElementTypeMapArray<UInt>
-// *> & connectivity,
-// Array<ElementTypeMapArray<UInt>
-// *> & facets) {
-// AKANTU_DEBUG_IN();
-
-// UInt spatial_dimension = mesh.getSpatialDimension();
-
-// /// init facet check tracking
-// ElementTypeMapArray<bool> facet_checked("facet_checked", id);
-
-// mesh.initElementTypeMapArray(facet_checked, 1, spatial_dimension - 1);
-
-// Mesh::type_iterator first = mesh.firstType(spatial_dimension - 1,
-// ghost_facets);
-// Mesh::type_iterator last = mesh.lastType(spatial_dimension - 1,
-// ghost_facets);
-
-// for (; first != last; ++first) {
-// ElementType type = *first;
-// Array<bool> & f_checked = facet_checked(type, ghost_facets);
-// UInt nb_facet = mesh.getNbElement(type, ghost_facets);
-// f_checked.resize(nb_facet);
-// }
-
-// const Array<UInt> & nodes_global_ids =
-// distributed_synchronizer.mesh.getGlobalNodesIds();
-
-// /// loop on every processor
-// for (UInt p = 0; p < nb_proc; ++p) {
-// if (p == rank) continue;
-
-// /// reset facet check
-// Mesh::type_iterator first = mesh.firstType(spatial_dimension - 1,
-// ghost_facets);
-// Mesh::type_iterator last = mesh.lastType(spatial_dimension - 1,
-// ghost_facets);
-
-// for (; first != last; ++first) {
-// ElementType type = *first;
-// Array<bool> & f_checked = facet_checked(type, ghost_facets);
-// f_checked.clear();
-// }
-
-// ElementTypeMapArray<UInt> & global_conn = (*connectivity(p));
-// const Array<Element> & elem = elements[p];
-// ElementTypeMapArray<UInt> & facet_list = (*facets(p));
-
-// UInt nb_element = elem.getSize();
-
-// /// loop on every send/recv element
-// for (UInt el = 0; el < nb_element; ++el) {
-// ElementType type = elem(el).type;
-// GhostType gt = elem(el).ghost_type;
-// UInt el_index = elem(el).element;
-
-// const Array<Element> & facet_to_element =
-// mesh.getSubelementToElement(type, gt);
-// UInt nb_facets_per_element = Mesh::getNbFacetsPerElement(type);
-// ElementType facet_type = Mesh::getFacetType(type);
-// UInt nb_nodes_per_facet = Mesh::getNbNodesPerElement(facet_type);
-// Vector<UInt> conn_tmp(nb_nodes_per_facet);
-
-// /// loop on every facet of the element
-// for (UInt f = 0; f < nb_facets_per_element; ++f) {
-
-// const Element & facet = facet_to_element(el_index, f);
-// if (facet == ElementNull) continue;
-// UInt facet_index = facet.element;
-// GhostType facet_gt = facet.ghost_type;
-
-// const Array<UInt> & t_to_f = rank_to_facet(facet_type, facet_gt);
-
-// /// exclude not ghost facets, facets assigned to other
-// /// processors
-// if (facet_gt != ghost_facets) continue;
-// if ((facet_gt == _ghost) && (t_to_f(facet_index) != p)) continue;
-
-// /// exclude facets that have already been added
-// Array<bool> & f_checked = facet_checked(facet_type, facet_gt);
-// if (f_checked(facet_index)) continue;
-// else f_checked(facet_index) = true;
-
-// /// add facet index
-// Array<UInt> & f_list = facet_list(facet_type, facet_gt);
-// f_list.push_back(facet_index);
-
-// /// add sorted facet global connectivity
-// const Array<UInt> & conn = mesh.getConnectivity(facet_type, facet_gt);
-// Array<UInt> & g_conn = global_conn(facet_type, facet_gt);
-
-// for (UInt n = 0; n < nb_nodes_per_facet; ++n)
-// conn_tmp(n) = nodes_global_ids(conn(facet_index, n));
-
-// std::sort(conn_tmp.storage(), conn_tmp.storage() + nb_nodes_per_facet);
-
-// g_conn.push_back(conn_tmp);
-// }
-// }
-// }
-
-// AKANTU_DEBUG_OUT();
-// }
diff --git a/src/synchronizer/grid_synchronizer.cc b/src/synchronizer/grid_synchronizer.cc
index 4532aed95..c117fdb4f 100644
--- a/src/synchronizer/grid_synchronizer.cc
+++ b/src/synchronizer/grid_synchronizer.cc
@@ -1,474 +1,485 @@
/**
* @file grid_synchronizer.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Oct 03 2011
* @date last modification: Tue Nov 07 2017
*
* @brief implementation of the grid synchronizer
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "grid_synchronizer.hh"
#include "aka_grid_dynamic.hh"
#include "communicator.hh"
#include "fe_engine.hh"
#include "integration_point.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class E>
void GridSynchronizer::createGridSynchronizer(const SpatialGrid<E> & grid) {
AKANTU_DEBUG_IN();
const Communicator & comm = this->mesh.getCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
- if (nb_proc == 1)
+ if (nb_proc == 1) {
return;
+ }
UInt spatial_dimension = this->mesh.getSpatialDimension();
BBox my_bounding_box(spatial_dimension);
const auto & lower = grid.getLowerBounds();
const auto & upper = grid.getUpperBounds();
const auto & spacing = grid.getSpacing();
my_bounding_box.getLowerBounds() = lower - spacing;
my_bounding_box.getUpperBounds() = upper + spacing;
AKANTU_DEBUG_INFO(
"Exchange of bounding box to detect the overlapping regions.");
auto && bboxes = my_bounding_box.allGather(comm);
std::vector<bool> intersects_proc(nb_proc);
std::fill(intersects_proc.begin(), intersects_proc.end(), true);
Matrix<Int> first_cells(spatial_dimension, nb_proc);
Matrix<Int> last_cells(spatial_dimension, nb_proc);
std::map<UInt, ElementTypeMapArray<UInt>> element_per_proc;
// check the overlapping between my box and the one from other processors
for (UInt p = 0; p < nb_proc; ++p) {
- if (p == my_rank)
+ if (p == my_rank) {
continue;
+ }
const auto & proc_bounding_box = bboxes[p];
auto intersection = my_bounding_box.intersection(proc_bounding_box);
Vector<Int> first_cell_p = first_cells(p);
Vector<Int> last_cell_p = last_cells(p);
intersects_proc[p] = intersection;
if (intersects_proc[p]) {
for (UInt s = 0; s < spatial_dimension; ++s) {
first_cell_p(s) = grid.getCellID(intersection.getLowerBounds()(s), s);
last_cell_p(s) = grid.getCellID(intersection.getUpperBounds()(s), s);
}
}
// create the list of cells in the overlapping
using CellID = typename SpatialGrid<E>::CellID;
std::vector<CellID> cell_ids;
if (intersects_proc[p]) {
AKANTU_DEBUG_INFO("I intersects with processor " << p);
CellID cell_id(spatial_dimension);
// for (UInt i = 0; i < spatial_dimension; ++i) {
// if(first_cell_p[i] != 0) --first_cell_p[i];
// if(last_cell_p[i] != 0) ++last_cell_p[i];
// }
for (Int fd = first_cell_p(0); fd <= last_cell_p(0); ++fd) {
cell_id.setID(0, fd);
if (spatial_dimension == 1) {
cell_ids.push_back(cell_id);
} else {
for (Int sd = first_cell_p(1); sd <= last_cell_p(1); ++sd) {
cell_id.setID(1, sd);
if (spatial_dimension == 2) {
cell_ids.push_back(cell_id);
} else {
for (Int ld = first_cell_p(2); ld <= last_cell_p(2); ++ld) {
cell_id.setID(2, ld);
cell_ids.push_back(cell_id);
}
}
}
}
}
// get the list of elements in the cells of the overlapping
std::set<Element> to_send;
for (auto & cur_cell_id : cell_ids) {
auto & cell = grid.getCell(cur_cell_id);
for (auto & element : cell) {
to_send.insert(element);
}
}
AKANTU_DEBUG_INFO("I have prepared " << to_send.size()
<< " elements to send to processor "
<< p);
auto & scheme = this->getCommunications().createSendScheme(p);
std::stringstream sstr;
sstr << "element_per_proc_" << p;
element_per_proc.emplace(
std::piecewise_construct, std::forward_as_tuple(p),
std::forward_as_tuple(sstr.str(), id, memory_id));
ElementTypeMapArray<UInt> & elempproc = element_per_proc[p];
for (auto elem : to_send) {
ElementType type = elem.type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
// /!\ this part must be slow due to the access in the
// ElementTypeMapArray<UInt>
- if (!elempproc.exists(type, _not_ghost))
+ if (!elempproc.exists(type, _not_ghost)) {
elempproc.alloc(0, nb_nodes_per_element, type, _not_ghost);
+ }
Vector<UInt> global_connect(nb_nodes_per_element);
Vector<UInt> local_connect = mesh.getConnectivity(type).begin(
nb_nodes_per_element)[elem.element];
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
global_connect(i) = mesh.getNodeGlobalId(local_connect(i));
AKANTU_DEBUG_ASSERT(
global_connect(i) < mesh.getNbGlobalNodes(),
"This global node send in the connectivity does not seem correct "
<< global_connect(i) << " corresponding to "
<< local_connect(i) << " from element " << elem.element);
}
elempproc(type).push_back(global_connect);
scheme.push_back(elem);
}
}
}
AKANTU_DEBUG_INFO("I have finished to compute intersection,"
<< " no it's time to communicate with my neighbors");
/**
* Sending loop, sends the connectivity asynchronously to all concerned proc
*/
std::vector<CommunicationRequest> isend_requests;
Tensor3<UInt> space(2, _max_element_type, nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
- if (p == my_rank)
+ if (p == my_rank) {
continue;
+ }
- if (not intersects_proc[p])
+ if (not intersects_proc[p]) {
continue;
+ }
Matrix<UInt> info_proc = space(p);
auto & elempproc = element_per_proc[p];
UInt count = 0;
for (auto type : elempproc.elementTypes(_all_dimensions, _not_ghost)) {
Array<UInt> & conn = elempproc(type, _not_ghost);
Vector<UInt> info = info_proc((UInt)type);
info[0] = (UInt)type;
info[1] = conn.size() * conn.getNbComponent();
AKANTU_DEBUG_INFO(
"I have " << conn.size() << " elements of type " << type
<< " to send to processor " << p << " (communication tag : "
<< Tag::genTag(my_rank, count, DATA_TAG) << ")");
isend_requests.push_back(
comm.asyncSend(info, p, Tag::genTag(my_rank, count, SIZE_TAG)));
- if (info[1] != 0)
+ if (info[1] != 0) {
isend_requests.push_back(comm.asyncSend<UInt>(
conn, p, Tag::genTag(my_rank, count, DATA_TAG)));
+ }
++count;
}
Vector<UInt> info = info_proc((UInt)_not_defined);
info[0] = (UInt)_not_defined;
info[1] = 0;
isend_requests.push_back(
comm.asyncSend(info, p, Tag::genTag(my_rank, count, SIZE_TAG)));
}
/**
* Receives the connectivity and store them in the ghosts elements
*/
MeshAccessor mesh_accessor(mesh);
auto & global_nodes_ids = mesh_accessor.getNodesGlobalIds();
auto & nodes_type = mesh_accessor.getNodesFlags();
std::vector<CommunicationRequest> isend_nodes_requests;
Vector<UInt> nb_nodes_to_recv(nb_proc);
UInt nb_total_nodes_to_recv = 0;
UInt nb_current_nodes = global_nodes_ids.size();
NewNodesEvent new_nodes;
NewElementsEvent new_elements;
std::map<UInt, std::vector<UInt>> ask_nodes_per_proc;
for (UInt p = 0; p < nb_proc; ++p) {
nb_nodes_to_recv(p) = 0;
- if (p == my_rank)
+ if (p == my_rank) {
continue;
+ }
- if (!intersects_proc[p])
+ if (!intersects_proc[p]) {
continue;
+ }
auto & scheme = this->getCommunications().createRecvScheme(p);
ask_nodes_per_proc.emplace(std::piecewise_construct,
std::forward_as_tuple(p),
std::forward_as_tuple(0));
auto & ask_nodes = ask_nodes_per_proc[p];
UInt count = 0;
ElementType type = _not_defined;
do {
Vector<UInt> info(2);
comm.receive(info, p, Tag::genTag(p, count, SIZE_TAG));
type = (ElementType)info[0];
- if (type == _not_defined)
+ if (type == _not_defined) {
break;
+ }
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt nb_element = info[1] / nb_nodes_per_element;
Array<UInt> tmp_conn(nb_element, nb_nodes_per_element);
- tmp_conn.clear();
- if (info[1] != 0)
+ tmp_conn.zero();
+ if (info[1] != 0) {
comm.receive<UInt>(tmp_conn, p, Tag::genTag(p, count, DATA_TAG));
+ }
AKANTU_DEBUG_INFO("I will receive "
<< nb_element << " elements of type "
<< ElementType(info[0]) << " from processor " << p
<< " (communication tag : "
<< Tag::genTag(p, count, DATA_TAG) << ")");
auto & ghost_connectivity = mesh_accessor.getConnectivity(type, _ghost);
auto & ghost_counter = mesh_accessor.getGhostsCounters(type, _ghost);
UInt nb_ghost_element = ghost_connectivity.size();
Element element{type, 0, _ghost};
Vector<UInt> conn(nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el) {
UInt nb_node_to_ask_for_elem = 0;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt gn = tmp_conn(el, n);
UInt ln = global_nodes_ids.find(gn);
AKANTU_DEBUG_ASSERT(gn < mesh.getNbGlobalNodes(),
"This global node seems not correct "
<< gn << " from element " << el << " node "
<< n);
if (ln == UInt(-1)) {
global_nodes_ids.push_back(gn);
nodes_type.push_back(NodeFlag::_pure_ghost); // pure ghost node
ln = nb_current_nodes;
new_nodes.getList().push_back(ln);
++nb_current_nodes;
ask_nodes.push_back(gn);
++nb_node_to_ask_for_elem;
}
conn[n] = ln;
}
// all the nodes are already known locally, the element should
// already exists
auto c = UInt(-1);
if (nb_node_to_ask_for_elem == 0) {
c = ghost_connectivity.find(conn);
element.element = c;
}
if (c == UInt(-1)) {
element.element = nb_ghost_element;
++nb_ghost_element;
ghost_connectivity.push_back(conn);
ghost_counter.push_back(1);
new_elements.getList().push_back(element);
} else {
++ghost_counter(c);
}
scheme.push_back(element);
}
count++;
} while (type != _not_defined);
AKANTU_DEBUG_INFO("I have "
<< ask_nodes.size()
<< " missing nodes for elements coming from processor "
<< p << " (communication tag : "
<< Tag::genTag(my_rank, 0, ASK_NODES_TAG) << ")");
ask_nodes.push_back(UInt(-1));
isend_nodes_requests.push_back(
comm.asyncSend(ask_nodes, p, Tag::genTag(my_rank, 0, ASK_NODES_TAG)));
nb_nodes_to_recv(p) = ask_nodes.size() - 1;
nb_total_nodes_to_recv += nb_nodes_to_recv(p);
}
- comm.waitAll(isend_requests);
- comm.freeCommunicationRequest(isend_requests);
+ Communicator::waitAll(isend_requests);
+ Communicator::freeCommunicationRequest(isend_requests);
/**
* Sends requested nodes to proc
*/
auto & nodes = const_cast<Array<Real> &>(mesh.getNodes());
UInt nb_nodes = nodes.size();
std::vector<CommunicationRequest> isend_coordinates_requests;
std::map<UInt, Array<Real>> nodes_to_send_per_proc;
for (UInt p = 0; p < nb_proc; ++p) {
- if (p == my_rank || !intersects_proc[p])
+ if (p == my_rank || !intersects_proc[p]) {
continue;
+ }
Array<UInt> asked_nodes;
CommunicationStatus status;
AKANTU_DEBUG_INFO("Waiting list of nodes to send to processor "
<< p << "(communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
comm.probe<UInt>(p, Tag::genTag(p, 0, ASK_NODES_TAG), status);
UInt nb_nodes_to_send = status.size();
asked_nodes.resize(nb_nodes_to_send);
AKANTU_DEBUG_INFO("I have " << nb_nodes_to_send - 1
<< " nodes to send to processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
AKANTU_DEBUG_INFO("Getting list of nodes to send to processor "
<< p << " (communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
comm.receive(asked_nodes, p, Tag::genTag(p, 0, ASK_NODES_TAG));
nb_nodes_to_send--;
asked_nodes.resize(nb_nodes_to_send);
nodes_to_send_per_proc.emplace(std::piecewise_construct,
std::forward_as_tuple(p),
std::forward_as_tuple(0, spatial_dimension));
auto & nodes_to_send = nodes_to_send_per_proc[p];
auto node_it = nodes.begin(spatial_dimension);
for (UInt n = 0; n < nb_nodes_to_send; ++n) {
UInt ln = global_nodes_ids.find(asked_nodes(n));
AKANTU_DEBUG_ASSERT(ln != UInt(-1), "The node ["
<< asked_nodes(n)
<< "] requested by proc " << p
<< " was not found locally!");
nodes_to_send.push_back(node_it + ln);
}
if (nb_nodes_to_send != 0) {
AKANTU_DEBUG_INFO("Sending the "
<< nb_nodes_to_send << " nodes to processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, SEND_NODES_TAG) << ")");
isend_coordinates_requests.push_back(comm.asyncSend(
nodes_to_send, p, Tag::genTag(my_rank, 0, SEND_NODES_TAG)));
}
#if not defined(AKANTU_NDEBUG)
else {
AKANTU_DEBUG_INFO("No nodes to send to processor " << p);
}
#endif
}
- comm.waitAll(isend_nodes_requests);
- comm.freeCommunicationRequest(isend_nodes_requests);
+ Communicator::waitAll(isend_nodes_requests);
+ Communicator::freeCommunicationRequest(isend_nodes_requests);
nodes.resize(nb_total_nodes_to_recv + nb_nodes);
for (UInt p = 0; p < nb_proc; ++p) {
if ((p != my_rank) && (nb_nodes_to_recv(p) > 0)) {
AKANTU_DEBUG_INFO("Receiving the "
<< nb_nodes_to_recv(p) << " nodes from processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, SEND_NODES_TAG) << ")");
Vector<Real> nodes_to_recv(nodes.storage() + nb_nodes * spatial_dimension,
nb_nodes_to_recv(p) * spatial_dimension);
comm.receive(nodes_to_recv, p, Tag::genTag(p, 0, SEND_NODES_TAG));
nb_nodes += nb_nodes_to_recv(p);
}
#if not defined(AKANTU_NDEBUG)
else {
if (p != my_rank) {
AKANTU_DEBUG_INFO("No nodes to receive from processor " << p);
}
}
#endif
}
- comm.waitAll(isend_coordinates_requests);
- comm.freeCommunicationRequest(isend_coordinates_requests);
+ Communicator::waitAll(isend_coordinates_requests);
+ Communicator::freeCommunicationRequest(isend_coordinates_requests);
mesh.sendEvent(new_nodes);
mesh.sendEvent(new_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template void GridSynchronizer::createGridSynchronizer<IntegrationPoint>(
const SpatialGrid<IntegrationPoint> & grid);
template void GridSynchronizer::createGridSynchronizer<Element>(
const SpatialGrid<Element> & grid);
} // namespace akantu
diff --git a/src/synchronizer/grid_synchronizer.hh b/src/synchronizer/grid_synchronizer.hh
index 37fe2fc2e..841752fa4 100644
--- a/src/synchronizer/grid_synchronizer.hh
+++ b/src/synchronizer/grid_synchronizer.hh
@@ -1,101 +1,101 @@
/**
* @file grid_synchronizer.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Synchronizer based on spatial grid
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_synchronizer.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_GRID_SYNCHRONIZER_HH__
-#define __AKANTU_GRID_SYNCHRONIZER_HH__
+#ifndef AKANTU_GRID_SYNCHRONIZER_HH_
+#define AKANTU_GRID_SYNCHRONIZER_HH_
namespace akantu {
class Mesh;
template <class T> class SpatialGrid;
class GridSynchronizer : public ElementSynchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
template <typename E>
GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
const ID & id = "grid_synchronizer", MemoryID memory_id = 0,
- const bool register_to_event_manager = true,
+ bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
template <typename E>
GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
SynchronizerRegistry & synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register,
const ID & id = "grid_synchronizer", MemoryID memory_id = 0,
- const bool register_to_event_manager = true,
+ bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
~GridSynchronizer() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/**
*Create the Grid Synchronizer:
*Compute intersection and send info to neighbours that will be stored in
*ghosts elements
*/
template <typename E>
void createGridSynchronizer(const SpatialGrid<E> & grid);
protected:
/// Define the tags that will be used in the send and receive instructions
enum CommTags {
SIZE_TAG = 0,
DATA_TAG = 1,
ASK_NODES_TAG = 2,
SEND_NODES_TAG = 3
};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
#include "grid_synchronizer_tmpl.hh"
-#endif /* __AKANTU_GRID_SYNCHRONIZER_HH__ */
+#endif /* AKANTU_GRID_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/grid_synchronizer_tmpl.hh b/src/synchronizer/grid_synchronizer_tmpl.hh
index 414645625..58a665ee3 100644
--- a/src/synchronizer/grid_synchronizer_tmpl.hh
+++ b/src/synchronizer/grid_synchronizer_tmpl.hh
@@ -1,74 +1,74 @@
/**
* @file grid_synchronizer_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 06 2017
* @date last modification: Wed Aug 09 2017
*
* @brief implementation of the templated part of the grid syncrhonizers
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "grid_synchronizer.hh"
-#ifndef __AKANTU_GRID_SYNCHRONIZER_TMPL_HH__
-#define __AKANTU_GRID_SYNCHRONIZER_TMPL_HH__
+#ifndef AKANTU_GRID_SYNCHRONIZER_TMPL_HH_
+#define AKANTU_GRID_SYNCHRONIZER_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename E>
GridSynchronizer::GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
const ID & id, MemoryID memory_id,
const bool register_to_event_manager,
EventHandlerPriority event_priority)
: ElementSynchronizer(mesh, id, memory_id, register_to_event_manager,
event_priority) {
AKANTU_DEBUG_IN();
this->createGridSynchronizer(grid);
AKANTU_DEBUG_OUT();
}
template <typename E>
GridSynchronizer::GridSynchronizer(
Mesh & mesh, const SpatialGrid<E> & grid,
SynchronizerRegistry & synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register, const ID & id,
MemoryID memory_id, const bool register_to_event_manager,
EventHandlerPriority event_priority)
: GridSynchronizer(mesh, grid, id, memory_id, register_to_event_manager,
event_priority) {
AKANTU_DEBUG_IN();
// Register the tags if any
- for (auto & tag : tags_to_register) {
+ for (const auto & tag : tags_to_register) {
synchronizer_registry.registerSynchronizer(*this, tag);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
-#endif /* __AKANTU_GRID_SYNCHRONIZER_TMPL_HH__ */
+#endif /* AKANTU_GRID_SYNCHRONIZER_TMPL_HH_ */
diff --git a/src/synchronizer/master_element_info_per_processor.cc b/src/synchronizer/master_element_info_per_processor.cc
index fcda3d110..1421dbd4f 100644
--- a/src/synchronizer/master_element_info_per_processor.cc
+++ b/src/synchronizer/master_element_info_per_processor.cc
@@ -1,450 +1,456 @@
/**
* @file master_element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
* @date last modification: Tue Feb 20 2018
*
* @brief Helper class to distribute a mesh
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
#include <tuple>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MasterElementInfoPerProc::MasterElementInfoPerProc(
ElementSynchronizer & synchronizer, UInt message_cnt, UInt root,
ElementType type, const MeshPartition & partition)
: ElementInfoPerProc(synchronizer, message_cnt, root, type),
partition(partition), all_nb_local_element(nb_proc, 0),
all_nb_ghost_element(nb_proc, 0), all_nb_element_to_send(nb_proc, 0) {
Vector<UInt> size(5);
size(0) = (UInt)type;
if (type != _not_defined) {
nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
nb_element = mesh.getNbElement(type);
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el) {
this->all_nb_local_element[partition_num(el)]++;
for (auto part = ghost_partition.begin(el);
part != ghost_partition.end(el); ++part) {
this->all_nb_ghost_element[*part]++;
}
this->all_nb_element_to_send[partition_num(el)] +=
ghost_partition.getNbCols(el) + 1;
}
/// tag info
auto && tag_names = this->mesh.getTagNames(type);
this->nb_tags = tag_names.size();
size(4) = nb_tags;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
size(1) = this->all_nb_local_element[p];
size(2) = this->all_nb_ghost_element[p];
size(3) = this->all_nb_element_to_send[p];
AKANTU_DEBUG_INFO(
"Sending connectivities informations to proc "
<< p << " TAG("
- << Tag::genTag(this->rank, this->message_count, Tag::_SIZES)
+ << Tag::genTag(this->rank, this->message_count, Tag::_sizes)
<< ")");
comm.send(size, p,
- Tag::genTag(this->rank, this->message_count, Tag::_SIZES));
+ Tag::genTag(this->rank, this->message_count, Tag::_sizes));
} else {
this->nb_local_element = this->all_nb_local_element[p];
this->nb_ghost_element = this->all_nb_ghost_element[p];
}
}
} else {
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p != this->root) {
AKANTU_DEBUG_INFO(
"Sending empty connectivities informations to proc "
<< p << " TAG("
- << Tag::genTag(this->rank, this->message_count, Tag::_SIZES)
+ << Tag::genTag(this->rank, this->message_count, Tag::_sizes)
<< ")");
comm.send(size, p,
- Tag::genTag(this->rank, this->message_count, Tag::_SIZES));
+ Tag::genTag(this->rank, this->message_count, Tag::_sizes));
}
}
}
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizeConnectivities() {
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->nb_proc);
const auto & connectivities =
this->mesh.getConnectivity(this->type, _not_ghost);
/// copying the local connectivity
for (auto && part_conn :
zip(partition_num,
make_view(connectivities, this->nb_nodes_per_element))) {
auto && part = std::get<0>(part_conn);
auto && conn = std::get<1>(part_conn);
for (UInt i = 0; i < conn.size(); ++i) {
buffers[part].push_back(conn[i]);
}
}
/// copying the connectivity of ghost element
for (auto && tuple :
enumerate(make_view(connectivities, this->nb_nodes_per_element))) {
auto && el = std::get<0>(tuple);
auto && conn = std::get<1>(tuple);
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part) {
UInt proc = *part;
for (UInt i = 0; i < conn.size(); ++i) {
buffers[proc].push_back(conn[i]);
}
}
}
#ifndef AKANTU_NDEBUG
for (auto p : arange(this->nb_proc)) {
UInt size = this->nb_nodes_per_element *
(this->all_nb_local_element[p] + this->all_nb_ghost_element[p]);
AKANTU_DEBUG_ASSERT(
buffers[p].size() == size,
"The connectivity data packed in the buffer are not correct");
}
#endif
/// send all connectivity and ghost information to all processors
std::vector<CommunicationRequest> requests;
for (auto p : arange(this->nb_proc)) {
- if (p == this->root)
+ if (p == this->root) {
continue;
+ }
auto && tag =
- Tag::genTag(this->rank, this->message_count, Tag::_CONNECTIVITY);
+ Tag::genTag(this->rank, this->message_count, Tag::_connectivity);
AKANTU_DEBUG_INFO("Sending connectivities to proc " << p << " TAG(" << tag
<< ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
Array<UInt> & old_nodes = this->getNodesGlobalIds();
/// create the renumbered connectivity
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh, buffers[root], all_nb_local_element[root],
all_nb_ghost_element[root], type, old_nodes);
- comm.waitAll(requests);
- comm.freeCommunicationRequest(requests);
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizePartitions() {
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->partition.getNbPartition());
/// splitting the partition information to send them to processors
Vector<UInt> count_by_proc(nb_proc, 0);
for (UInt el = 0; el < nb_element; ++el) {
UInt proc = partition_num(el);
buffers[proc].push_back(ghost_partition.getNbCols(el));
UInt i(0);
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part, ++i) {
buffers[proc].push_back(*part);
}
}
for (UInt el = 0; el < nb_element; ++el) {
UInt i(0);
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part, ++i) {
buffers[*part].push_back(partition_num(el));
}
}
#ifndef AKANTU_NDEBUG
for (UInt p = 0; p < this->nb_proc; ++p) {
AKANTU_DEBUG_ASSERT(buffers[p].size() == (this->all_nb_ghost_element[p] +
this->all_nb_element_to_send[p]),
"Data stored in the buffer are most probably wrong");
}
#endif
std::vector<CommunicationRequest> requests;
/// last data to compute the communication scheme
for (UInt p = 0; p < this->nb_proc; ++p) {
- if (p == this->root)
+ if (p == this->root) {
continue;
+ }
auto && tag =
- Tag::genTag(this->rank, this->message_count, Tag::_PARTITIONS);
+ Tag::genTag(this->rank, this->message_count, Tag::_partitions);
AKANTU_DEBUG_INFO("Sending partition informations to proc " << p << " TAG("
<< tag << ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
if (Mesh::getSpatialDimension(this->type) ==
this->mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
this->fillCommunicationScheme(buffers[this->rank]);
}
- comm.waitAll(requests);
- comm.freeCommunicationRequest(requests);
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeTags() {
AKANTU_DEBUG_IN();
if (this->nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
/// tag info
auto tag_names = mesh.getTagNames(type);
// Make sure the tags are sorted (or at least not in random order),
// because they come from a map !!
std::sort(tag_names.begin(), tag_names.end());
// Sending information about the tags in mesh_data: name, data type and
// number of components of the underlying array associated to the current
// type
DynamicCommunicationBuffer mesh_data_sizes_buffer;
for (auto && tag_name : tag_names) {
mesh_data_sizes_buffer << tag_name;
mesh_data_sizes_buffer << mesh.getTypeCode(tag_name);
mesh_data_sizes_buffer << mesh.getNbComponent(tag_name, type);
}
AKANTU_DEBUG_INFO(
"Broadcasting the size of the information about the mesh data tags: ("
<< mesh_data_sizes_buffer.size() << ").");
AKANTU_DEBUG_INFO(
"Broadcasting the information about the mesh data tags, addr "
<< (void *)mesh_data_sizes_buffer.storage());
comm.broadcast(mesh_data_sizes_buffer, root);
- if (mesh_data_sizes_buffer.size() == 0)
+ if (mesh_data_sizes_buffer.empty()) {
return;
+ }
// Sending the actual data to each processor
std::vector<DynamicCommunicationBuffer> buffers(nb_proc);
// Loop over each tag for the current type
for (auto && tag_name : tag_names) {
// Type code of the current tag (i.e. the tag named *names_it)
this->fillTagBuffer(buffers, tag_name);
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
- if (p == root)
+ if (p == root) {
continue;
+ }
- auto && tag = Tag::genTag(this->rank, this->message_count, Tag::_MESH_DATA);
+ auto && tag = Tag::genTag(this->rank, this->message_count, Tag::_mesh_data);
AKANTU_DEBUG_INFO("Sending " << buffers[p].size()
<< " bytes of mesh data to proc " << p
<< " TAG(" << tag << ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
// Loop over each tag for the current type
for (auto && tag_name : tag_names) {
// Reinitializing the mesh data on the master
this->fillMeshData(buffers[root], tag_name, mesh.getTypeCode(tag_name),
mesh.getNbComponent(tag_name, type));
}
- comm.waitAll(requests);
- comm.freeCommunicationRequest(requests);
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void MasterElementInfoPerProc::fillTagBufferTemplated(
std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name) {
const auto & data = mesh.getElementalDataArray<T>(tag_name, type);
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
// Not possible to use the iterator because it potentially triggers the
// creation of complex
// type templates (such as akantu::Vector< std::vector<Element> > which don't
// implement the right interface
// (e.g. operator<< in that case).
// typename Array<T>::template const_iterator< Vector<T> > data_it =
// data.begin(data.getNbComponent());
// typename Array<T>::template const_iterator< Vector<T> > data_end =
// data.end(data.getNbComponent());
const T * data_it = data.storage();
const T * data_end = data.storage() + data.size() * data.getNbComponent();
const UInt * part = partition_num.storage();
/// copying the data, element by element
for (; data_it != data_end; ++part) {
for (UInt j(0); j < data.getNbComponent(); ++j, ++data_it) {
buffers[*part] << *data_it;
}
}
data_it = data.storage();
/// copying the data for the ghost element
for (UInt el(0); data_it != data_end;
data_it += data.getNbComponent(), ++el) {
auto it = ghost_partition.begin(el);
auto end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
for (UInt j(0); j < data.getNbComponent(); ++j) {
buffers[proc] << data_it[j];
}
}
}
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::fillTagBuffer(
std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
this->fillTagBufferTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(buffers, \
tag_name); \
break; \
}
MeshDataTypeCode data_type_code = mesh.getTypeCode(tag_name);
switch (data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not obtain the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
std::vector<DynamicCommunicationBuffer> buffers(nb_proc);
using ElementToGroup = std::vector<std::vector<std::string>>;
ElementToGroup element_to_group(nb_element);
for (auto & eg : mesh.iterateElementGroups()) {
const auto & name = eg.getName();
for (const auto & element : eg.getElements(type, _not_ghost)) {
element_to_group[element].push_back(name);
}
auto eit = eg.begin(type, _not_ghost);
- if (eit != eg.end(type, _not_ghost))
- const_cast<Array<UInt> &>(eg.getElements(type)).empty();
+ if (eit != eg.end(type, _not_ghost)) {
+ const_cast<Array<UInt> &>(eg.getElements(type)).zero();
+ }
}
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
/// copying the data, element by element
for (auto && pair : zip(partition_num, element_to_group)) {
buffers[std::get<0>(pair)] << std::get<1>(pair);
}
/// copying the data for the ghost element
for (auto && pair : enumerate(element_to_group)) {
auto && el = std::get<0>(pair);
auto it = ghost_partition.begin(el);
auto end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
buffers[proc] << std::get<1>(pair);
}
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
- if (p == this->rank)
+ if (p == this->rank) {
continue;
+ }
- auto && tag = Tag::genTag(this->rank, p, Tag::_ELEMENT_GROUP);
+ auto && tag = Tag::genTag(this->rank, p, Tag::_element_group);
AKANTU_DEBUG_INFO("Sending element groups to proc " << p << " TAG(" << tag
<< ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
this->fillElementGroupsFromBuffer(buffers[this->rank]);
- comm.waitAll(requests);
- comm.freeCommunicationRequest(requests);
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/mpi_communicator_data.hh b/src/synchronizer/mpi_communicator_data.hh
index 59cdfdb89..571d5d3e3 100644
--- a/src/synchronizer/mpi_communicator_data.hh
+++ b/src/synchronizer/mpi_communicator_data.hh
@@ -1,136 +1,139 @@
/**
* @file mpi_communicator_data.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Mon Feb 05 2018
*
* @brief Wrapper on MPI types to have a better separation between libraries
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#if __cplusplus > 199711L
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wliteral-suffix"
#endif
#endif
#include <mpi.h>
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#if __cplusplus > 199711L
#pragma GCC diagnostic pop
#endif
#endif
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MPI_TYPE_WRAPPER_HH__
-#define __AKANTU_MPI_TYPE_WRAPPER_HH__
+#ifndef AKANTU_MPI_TYPE_WRAPPER_HH_
+#define AKANTU_MPI_TYPE_WRAPPER_HH_
namespace akantu {
class MPICommunicatorData : public CommunicatorInternalData {
public:
MPICommunicatorData() {
MPI_Initialized(&is_externaly_initialized);
- if (not is_externaly_initialized) {
+ if (is_externaly_initialized == 0) {
MPI_Init(nullptr, nullptr); // valid according to the spec
}
MPI_Comm_create_errhandler(MPICommunicatorData::errorHandler,
&error_handler);
MPI_Comm_set_errhandler(MPI_COMM_WORLD, error_handler);
setMPICommunicator(MPI_COMM_WORLD);
}
~MPICommunicatorData() override {
- if (not is_externaly_initialized) {
+ if (is_externaly_initialized == 0) {
MPI_Comm_set_errhandler(communicator, save_error_handler);
MPI_Errhandler_free(&error_handler);
MPI_Finalize();
}
}
inline void setMPICommunicator(MPI_Comm comm) {
MPI_Comm_set_errhandler(communicator, save_error_handler);
communicator = comm;
MPI_Comm_get_errhandler(comm, &save_error_handler);
MPI_Comm_set_errhandler(comm, error_handler);
}
inline int rank() const {
int prank;
MPI_Comm_rank(communicator, &prank);
return prank;
}
inline int size() const {
int psize;
MPI_Comm_size(communicator, &psize);
return psize;
}
inline MPI_Comm getMPICommunicator() const { return communicator; }
- inline int getMaxTag() const {
+ static int getMaxTag() {
int flag;
int * value;
// not defined on derived intra-communicator
MPI_Comm_get_attr(MPI_COMM_WORLD, MPI_TAG_UB, &value, &flag);
AKANTU_DEBUG_ASSERT(flag, "No attribute MPI_TAG_UB.");
return *value;
}
private:
MPI_Comm communicator{MPI_COMM_WORLD};
MPI_Errhandler save_error_handler{MPI_ERRORS_ARE_FATAL};
static int is_externaly_initialized;
/* ------------------------------------------------------------------------ */
MPI_Errhandler error_handler;
- static void errorHandler(MPI_Comm * /*comm*/, int * error_code, ...) {
+ static void
+ errorHandler(MPI_Comm * /*comm*/,
+ int * error_code, // NOLINT(readability-non-const-parameter)
+ ...) {
char error_string[MPI_MAX_ERROR_STRING];
int str_len;
MPI_Error_string(*error_code, error_string, &str_len);
AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
"MPI failed with the error code "
<< *error_code << ": \"" << error_string
<< "\"");
}
};
} // namespace akantu
-#endif /* __AKANTU_MPI_TYPE_WRAPPER_HH__ */
+#endif /* AKANTU_MPI_TYPE_WRAPPER_HH_ */
diff --git a/src/synchronizer/node_info_per_processor.cc b/src/synchronizer/node_info_per_processor.cc
index b9988812c..eeee66941 100644
--- a/src/synchronizer/node_info_per_processor.cc
+++ b/src/synchronizer/node_info_per_processor.cc
@@ -1,840 +1,846 @@
/**
* @file node_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
* @date last modification: Wed Nov 08 2017
*
* @brief Please type the brief for file: Helper classes to create the
* distributed synchronizer and distribute a mesh
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_info_per_processor.hh"
#include "communicator.hh"
#include "node_group.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeInfoPerProc::NodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: MeshAccessor(synchronizer.getMesh()), synchronizer(synchronizer),
comm(synchronizer.getCommunicator()), rank(comm.whoAmI()),
nb_proc(comm.getNbProc()), root(root), mesh(synchronizer.getMesh()),
spatial_dimension(synchronizer.getMesh().getSpatialDimension()),
message_count(message_cnt) {}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::synchronize() {
synchronizeNodes();
synchronizeTypes();
synchronizeGroups();
synchronizePeriodicity();
synchronizeTags();
}
/* -------------------------------------------------------------------------- */
template <class CommunicationBuffer>
void NodeInfoPerProc::fillNodeGroupsFromBuffer(CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
std::vector<std::vector<std::string>> node_to_group;
buffer >> node_to_group;
AKANTU_DEBUG_ASSERT(node_to_group.size() == mesh.getNbGlobalNodes(),
"Not the good amount of nodes where transmitted");
const auto & global_nodes = mesh.getGlobalNodesIds();
for (auto && data : enumerate(global_nodes)) {
for (const auto & node : node_to_group[std::get<1>(data)]) {
mesh.getNodeGroup(node).add(std::get<0>(data), false);
}
}
for (auto && ng_data : mesh.iterateNodeGroups()) {
ng_data.optimize();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillNodesType() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
auto & nodes_flags = this->getNodesFlags();
Array<UInt> nodes_set(nb_nodes);
nodes_set.set(0);
enum NodeSet {
NORMAL_SET = 1,
GHOST_SET = 2,
};
Array<bool> already_seen(nb_nodes, 1, false);
for (auto gt : ghost_types) {
UInt set = NORMAL_SET;
- if (gt == _ghost)
+ if (gt == _ghost) {
set = GHOST_SET;
+ }
already_seen.set(false);
for (auto && type :
mesh.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
const auto & connectivity = mesh.getConnectivity(type, gt);
- for (auto & conn :
+ for (const auto & conn :
make_view(connectivity, connectivity.getNbComponent())) {
for (UInt n = 0; n < conn.size(); ++n) {
AKANTU_DEBUG_ASSERT(conn(n) < nb_nodes,
"Node " << conn(n)
<< " bigger than number of nodes "
<< nb_nodes);
if (!already_seen(conn(n))) {
nodes_set(conn(n)) += set;
already_seen(conn(n)) = true;
}
}
}
}
}
nodes_flags.resize(nb_nodes);
for (UInt i = 0; i < nb_nodes; ++i) {
- if (nodes_set(i) == NORMAL_SET)
+ if (nodes_set(i) == NORMAL_SET) {
nodes_flags(i) = NodeFlag::_normal;
- else if (nodes_set(i) == GHOST_SET)
+ } else if (nodes_set(i) == GHOST_SET) {
nodes_flags(i) = NodeFlag::_pure_ghost;
- else if (nodes_set(i) == (GHOST_SET + NORMAL_SET))
+ } else if (nodes_set(i) == (GHOST_SET + NORMAL_SET)) {
nodes_flags(i) = NodeFlag::_master;
- else {
+ } else {
AKANTU_EXCEPTION("Gni ?");
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillCommunicationScheme(const Array<UInt> & master_info) {
AKANTU_DEBUG_IN();
Communications<UInt> & communications =
this->synchronizer.getCommunications();
{ // send schemes
std::map<UInt, Array<UInt>> send_array_per_proc;
for (const auto & send_info : make_view(master_info, 2)) {
send_array_per_proc[send_info(0)].push_back(send_info(1));
}
for (auto & send_schemes : send_array_per_proc) {
auto & scheme = communications.createSendScheme(send_schemes.first);
auto & sends = send_schemes.second;
std::sort(sends.begin(), sends.end());
std::transform(sends.begin(), sends.end(), sends.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(sends);
AKANTU_DEBUG_INFO("Proc " << rank << " has " << sends.size()
<< " nodes to send to to proc "
<< send_schemes.first);
}
}
{ // receive schemes
std::map<UInt, Array<UInt>> recv_array_per_proc;
for (auto node : arange(mesh.getNbNodes())) {
if (mesh.isSlaveNode(node)) {
recv_array_per_proc[mesh.getNodePrank(node)].push_back(
mesh.getNodeGlobalId(node));
}
}
for (auto & recv_schemes : recv_array_per_proc) {
auto & scheme = communications.createRecvScheme(recv_schemes.first);
auto & recvs = recv_schemes.second;
std::sort(recvs.begin(), recvs.end());
std::transform(recvs.begin(), recvs.end(), recvs.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(recvs);
AKANTU_DEBUG_INFO("Proc " << rank << " will receive " << recvs.size()
<< " nodes from proc " << recv_schemes.first);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillPeriodicPairs(const Array<UInt> & global_pairs,
std::vector<UInt> & missing_nodes) {
this->wipePeriodicInfo();
auto & nodes_flags = this->getNodesFlags();
auto checkIsLocal = [&](auto && global_node) {
auto && node = mesh.getNodeLocalId(global_node);
if (node == UInt(-1)) {
auto & global_nodes = this->getNodesGlobalIds();
node = global_nodes.size();
global_nodes.push_back(global_node);
nodes_flags.push_back(NodeFlag::_pure_ghost);
missing_nodes.push_back(global_node);
std::cout << "Missing node " << node << std::endl;
}
return node;
};
for (auto && pairs : make_view(global_pairs, 2)) {
UInt slave = checkIsLocal(pairs(0));
UInt master = checkIsLocal(pairs(1));
this->addPeriodicSlave(slave, master);
}
this->markMeshPeriodic();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::receiveMissingPeriodic(
DynamicCommunicationBuffer & buffer) {
auto & nodes = this->getNodes();
Communications<UInt> & communications =
this->synchronizer.getCommunications();
std::size_t nb_nodes;
buffer >> nb_nodes;
for (auto _ [[gnu::unused]] : arange(nb_nodes)) {
Vector<Real> pos(spatial_dimension);
Int prank;
buffer >> pos;
buffer >> prank;
UInt node = nodes.size();
this->setNodePrank(node, prank);
nodes.push_back(pos);
auto & scheme = communications.createRecvScheme(prank);
scheme.push_back(node);
}
while (buffer.getLeftToUnpack() != 0) {
Int prank;
UInt gnode;
buffer >> gnode;
buffer >> prank;
auto node = mesh.getNodeLocalId(gnode);
AKANTU_DEBUG_ASSERT(node != UInt(-1),
"I cannot send the node "
<< gnode << " to proc " << prank
<< " because it is note a local node");
auto & scheme = communications.createSendScheme(prank);
scheme.push_back(node);
}
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillNodalData(DynamicCommunicationBuffer & buffer,
- std::string tag_name) {
+ const std::string & tag_name) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, _, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
auto & nodal_data = \
mesh.getNodalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(tag_name); \
nodal_data.resize(mesh.getNbNodes()); \
for (auto && data : make_view(nodal_data)) { \
buffer >> data; \
} \
break; \
}
MeshDataTypeCode data_type_code =
mesh.getTypeCode(tag_name, MeshDataType::_nodal);
switch (data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not obtain the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
MasterNodeInfoPerProc::MasterNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root),
all_nodes(0, synchronizer.getMesh().getSpatialDimension()) {
UInt nb_global_nodes = this->mesh.getNbGlobalNodes();
this->comm.broadcast(nb_global_nodes, this->root);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeNodes() {
this->nodes_per_proc.resize(nb_proc);
this->nb_nodes_per_proc.resize(nb_proc);
Array<Real> local_nodes(0, spatial_dimension);
Array<Real> & nodes = this->getNodes();
all_nodes.copy(nodes);
nodes_pranks.resize(nodes.size(), UInt(-1));
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_nodes = 0;
// UInt * buffer;
- Array<Real> * nodes_to_send;
+ Array<Real> * nodes_to_send{nullptr};
Array<UInt> & nodespp = nodes_per_proc[p];
if (p != root) {
nodes_to_send = new Array<Real>(0, spatial_dimension);
AKANTU_DEBUG_INFO("Receiving number of nodes from proc "
- << p << " " << Tag::genTag(p, 0, Tag::_NB_NODES));
- comm.receive(nb_nodes, p, Tag::genTag(p, 0, Tag::_NB_NODES));
+ << p << " " << Tag::genTag(p, 0, Tag::_nb_nodes));
+ comm.receive(nb_nodes, p, Tag::genTag(p, 0, Tag::_nb_nodes));
nodespp.resize(nb_nodes);
this->nb_nodes_per_proc(p) = nb_nodes;
AKANTU_DEBUG_INFO("Receiving list of nodes from proc "
- << p << " " << Tag::genTag(p, 0, Tag::_NODES));
- comm.receive(nodespp, p, Tag::genTag(p, 0, Tag::_NODES));
+ << p << " " << Tag::genTag(p, 0, Tag::_nodes));
+ comm.receive(nodespp, p, Tag::genTag(p, 0, Tag::_nodes));
} else {
Array<UInt> & local_ids = this->getNodesGlobalIds();
this->nb_nodes_per_proc(p) = local_ids.size();
nodespp.copy(local_ids);
nodes_to_send = &local_nodes;
}
/// get the coordinates for the selected nodes
for (const auto & node : nodespp) {
Vector<Real> coord(nodes.storage() + spatial_dimension * node,
spatial_dimension);
nodes_to_send->push_back(coord);
}
if (p != root) { /// send them for distant processors
AKANTU_DEBUG_INFO("Sending coordinates to proc "
<< p << " "
- << Tag::genTag(this->rank, 0, Tag::_COORDINATES));
+ << Tag::genTag(this->rank, 0, Tag::_coordinates));
comm.send(*nodes_to_send, p,
- Tag::genTag(this->rank, 0, Tag::_COORDINATES));
+ Tag::genTag(this->rank, 0, Tag::_coordinates));
+
delete nodes_to_send;
}
}
/// construct the local nodes coordinates
nodes.copy(local_nodes);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeTypes() {
// <global_id, <proc, local_id> >
std::multimap<UInt, std::pair<UInt, UInt>> nodes_to_proc;
std::vector<Array<NodeFlag>> nodes_flags_per_proc(nb_proc);
std::vector<Array<Int>> nodes_prank_per_proc(nb_proc);
- if (mesh.isPeriodic())
+ if (mesh.isPeriodic()) {
all_periodic_flags.copy(this->getNodesFlags());
+ }
// arrays containing pairs of (proc, node)
std::vector<Array<UInt>> nodes_to_send_per_proc(nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
nodes_flags_per_proc[p].resize(nb_nodes_per_proc(p), NodeFlag(0xFF));
nodes_prank_per_proc[p].resize(nb_nodes_per_proc(p), -1);
}
this->fillNodesType();
auto is_master = [](auto && flag) {
return (flag & NodeFlag::_shared_mask) == NodeFlag::_master;
};
auto is_local = [](auto && flag) {
return (flag & NodeFlag::_shared_mask) == NodeFlag::_normal;
};
for (auto p : arange(nb_proc)) {
auto & nodes_flags = nodes_flags_per_proc[p];
if (p != root) {
AKANTU_DEBUG_INFO(
"Receiving first nodes types from proc "
<< p << " "
- << Tag::genTag(this->rank, this->message_count, Tag::_NODES_TYPE));
- comm.receive(nodes_flags, p, Tag::genTag(p, 0, Tag::_NODES_TYPE));
+ << Tag::genTag(this->rank, this->message_count, Tag::_nodes_type));
+ comm.receive(nodes_flags, p, Tag::genTag(p, 0, Tag::_nodes_type));
} else {
nodes_flags.copy(this->getNodesFlags());
}
// stack all processors claiming to be master for a node
for (auto local_node : arange(nb_nodes_per_proc(p))) {
auto global_node = nodes_per_proc[p](local_node);
if (is_master(nodes_flags(local_node))) {
nodes_to_proc.insert(
std::make_pair(global_node, std::make_pair(p, local_node)));
} else if (is_local(nodes_flags(local_node))) {
nodes_pranks[global_node] = p;
}
}
}
for (auto i : arange(mesh.getNbGlobalNodes())) {
auto it_range = nodes_to_proc.equal_range(i);
- if (it_range.first == nodes_to_proc.end() || it_range.first->first != i)
+ if (it_range.first == nodes_to_proc.end() || it_range.first->first != i) {
continue;
+ }
// pick the first processor out of the multi-map as the actual master
UInt master_proc = (it_range.first)->second.first;
nodes_pranks[i] = master_proc;
for (auto && data : range(it_range.first, it_range.second)) {
auto proc = data.second.first;
auto node = data.second.second;
if (proc != master_proc) {
// store the info on all the slaves for a given master
nodes_flags_per_proc[proc](node) = NodeFlag::_slave;
nodes_to_send_per_proc[master_proc].push_back(proc);
nodes_to_send_per_proc[master_proc].push_back(i);
}
}
}
/// Fills the nodes prank per proc
for (auto && data : zip(arange(nb_proc), nodes_per_proc, nodes_prank_per_proc,
nodes_flags_per_proc)) {
for (auto && node_data :
zip(std::get<1>(data), std::get<2>(data), std::get<3>(data))) {
if (std::get<2>(node_data) == NodeFlag::_normal) {
std::get<1>(node_data) = std::get<0>(data);
} else {
std::get<1>(node_data) = nodes_pranks(std::get<0>(node_data));
}
}
}
std::vector<CommunicationRequest> requests_send_type;
std::vector<CommunicationRequest> requests_send_master_info;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
- auto tag0 = Tag::genTag(this->rank, 0, Tag::_NODES_TYPE);
+ auto tag0 = Tag::genTag(this->rank, 0, Tag::_nodes_type);
AKANTU_DEBUG_INFO("Sending nodes types to proc " << p << " " << tag0);
requests_send_type.push_back(
comm.asyncSend(nodes_flags_per_proc[p], p, tag0));
- auto tag2 = Tag::genTag(this->rank, 2, Tag::_NODES_TYPE);
+ auto tag2 = Tag::genTag(this->rank, 2, Tag::_nodes_type);
AKANTU_DEBUG_INFO("Sending nodes pranks to proc " << p << " " << tag2);
requests_send_type.push_back(
comm.asyncSend(nodes_prank_per_proc[p], p, tag2));
auto & nodes_to_send = nodes_to_send_per_proc[p];
- auto tag1 = Tag::genTag(this->rank, 1, Tag::_NODES_TYPE);
+ auto tag1 = Tag::genTag(this->rank, 1, Tag::_nodes_type);
AKANTU_DEBUG_INFO("Sending nodes master info to proc " << p << " "
<< tag1);
requests_send_master_info.push_back(
comm.asyncSend(nodes_to_send, p, tag1));
} else {
this->getNodesFlags().copy(nodes_flags_per_proc[p]);
for (auto && data : enumerate(nodes_prank_per_proc[p])) {
auto node = std::get<0>(data);
if (not(mesh.isMasterNode(node) or mesh.isLocalNode(node))) {
this->setNodePrank(node, std::get<1>(data));
}
}
this->fillCommunicationScheme(nodes_to_send_per_proc[root]);
}
}
- comm.waitAll(requests_send_type);
- comm.freeCommunicationRequest(requests_send_type);
- requests_send_type.clear();
+ Communicator::waitAll(requests_send_type);
+ Communicator::freeCommunicationRequest(requests_send_type);
- comm.waitAll(requests_send_master_info);
- comm.freeCommunicationRequest(requests_send_master_info);
+ Communicator::waitAll(requests_send_master_info);
+ Communicator::freeCommunicationRequest(requests_send_master_info);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
UInt nb_total_nodes = mesh.getNbGlobalNodes();
DynamicCommunicationBuffer buffer;
using NodeToGroup = std::vector<std::vector<std::string>>;
NodeToGroup node_to_group;
node_to_group.resize(nb_total_nodes);
for (auto & ng : mesh.iterateNodeGroups()) {
std::string name = ng.getName();
for (auto && node : ng.getNodes()) {
node_to_group[node].push_back(name);
}
- ng.empty();
+ ng.clear();
}
buffer << node_to_group;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
- if (p == this->rank)
+ if (p == this->rank) {
continue;
+ }
AKANTU_DEBUG_INFO("Sending node groups to proc "
<< p << " "
- << Tag::genTag(this->rank, p, Tag::_NODE_GROUP));
+ << Tag::genTag(this->rank, p, Tag::_node_group));
requests.push_back(comm.asyncSend(
- buffer, p, Tag::genTag(this->rank, p, Tag::_NODE_GROUP)));
+ buffer, p, Tag::genTag(this->rank, p, Tag::_node_group)));
}
this->fillNodeGroupsFromBuffer(buffer);
- comm.waitAll(requests);
- comm.freeCommunicationRequest(requests);
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizePeriodicity() {
bool is_periodic = mesh.isPeriodic();
comm.broadcast(is_periodic, root);
- if (not is_periodic)
+ if (not is_periodic) {
return;
+ }
std::vector<CommunicationRequest> requests;
std::vector<Array<UInt>> periodic_info_to_send_per_proc;
for (auto p : arange(nb_proc)) {
periodic_info_to_send_per_proc.emplace_back(0, 2);
auto && periodic_info = periodic_info_to_send_per_proc.back();
for (UInt proc_local_node : arange(nb_nodes_per_proc(p))) {
UInt global_node = nodes_per_proc[p](proc_local_node);
if ((all_periodic_flags[global_node] & NodeFlag::_periodic_mask) ==
NodeFlag::_periodic_slave) {
periodic_info.push_back(
Vector<UInt>{global_node, mesh.getPeriodicMaster(global_node)});
}
}
- if (p == root)
+ if (p == root) {
continue;
+ }
- auto && tag = Tag::genTag(this->rank, p, Tag::_PERIODIC_SLAVES);
+ auto && tag = Tag::genTag(this->rank, p, Tag::_periodic_slaves);
AKANTU_DEBUG_INFO("Sending periodic info to proc " << p << " " << tag);
requests.push_back(comm.asyncSend(periodic_info, p, tag));
}
CommunicationStatus status;
std::vector<DynamicCommunicationBuffer> buffers(nb_proc);
std::vector<std::vector<UInt>> proc_missings(nb_proc);
auto nodes_it = all_nodes.begin(spatial_dimension);
for (UInt p = 0; p < nb_proc; ++p) {
auto & proc_missing = proc_missings[p];
if (p != root) {
- auto && tag = Tag::genTag(p, 0, Tag::_PERIODIC_NODES);
+ auto && tag = Tag::genTag(p, 0, Tag::_periodic_nodes);
comm.probe<UInt>(p, tag, status);
proc_missing.resize(status.size());
comm.receive(proc_missing, p, tag);
} else {
fillPeriodicPairs(periodic_info_to_send_per_proc[root], proc_missing);
}
auto & buffer = buffers[p];
buffer.reserve((spatial_dimension * sizeof(Real) + sizeof(Int)) *
proc_missing.size());
buffer << proc_missing.size();
for (auto && node : proc_missing) {
buffer << *(nodes_it + node);
buffer << nodes_pranks(node);
}
}
for (UInt p = 0; p < nb_proc; ++p) {
for (auto && node : proc_missings[p]) {
auto & buffer = buffers[nodes_pranks(node)];
buffer << node;
buffer << p;
}
}
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
- auto && tag_send = Tag::genTag(p, 1, Tag::_PERIODIC_NODES);
+ auto && tag_send = Tag::genTag(p, 1, Tag::_periodic_nodes);
requests.push_back(comm.asyncSend(buffers[p], p, tag_send));
} else {
receiveMissingPeriodic(buffers[p]);
}
}
- comm.waitAll(requests);
- comm.freeCommunicationRequest(requests);
- requests.clear();
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::fillTagBuffers(
std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, _, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
auto & nodal_data = \
mesh.getNodalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(tag_name); \
for (auto && data : enumerate(nodes_per_proc)) { \
auto proc = std::get<0>(data); \
auto & nodes = std::get<1>(data); \
auto & buffer = buffers[proc]; \
for (auto & node : nodes) { \
for (auto i : arange(nodal_data.getNbComponent())) { \
buffer << nodal_data(node, i); \
} \
} \
} \
break; \
}
MeshDataTypeCode data_type_code =
mesh.getTypeCode(tag_name, MeshDataType::_nodal);
switch (data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not obtain the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
} // namespace akantu
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeTags() {
/// tag info
auto tag_names = mesh.getTagNames();
DynamicCommunicationBuffer tags_buffer;
for (auto && tag_name : tag_names) {
tags_buffer << tag_name;
tags_buffer << mesh.getTypeCode(tag_name, MeshDataType::_nodal);
tags_buffer << mesh.getNbComponent(tag_name);
}
AKANTU_DEBUG_INFO(
"Broadcasting the information about the nodes mesh data tags: ("
<< tags_buffer.size() << ").");
comm.broadcast(tags_buffer, root);
for (auto && tag_data : enumerate(tag_names)) {
auto tag_count = std::get<0>(tag_data);
auto & tag_name = std::get<1>(tag_data);
std::vector<DynamicCommunicationBuffer> buffers;
std::vector<CommunicationRequest> requests;
buffers.resize(nb_proc);
fillTagBuffers(buffers, tag_name);
for (auto && data : enumerate(buffers)) {
auto && proc = std::get<0>(data);
auto & buffer = std::get<1>(data);
if (proc == root) {
fillNodalData(buffer, tag_name);
} else {
- auto && tag = Tag::genTag(this->rank, tag_count, Tag::_MESH_DATA);
+ auto && tag = Tag::genTag(this->rank, tag_count, Tag::_mesh_data);
requests.push_back(comm.asyncSend(buffer, proc, tag));
}
}
- comm.waitAll(requests);
- comm.freeCommunicationRequest(requests);
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
}
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
SlaveNodeInfoPerProc::SlaveNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root) {
UInt nb_global_nodes = 0;
comm.broadcast(nb_global_nodes, root);
this->setNbGlobalNodes(nb_global_nodes);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeNodes() {
AKANTU_DEBUG_INFO("Sending list of nodes to proc "
- << root << " " << Tag::genTag(this->rank, 0, Tag::_NB_NODES)
- << " " << Tag::genTag(this->rank, 0, Tag::_NODES));
+ << root << " " << Tag::genTag(this->rank, 0, Tag::_nb_nodes)
+ << " " << Tag::genTag(this->rank, 0, Tag::_nodes));
Array<UInt> & local_ids = this->getNodesGlobalIds();
Array<Real> & nodes = this->getNodes();
UInt nb_nodes = local_ids.size();
- comm.send(nb_nodes, root, Tag::genTag(this->rank, 0, Tag::_NB_NODES));
- comm.send(local_ids, root, Tag::genTag(this->rank, 0, Tag::_NODES));
+ comm.send(nb_nodes, root, Tag::genTag(this->rank, 0, Tag::_nb_nodes));
+ comm.send(local_ids, root, Tag::genTag(this->rank, 0, Tag::_nodes));
/* --------<<<<-COORDINATES---------------------------------------------- */
nodes.resize(nb_nodes);
AKANTU_DEBUG_INFO("Receiving coordinates from proc "
- << root << " " << Tag::genTag(root, 0, Tag::_COORDINATES));
- comm.receive(nodes, root, Tag::genTag(root, 0, Tag::_COORDINATES));
+ << root << " " << Tag::genTag(root, 0, Tag::_coordinates));
+ comm.receive(nodes, root, Tag::genTag(root, 0, Tag::_coordinates));
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeTypes() {
this->fillNodesType();
auto & nodes_flags = this->getNodesFlags();
AKANTU_DEBUG_INFO("Sending first nodes types to proc "
<< root << ""
- << Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
- comm.send(nodes_flags, root, Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
+ << Tag::genTag(this->rank, 0, Tag::_nodes_type));
+ comm.send(nodes_flags, root, Tag::genTag(this->rank, 0, Tag::_nodes_type));
AKANTU_DEBUG_INFO("Receiving nodes types from proc "
- << root << " " << Tag::genTag(root, 0, Tag::_NODES_TYPE));
- comm.receive(nodes_flags, root, Tag::genTag(root, 0, Tag::_NODES_TYPE));
+ << root << " " << Tag::genTag(root, 0, Tag::_nodes_type));
+ comm.receive(nodes_flags, root, Tag::genTag(root, 0, Tag::_nodes_type));
Array<Int> nodes_prank(nodes_flags.size());
AKANTU_DEBUG_INFO("Receiving nodes pranks from proc "
- << root << " " << Tag::genTag(root, 2, Tag::_NODES_TYPE));
- comm.receive(nodes_prank, root, Tag::genTag(root, 2, Tag::_NODES_TYPE));
+ << root << " " << Tag::genTag(root, 2, Tag::_nodes_type));
+ comm.receive(nodes_prank, root, Tag::genTag(root, 2, Tag::_nodes_type));
for (auto && data : enumerate(nodes_prank)) {
auto node = std::get<0>(data);
if (not(mesh.isMasterNode(node) or mesh.isLocalNode(node))) {
this->setNodePrank(node, std::get<1>(data));
}
}
AKANTU_DEBUG_INFO("Receiving nodes master info from proc "
- << root << " " << Tag::genTag(root, 1, Tag::_NODES_TYPE));
+ << root << " " << Tag::genTag(root, 1, Tag::_nodes_type));
CommunicationStatus status;
- comm.probe<UInt>(root, Tag::genTag(root, 1, Tag::_NODES_TYPE), status);
+ comm.probe<UInt>(root, Tag::genTag(root, 1, Tag::_nodes_type), status);
Array<UInt> nodes_master_info(status.size());
- comm.receive(nodes_master_info, root, Tag::genTag(root, 1, Tag::_NODES_TYPE));
+ comm.receive(nodes_master_info, root, Tag::genTag(root, 1, Tag::_nodes_type));
this->fillCommunicationScheme(nodes_master_info);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Receiving node groups from proc "
<< root << " "
- << Tag::genTag(root, this->rank, Tag::_NODE_GROUP));
+ << Tag::genTag(root, this->rank, Tag::_node_group));
DynamicCommunicationBuffer buffer;
- comm.receive(buffer, root, Tag::genTag(root, this->rank, Tag::_NODE_GROUP));
+ comm.receive(buffer, root, Tag::genTag(root, this->rank, Tag::_node_group));
this->fillNodeGroupsFromBuffer(buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizePeriodicity() {
bool is_periodic;
comm.broadcast(is_periodic, root);
- if (not is_periodic)
+ if (not is_periodic) {
return;
+ }
CommunicationStatus status;
- auto && tag = Tag::genTag(root, this->rank, Tag::_PERIODIC_SLAVES);
+ auto && tag = Tag::genTag(root, this->rank, Tag::_periodic_slaves);
comm.probe<UInt>(root, tag, status);
Array<UInt> periodic_info(status.size() / 2, 2);
comm.receive(periodic_info, root, tag);
std::vector<UInt> proc_missing;
fillPeriodicPairs(periodic_info, proc_missing);
auto && tag_missing_request =
- Tag::genTag(this->rank, 0, Tag::_PERIODIC_NODES);
+ Tag::genTag(this->rank, 0, Tag::_periodic_nodes);
comm.send(proc_missing, root, tag_missing_request);
DynamicCommunicationBuffer buffer;
- auto && tag_missing = Tag::genTag(this->rank, 1, Tag::_PERIODIC_NODES);
+ auto && tag_missing = Tag::genTag(this->rank, 1, Tag::_periodic_nodes);
comm.receive(buffer, root, tag_missing);
receiveMissingPeriodic(buffer);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeTags() {
DynamicCommunicationBuffer tags_buffer;
comm.broadcast(tags_buffer, root);
std::vector<std::string> tag_names;
while (tags_buffer.getLeftToUnpack() > 0) {
std::string name;
MeshDataTypeCode code;
UInt nb_components;
tags_buffer >> name;
tags_buffer >> code;
tags_buffer >> nb_components;
mesh.registerNodalData(name, nb_components, code);
tag_names.push_back(name);
}
for (auto && tag_data : enumerate(tag_names)) {
auto tag_count = std::get<0>(tag_data);
auto & tag_name = std::get<1>(tag_data);
DynamicCommunicationBuffer buffer;
- auto && tag = Tag::genTag(this->root, tag_count, Tag::_MESH_DATA);
+ auto && tag = Tag::genTag(this->root, tag_count, Tag::_mesh_data);
comm.receive(buffer, this->root, tag);
fillNodalData(buffer, tag_name);
}
}
} // namespace akantu
diff --git a/src/synchronizer/node_info_per_processor.hh b/src/synchronizer/node_info_per_processor.hh
index 0b1cff4f2..b548a9a1b 100644
--- a/src/synchronizer/node_info_per_processor.hh
+++ b/src/synchronizer/node_info_per_processor.hh
@@ -1,126 +1,128 @@
/**
* @file node_info_per_processor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
* @date last modification: Wed Nov 08 2017
*
* @brief Helper classes to create the distributed synchronizer and distribute
* a mesh
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NODE_INFO_PER_PROCESSOR_HH__
-#define __AKANTU_NODE_INFO_PER_PROCESSOR_HH__
+#ifndef AKANTU_NODE_INFO_PER_PROCESSOR_HH_
+#define AKANTU_NODE_INFO_PER_PROCESSOR_HH_
namespace akantu {
class NodeSynchronizer;
class Communicator;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
class NodeInfoPerProc : protected MeshAccessor {
public:
NodeInfoPerProc(NodeSynchronizer & synchronizer, UInt message_cnt, UInt root);
void synchronize();
protected:
virtual void synchronizeNodes() = 0;
virtual void synchronizeTypes() = 0;
virtual void synchronizeGroups() = 0;
virtual void synchronizePeriodicity() = 0;
virtual void synchronizeTags() = 0;
protected:
template <class CommunicationBuffer>
void fillNodeGroupsFromBuffer(CommunicationBuffer & buffer);
void fillNodesType();
- void fillCommunicationScheme(const Array<UInt> &);
- void fillNodalData(DynamicCommunicationBuffer & buffer, std::string tag_name);
+ void fillCommunicationScheme(const Array<UInt> & /*master_info*/);
+ void fillNodalData(DynamicCommunicationBuffer & buffer,
+ const std::string & tag_name);
- void fillPeriodicPairs(const Array<UInt> &, std::vector<UInt> &);
- void receiveMissingPeriodic(DynamicCommunicationBuffer &);
+ void fillPeriodicPairs(const Array<UInt> & /*global_pairs*/,
+ std::vector<UInt> & /*missing_nodes*/);
+ void receiveMissingPeriodic(DynamicCommunicationBuffer & /*buffer*/);
protected:
NodeSynchronizer & synchronizer;
const Communicator & comm;
UInt rank;
UInt nb_proc;
UInt root;
Mesh & mesh;
UInt spatial_dimension;
UInt message_count;
};
/* -------------------------------------------------------------------------- */
class MasterNodeInfoPerProc : public NodeInfoPerProc {
public:
MasterNodeInfoPerProc(NodeSynchronizer & synchronizer, UInt message_cnt,
UInt root);
void synchronizeNodes() override;
void synchronizeTypes() override;
void synchronizeGroups() override;
void synchronizePeriodicity() override;
void synchronizeTags() override;
private:
void fillTagBuffers(std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name);
/// get the list of nodes to send and send them
std::vector<Array<UInt>> nodes_per_proc;
Array<UInt> nb_nodes_per_proc;
Array<Real> all_nodes;
Array<NodeFlag> all_periodic_flags;
Array<Int> nodes_pranks;
};
/* -------------------------------------------------------------------------- */
class SlaveNodeInfoPerProc : public NodeInfoPerProc {
public:
SlaveNodeInfoPerProc(NodeSynchronizer & synchronizer, UInt message_cnt,
UInt root);
void synchronizeNodes() override;
void synchronizeTypes() override;
void synchronizeGroups() override;
void synchronizePeriodicity() override;
void synchronizeTags() override;
private:
};
} // namespace akantu
-#endif /* __AKANTU_NODE_INFO_PER_PROCESSOR_HH__ */
+#endif /* AKANTU_NODE_INFO_PER_PROCESSOR_HH_ */
diff --git a/src/synchronizer/node_synchronizer.cc b/src/synchronizer/node_synchronizer.cc
index e1d02fada..f791dc24f 100644
--- a/src/synchronizer/node_synchronizer.cc
+++ b/src/synchronizer/node_synchronizer.cc
@@ -1,243 +1,245 @@
/**
* @file node_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 15 2017
*
* @brief Implementation of the node synchronizer
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_synchronizer.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeSynchronizer::NodeSynchronizer(Mesh & mesh, const ID & id,
MemoryID memory_id,
const bool register_to_event_manager,
EventHandlerPriority event_priority)
: SynchronizerImpl<UInt>(mesh.getCommunicator(), id, memory_id),
mesh(mesh) {
AKANTU_DEBUG_IN();
if (register_to_event_manager) {
this->mesh.registerEventHandler(*this, event_priority);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NodeSynchronizer::~NodeSynchronizer() = default;
/* -------------------------------------------------------------------------- */
Int NodeSynchronizer::getRank(const UInt & node) const {
return this->mesh.getNodePrank(node);
}
/* -------------------------------------------------------------------------- */
void NodeSynchronizer::onNodesAdded(const Array<UInt> & /*nodes_list*/,
- const NewNodesEvent &) {
+ const NewNodesEvent & /*unused*/) {
std::map<UInt, std::vector<UInt>> nodes_per_proc;
// recreates fully the schemes due to changes of global ids
// \TODO add an event to handle global id changes
for (auto && data : communications.iterateSchemes(_recv)) {
auto & scheme = data.second;
scheme.resize(0);
}
for (auto && local_id : arange(mesh.getNbNodes())) {
- if (not mesh.isSlaveNode(local_id))
+ if (not mesh.isSlaveNode(local_id)) {
continue; // local, master or pure ghost
+ }
auto global_id = mesh.getNodeGlobalId(local_id);
auto proc = mesh.getNodePrank(local_id);
AKANTU_DEBUG_ASSERT(
proc != -1,
"The node " << local_id << " does not have a valid associated prank");
nodes_per_proc[proc].push_back(global_id);
auto & scheme = communications.createScheme(proc, _recv);
scheme.push_back(local_id);
}
std::vector<CommunicationRequest> send_requests;
for (auto && pair : communications.iterateSchemes(_recv)) {
auto proc = pair.first;
AKANTU_DEBUG_ASSERT(proc != UInt(-1),
"For real I should send something to proc -1");
// if proc not in nodes_per_proc this should insert an empty array to send
send_requests.push_back(communicator.asyncSend(
nodes_per_proc[proc], proc, Tag::genTag(rank, proc, 0xcafe)));
}
for (auto && data : communications.iterateSchemes(_send)) {
auto proc = data.first;
auto & scheme = data.second;
CommunicationStatus status;
auto tag = Tag::genTag(proc, rank, 0xcafe);
communicator.probe<UInt>(proc, tag, status);
scheme.resize(status.size());
communicator.receive(scheme, proc, tag);
std::transform(scheme.begin(), scheme.end(), scheme.begin(),
[&](auto & gnode) { return mesh.getNodeLocalId(gnode); });
}
// communicator.receiveAnyNumber<UInt>(
// send_requests,
// [&](auto && proc, auto && nodes) {
// auto & scheme = communications.createScheme(proc, _send);
// scheme.resize(nodes.size());
// for (auto && data : enumerate(nodes)) {
// auto global_id = std::get<1>(data);
// auto local_id = mesh.getNodeLocalId(global_id);
// AKANTU_DEBUG_ASSERT(local_id != UInt(-1),
// "The global node " << global_id
// << "is not known on rank "
// << rank);
// scheme[std::get<0>(data)] = local_id;
// }
// },
// Tag::genTag(rank, count, 0xcafe));
// ++count;
- communicator.waitAll(send_requests);
- communicator.freeCommunicationRequest(send_requests);
+ Communicator::waitAll(send_requests);
+ Communicator::freeCommunicationRequest(send_requests);
this->entities_changed = true;
}
/* -------------------------------------------------------------------------- */
UInt NodeSynchronizer::sanityCheckDataSize(const Array<UInt> & nodes,
const SynchronizationTag & tag,
bool from_comm_desc) const {
UInt size =
SynchronizerImpl<UInt>::sanityCheckDataSize(nodes, tag, from_comm_desc);
// global id
if (tag != SynchronizationTag::_giu_global_conn) {
size += sizeof(UInt) * nodes.size();
}
// flag
size += sizeof(NodeFlag) * nodes.size();
// positions
size += mesh.getSpatialDimension() * sizeof(Real) * nodes.size();
return size;
}
/* -------------------------------------------------------------------------- */
void NodeSynchronizer::packSanityCheckData(
CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) const {
auto dim = mesh.getSpatialDimension();
for (auto && node : nodes) {
if (tag != SynchronizationTag::_giu_global_conn) {
buffer << mesh.getNodeGlobalId(node);
}
buffer << mesh.getNodeFlag(node);
buffer << Vector<Real>(mesh.getNodes().begin(dim)[node]);
}
}
/* -------------------------------------------------------------------------- */
void NodeSynchronizer::unpackSanityCheckData(CommunicationBuffer & buffer,
const Array<UInt> & nodes,
const SynchronizationTag & tag,
UInt proc, UInt rank) const {
auto dim = mesh.getSpatialDimension();
auto periodic = [&](auto && flag) { return flag & NodeFlag::_periodic_mask; };
auto distrib = [&](auto && flag) { return flag & NodeFlag::_shared_mask; };
for (auto && node : nodes) {
if (tag != SynchronizationTag::_giu_global_conn) {
UInt global_id;
buffer >> global_id;
AKANTU_DEBUG_ASSERT(global_id == mesh.getNodeGlobalId(node),
"The nodes global ids do not match: "
<< global_id
<< " != " << mesh.getNodeGlobalId(node));
}
NodeFlag flag;
buffer >> flag;
AKANTU_DEBUG_ASSERT(
(periodic(flag) == periodic(mesh.getNodeFlag(node))) and
(((distrib(flag) == NodeFlag::_master) and
(distrib(mesh.getNodeFlag(node)) ==
NodeFlag::_slave)) or // master to slave
((distrib(flag) == NodeFlag::_slave) and
(distrib(mesh.getNodeFlag(node)) ==
NodeFlag::_master)) or // reverse comm slave to master
(distrib(mesh.getNodeFlag(node)) ==
NodeFlag::_pure_ghost or // pure ghost nodes
distrib(flag) == NodeFlag::_pure_ghost)),
"The node flags: " << flag << " and " << mesh.getNodeFlag(node));
Vector<Real> pos_remote(dim);
buffer >> pos_remote;
Vector<Real> pos(mesh.getNodes().begin(dim)[node]);
auto dist = pos_remote.distance(pos);
if (not Math::are_float_equal(dist, 0.)) {
AKANTU_EXCEPTION("Unpacking an unknown value for the node "
<< node << "(position " << pos << " != buffer "
<< pos_remote << ") [" << dist << "] - tag: " << tag
<< " comm from " << proc << " to " << rank);
}
}
}
/* -------------------------------------------------------------------------- */
void NodeSynchronizer::fillEntityToSend(Array<UInt> & nodes_to_send) {
UInt nb_nodes = mesh.getNbNodes();
this->entities_from_root.clear();
nodes_to_send.resize(0);
for (UInt n : arange(nb_nodes)) {
- if (not mesh.isLocalOrMasterNode(n))
+ if (not mesh.isLocalOrMasterNode(n)) {
continue;
+ }
entities_from_root.push_back(n);
}
for (auto n : entities_from_root) {
UInt global_node = mesh.getNodeGlobalId(n);
nodes_to_send.push_back(global_node);
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/node_synchronizer.hh b/src/synchronizer/node_synchronizer.hh
index 79d02dd33..2cf5a2b65 100644
--- a/src/synchronizer/node_synchronizer.hh
+++ b/src/synchronizer/node_synchronizer.hh
@@ -1,110 +1,113 @@
/**
* @file node_synchronizer.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 08 2016
* @date last modification: Tue Feb 20 2018
*
* @brief Synchronizer for nodal information
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_events.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NODE_SYNCHRONIZER_HH__
-#define __AKANTU_NODE_SYNCHRONIZER_HH__
+#ifndef AKANTU_NODE_SYNCHRONIZER_HH_
+#define AKANTU_NODE_SYNCHRONIZER_HH_
namespace akantu {
class NodeSynchronizer : public MeshEventHandler,
public SynchronizerImpl<UInt> {
public:
NodeSynchronizer(Mesh & mesh, const ID & id = "element_synchronizer",
MemoryID memory_id = 0,
- const bool register_to_event_manager = true,
+ bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
~NodeSynchronizer() override;
UInt sanityCheckDataSize(const Array<UInt> & nodes,
const SynchronizationTag & tag,
bool from_comm_desc) const override;
void packSanityCheckData(CommunicationBuffer & buffer,
const Array<UInt> & nodes,
const SynchronizationTag & /*tag*/) const override;
void unpackSanityCheckData(CommunicationBuffer & buffer,
const Array<UInt> & nodes,
const SynchronizationTag & tag, UInt proc,
UInt rank) const override;
/// function to implement to react on akantu::NewNodesEvent
- void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override;
+ void onNodesAdded(const Array<UInt> & /*unused*/,
+ const NewNodesEvent & /*unused*/) override;
/// function to implement to react on akantu::RemovedNodesEvent
- void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
- const RemovedNodesEvent &) override {}
+ void onNodesRemoved(const Array<UInt> & /*unused*/,
+ const Array<UInt> & /*unused*/,
+ const RemovedNodesEvent & /*unused*/) override {}
/// function to implement to react on akantu::NewElementsEvent
- void onElementsAdded(const Array<Element> &,
- const NewElementsEvent &) override {}
+ void onElementsAdded(const Array<Element> & /*unused*/,
+ const NewElementsEvent & /*unused*/) override {}
/// function to implement to react on akantu::RemovedElementsEvent
- void onElementsRemoved(const Array<Element> &,
- const ElementTypeMapArray<UInt> &,
- const RemovedElementsEvent &) override {}
+ void onElementsRemoved(const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const RemovedElementsEvent & /*unused*/) override {}
/// function to implement to react on akantu::ChangedElementsEvent
- void onElementsChanged(const Array<Element> &, const Array<Element> &,
- const ElementTypeMapArray<UInt> &,
- const ChangedElementsEvent &) override {}
+ void onElementsChanged(const Array<Element> & /*unused*/,
+ const Array<Element> & /*unused*/,
+ const ElementTypeMapArray<UInt> & /*unused*/,
+ const ChangedElementsEvent & /*unused*/) override {}
/* ------------------------------------------------------------------------ */
NodeSynchronizer & operator=(const NodeSynchronizer & other) {
copySchemes(other);
return *this;
}
friend class NodeInfoPerProc;
protected:
- void fillEntityToSend(Array<UInt> & entities_to_send) override;
+ void fillEntityToSend(Array<UInt> & nodes_to_send) override;
public:
AKANTU_GET_MACRO(Mesh, mesh, Mesh &);
inline UInt canScatterSize() override;
inline UInt gatheredSize() override;
inline UInt localToGlobalEntity(const UInt & local) override;
protected:
Int getRank(const UInt & node) const final;
protected:
Mesh & mesh;
};
} // namespace akantu
#include "node_synchronizer_inline_impl.hh"
-#endif /* __AKANTU_NODE_SYNCHRONIZER_HH__ */
+#endif /* AKANTU_NODE_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/node_synchronizer_inline_impl.hh b/src/synchronizer/node_synchronizer_inline_impl.hh
index cbdd5a031..41cfaf626 100644
--- a/src/synchronizer/node_synchronizer_inline_impl.hh
+++ b/src/synchronizer/node_synchronizer_inline_impl.hh
@@ -1,55 +1,55 @@
/**
* @file node_synchronizer_inline_impl.hh
*
* @author Nicolas Richart
*
* @date creation mar jan 14 2020
*
* @brief A Documented file.
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_synchronizer.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_NODE_SYNCHRONIZER_INLINE_IMPL_HH__
-#define __AKANTU_NODE_SYNCHRONIZER_INLINE_IMPL_HH__
+#ifndef AKANTU_NODE_SYNCHRONIZER_INLINE_IMPL_HH_
+#define AKANTU_NODE_SYNCHRONIZER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt NodeSynchronizer::canScatterSize() {
return mesh.getNbNodes();
}
/* -------------------------------------------------------------------------- */
inline UInt NodeSynchronizer::gatheredSize() {
return mesh.getNbGlobalNodes();
}
/* -------------------------------------------------------------------------- */
inline UInt NodeSynchronizer::localToGlobalEntity(const UInt & local) {
return mesh.getNodeGlobalId(local);
}
} // akantu
-#endif // __AKANTU_NODE_SYNCHRONIZER_INLINE_IMPL_HH__
+#endif // AKANTU_NODE_SYNCHRONIZER_INLINE_IMPL_HH_
diff --git a/src/synchronizer/periodic_node_synchronizer.cc b/src/synchronizer/periodic_node_synchronizer.cc
index fbac2a0fa..cb6286a93 100644
--- a/src/synchronizer/periodic_node_synchronizer.cc
+++ b/src/synchronizer/periodic_node_synchronizer.cc
@@ -1,130 +1,131 @@
/**
* @file periodic_node_synchronizer.cc
*
* @author Nicolas Richart
*
* @date creation Tue May 29 2018
*
* @brief Implementation of the periodic node synchronizer
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "periodic_node_synchronizer.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
PeriodicNodeSynchronizer::PeriodicNodeSynchronizer(
Mesh & mesh, const ID & id, MemoryID memory_id,
const bool register_to_event_manager, EventHandlerPriority event_priority)
: NodeSynchronizer(mesh, id + ":masters", memory_id,
register_to_event_manager, event_priority) {}
/* -------------------------------------------------------------------------- */
void PeriodicNodeSynchronizer::update() {
static int count = 0;
const auto & masters_to_slaves = this->mesh.getPeriodicMasterSlaves();
masters_list.resize(0);
masters_list.reserve(masters_to_slaves.size());
slaves_list.resize(0);
slaves_list.reserve(masters_to_slaves.size());
reset();
std::set<UInt> masters_to_receive;
for (auto && data : masters_to_slaves) {
auto master = std::get<0>(data);
auto slave = std::get<1>(data);
masters_list.push_back(master);
slaves_list.push_back(slave);
if (not(mesh.isMasterNode(master) or mesh.isLocalNode(master))) {
masters_to_receive.insert(master);
}
}
- if (not mesh.isDistributed() or nb_proc == 1)
+ if (not mesh.isDistributed() or nb_proc == 1) {
return;
+ }
std::map<Int, Array<UInt>> buffers;
for (auto node : masters_to_receive) {
auto && proc = mesh.getNodePrank(node);
auto && scheme = this->communications.createRecvScheme(proc);
scheme.push_back(node);
buffers[proc].push_back(mesh.getNodeGlobalId(node));
}
- auto tag = Tag::genTag(0, count, Tag::_MODIFY_SCHEME);
+ auto tag = Tag::genTag(0, count, Tag::_modify_scheme);
std::vector<CommunicationRequest> requests;
for (auto && data : buffers) {
auto proc = std::get<0>(data);
auto & buffer = std::get<1>(data);
requests.push_back(communicator.asyncSend(buffer, proc, tag,
CommunicationMode::_synchronous));
std::cout << "Recv from proc : " << proc << " -> "
<< this->communications.getScheme(proc, _recv).size()
<< std::endl;
}
communicator.receiveAnyNumber<UInt>(
requests,
[&](auto && proc, auto && msg) {
auto && scheme = this->communications.createSendScheme(proc);
for (auto node : msg) {
scheme.push_back(mesh.getNodeLocalId(node));
}
std::cout << "Send to proc : " << proc << " -> " << scheme.size()
<< " [" << tag << "]" << std::endl;
},
tag);
++count;
}
/* -------------------------------------------------------------------------- */
void PeriodicNodeSynchronizer::synchronizeOnceImpl(
DataAccessor<UInt> & data_accessor, const SynchronizationTag & tag) const {
NodeSynchronizer::synchronizeOnceImpl(data_accessor, tag);
auto size = data_accessor.getNbData(masters_list, tag);
CommunicationBuffer buffer(size);
data_accessor.packData(buffer, masters_list, tag);
data_accessor.unpackData(buffer, slaves_list, tag);
}
/* -------------------------------------------------------------------------- */
void PeriodicNodeSynchronizer::waitEndSynchronizeImpl(
DataAccessor<UInt> & data_accessor, const SynchronizationTag & tag) {
NodeSynchronizer::waitEndSynchronizeImpl(data_accessor, tag);
auto size = data_accessor.getNbData(masters_list, tag);
CommunicationBuffer buffer(size);
data_accessor.packData(buffer, masters_list, tag);
data_accessor.unpackData(buffer, slaves_list, tag);
}
} // namespace akantu
diff --git a/src/synchronizer/periodic_node_synchronizer.hh b/src/synchronizer/periodic_node_synchronizer.hh
index b048a46de..7d90ed7f3 100644
--- a/src/synchronizer/periodic_node_synchronizer.hh
+++ b/src/synchronizer/periodic_node_synchronizer.hh
@@ -1,93 +1,93 @@
/**
* @file periodic_node_synchronizer.hh
*
* @author Nicolas Richart
*
* @date creation Tue May 29 2018
*
* @brief PeriodicNodeSynchronizer definition
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PERIODIC_NODE_SYNCHRONIZER_HH__
-#define __AKANTU_PERIODIC_NODE_SYNCHRONIZER_HH__
+#ifndef AKANTU_PERIODIC_NODE_SYNCHRONIZER_HH_
+#define AKANTU_PERIODIC_NODE_SYNCHRONIZER_HH_
namespace akantu {
class PeriodicNodeSynchronizer : public NodeSynchronizer {
public:
PeriodicNodeSynchronizer(
Mesh & mesh, const ID & id = "periodic_node_synchronizer",
- MemoryID memory_id = 0, const bool register_to_event_manager = true,
+ MemoryID memory_id = 0, bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void update();
/// Uses the synchronizer to perform a reduction on the vector
template <template <class> class Op, typename T>
void reduceSynchronizeWithPBCSlaves(Array<T> & array) const;
/// synchronize ghosts without state
void synchronizeOnceImpl(DataAccessor<UInt> & data_accessor,
const SynchronizationTag & tag) const override;
// /// asynchronous synchronization of ghosts
// void asynchronousSynchronizeImpl(const DataAccessor<UInt> & data_accessor,
// const SynchronizationTag & tag) override;
/// wait end of asynchronous synchronization of ghosts
void waitEndSynchronizeImpl(DataAccessor<UInt> & data_accessor,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
// NodeSynchronizer master_to_slaves_synchronizer;
Array<UInt> masters_list;
Array<UInt> slaves_list;
};
/* -------------------------------------------------------------------------- */
template <template <class> class Op, typename T>
void PeriodicNodeSynchronizer::reduceSynchronizeWithPBCSlaves(
Array<T> & array) const {
ReduceDataAccessor<UInt, Op, T> data_accessor(array,
SynchronizationTag::_whatever);
auto size =
data_accessor.getNbData(slaves_list, SynchronizationTag::_whatever);
CommunicationBuffer buffer(size);
data_accessor.packData(buffer, slaves_list, SynchronizationTag::_whatever);
data_accessor.unpackData(buffer, masters_list, SynchronizationTag::_whatever);
this->reduceSynchronizeArray<Op>(array);
}
} // namespace akantu
-#endif /* __AKANTU_PERIODIC_NODE_SYNCHRONIZER_HH__ */
+#endif /* AKANTU_PERIODIC_NODE_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/slave_element_info_per_processor.cc b/src/synchronizer/slave_element_info_per_processor.cc
index e25135516..b0f8e94d0 100644
--- a/src/synchronizer/slave_element_info_per_processor.cc
+++ b/src/synchronizer/slave_element_info_per_processor.cc
@@ -1,191 +1,193 @@
/**
* @file slave_element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
* @date last modification: Tue Nov 07 2017
*
* @brief Helper class to distribute a mesh
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SlaveElementInfoPerProc::SlaveElementInfoPerProc(
ElementSynchronizer & synchronizer, UInt message_cnt, UInt root)
: ElementInfoPerProc(synchronizer, message_cnt, root, _not_defined) {
Vector<UInt> size(5);
comm.receive(size, this->root,
- Tag::genTag(this->root, this->message_count, Tag::_SIZES));
+ Tag::genTag(this->root, this->message_count, Tag::_sizes));
this->type = (ElementType)size[0];
this->nb_local_element = size[1];
this->nb_ghost_element = size[2];
this->nb_element_to_receive = size[3];
this->nb_tags = size[4];
- if (this->type != _not_defined)
+ if (this->type != _not_defined) {
this->nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
+ }
}
/* -------------------------------------------------------------------------- */
bool SlaveElementInfoPerProc::needSynchronize() {
return this->type != _not_defined;
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeConnectivities() {
Array<UInt> local_connectivity(
(this->nb_local_element + this->nb_ghost_element) *
this->nb_nodes_per_element);
AKANTU_DEBUG_INFO("Receiving connectivities from proc " << root);
comm.receive(
local_connectivity, this->root,
- Tag::genTag(this->root, this->message_count, Tag::_CONNECTIVITY));
+ Tag::genTag(this->root, this->message_count, Tag::_connectivity));
auto & old_nodes = this->getNodesGlobalIds();
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(this->mesh, local_connectivity,
this->nb_local_element, this->nb_ghost_element,
this->type, old_nodes);
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizePartitions() {
Array<UInt> local_partitions(this->nb_element_to_receive +
this->nb_ghost_element * 2);
AKANTU_DEBUG_INFO("Receiving partition informations from proc " << root);
this->comm.receive(local_partitions, this->root,
- Tag::genTag(root, this->message_count, Tag::_PARTITIONS));
+ Tag::genTag(root, this->message_count, Tag::_partitions));
if (Mesh::getSpatialDimension(this->type) ==
this->mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
this->fillCommunicationScheme(local_partitions);
}
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeTags() {
AKANTU_DEBUG_IN();
if (this->nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
/* --------<<<<-TAGS------------------------------------------------- */
DynamicCommunicationBuffer mesh_data_sizes_buffer;
comm.broadcast(mesh_data_sizes_buffer, root);
AKANTU_DEBUG_INFO("Size of the information about the mesh data: "
<< mesh_data_sizes_buffer.size());
- if (mesh_data_sizes_buffer.size() == 0)
+ if (mesh_data_sizes_buffer.empty()) {
return;
+ }
AKANTU_DEBUG_INFO("Receiving the information about the mesh data tags, addr "
<< (void *)mesh_data_sizes_buffer.storage());
std::vector<std::string> tag_names;
std::vector<MeshDataTypeCode> tag_type_codes;
std::vector<UInt> tag_nb_component;
tag_names.resize(nb_tags);
tag_type_codes.resize(nb_tags);
tag_nb_component.resize(nb_tags);
CommunicationBuffer mesh_data_buffer;
UInt type_code_int;
for (UInt i(0); i < nb_tags; ++i) {
mesh_data_sizes_buffer >> tag_names[i];
mesh_data_sizes_buffer >> type_code_int;
tag_type_codes[i] = static_cast<MeshDataTypeCode>(type_code_int);
mesh_data_sizes_buffer >> tag_nb_component[i];
}
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
CommunicationStatus mesh_data_comm_status;
AKANTU_DEBUG_INFO("Checking size of data to receive for mesh data TAG("
- << Tag::genTag(root, this->message_count, Tag::_MESH_DATA)
+ << Tag::genTag(root, this->message_count, Tag::_mesh_data)
<< ")");
comm.probe<char>(root,
- Tag::genTag(root, this->message_count, Tag::_MESH_DATA),
+ Tag::genTag(root, this->message_count, Tag::_mesh_data),
mesh_data_comm_status);
UInt mesh_data_buffer_size(mesh_data_comm_status.size());
AKANTU_DEBUG_INFO("Receiving "
<< mesh_data_buffer_size << " bytes of mesh data TAG("
- << Tag::genTag(root, this->message_count, Tag::_MESH_DATA)
+ << Tag::genTag(root, this->message_count, Tag::_mesh_data)
<< ")");
mesh_data_buffer.resize(mesh_data_buffer_size);
comm.receive(mesh_data_buffer, root,
- Tag::genTag(root, this->message_count, Tag::_MESH_DATA));
+ Tag::genTag(root, this->message_count, Tag::_mesh_data));
// Loop over each tag for the current type
UInt k(0);
for (; names_it != names_end; ++names_it, ++k) {
this->fillMeshData(mesh_data_buffer, *names_it, tag_type_codes[k],
tag_nb_component[k]);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
const Communicator & comm = mesh.getCommunicator();
UInt my_rank = comm.whoAmI();
AKANTU_DEBUG_INFO("Receiving element groups from proc "
<< root << " TAG("
- << Tag::genTag(root, my_rank, Tag::_ELEMENT_GROUP) << ")");
+ << Tag::genTag(root, my_rank, Tag::_element_group) << ")");
CommunicationStatus status;
- comm.probe<char>(root, Tag::genTag(root, my_rank, Tag::_ELEMENT_GROUP),
+ comm.probe<char>(root, Tag::genTag(root, my_rank, Tag::_element_group),
status);
CommunicationBuffer buffer(status.size());
- comm.receive(buffer, root, Tag::genTag(root, my_rank, Tag::_ELEMENT_GROUP));
+ comm.receive(buffer, root, Tag::genTag(root, my_rank, Tag::_element_group));
this->fillElementGroupsFromBuffer(buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/synchronizer.cc b/src/synchronizer/synchronizer.cc
index fd203707e..9ed1aebaf 100644
--- a/src/synchronizer/synchronizer.cc
+++ b/src/synchronizer/synchronizer.cc
@@ -1,54 +1,55 @@
/**
* @file synchronizer.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Wed Nov 15 2017
*
* @brief implementation of the common part
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "synchronizer.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Synchronizer::Synchronizer(const Communicator & comm, const ID & id,
MemoryID memory_id)
: Memory(id, memory_id), communicator(comm) {
int max_tag = comm.getMaxTag();
this->hash_id = std::hash<std::string>()(this->getID());
- if (max_tag != 0)
+ if (max_tag != 0) {
this->hash_id = this->hash_id % max_tag;
+ }
this->nb_proc = communicator.getNbProc();
this->rank = communicator.whoAmI();
}
} // namespace akantu
diff --git a/src/synchronizer/synchronizer.hh b/src/synchronizer/synchronizer.hh
index 846b8b2f0..289fdbe0a 100644
--- a/src/synchronizer/synchronizer.hh
+++ b/src/synchronizer/synchronizer.hh
@@ -1,129 +1,129 @@
/**
* @file synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Common interface for synchronizers
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SYNCHRONIZER_HH__
-#define __AKANTU_SYNCHRONIZER_HH__
+#ifndef AKANTU_SYNCHRONIZER_HH_
+#define AKANTU_SYNCHRONIZER_HH_
namespace akantu {
class Communicator;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Base class for synchronizers */
/* -------------------------------------------------------------------------- */
class Synchronizer : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Synchronizer(const Communicator & comm, const ID & id = "synchronizer",
MemoryID memory_id = 0);
Synchronizer(const Synchronizer & other) = default;
~Synchronizer() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronous communications form slaves to master
template <class DataAccessor>
void slaveReductionOnce(DataAccessor & data_accessor,
const SynchronizationTag & tag) const;
/// synchronize ghosts without state
template <class DataAccessor>
void synchronizeOnce(DataAccessor & data_accessor,
const SynchronizationTag & tag) const;
/// synchronize ghosts
template <class DataAccessor>
void synchronize(DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// asynchronous synchronization of ghosts
template <class DataAccessor>
void asynchronousSynchronize(const DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// wait end of asynchronous synchronization of ghosts
template <class DataAccessor>
void waitEndSynchronize(DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// compute buffer size for a given tag and data accessor
template <class DataAccessor>
void computeBufferSize(const DataAccessor & data_accessor,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Communicator, communicator, const Communicator &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the synchronizer
ID id;
/// hashed version of the id
int hash_id;
/// message counter per tag
std::map<SynchronizationTag, UInt> tag_counter;
/// the static memory instance
const Communicator & communicator;
/// nb processors in the communicator
UInt nb_proc;
/// rank in the communicator
UInt rank;
};
} // namespace akantu
#include "synchronizer_tmpl.hh"
-#endif /* __AKANTU_SYNCHRONIZER_HH__ */
+#endif /* AKANTU_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/synchronizer_impl.hh b/src/synchronizer/synchronizer_impl.hh
index 91e90ab35..63ee56c53 100644
--- a/src/synchronizer/synchronizer_impl.hh
+++ b/src/synchronizer/synchronizer_impl.hh
@@ -1,216 +1,216 @@
/**
* @file synchronizer_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the generic part of synchronizers
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communications.hh"
#include "synchronizer.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SYNCHRONIZER_IMPL_HH__
-#define __AKANTU_SYNCHRONIZER_IMPL_HH__
+#ifndef AKANTU_SYNCHRONIZER_IMPL_HH_
+#define AKANTU_SYNCHRONIZER_IMPL_HH_
namespace akantu {
template <class Entity> class SynchronizerImpl : public Synchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SynchronizerImpl(const Communicator & communicator,
const ID & id = "synchronizer", MemoryID memory_id = 0);
SynchronizerImpl(const SynchronizerImpl & other, const ID & id);
~SynchronizerImpl() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
void communicateOnce(
const std::tuple<CommunicationSendRecv, CommunicationSendRecv> &
send_recv_schemes,
const Tag::CommTags & comm_tag, DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const;
public:
/// synchronous synchronization without state
virtual void slaveReductionOnceImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const;
/// synchronous synchronization without state
virtual void synchronizeOnceImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const;
/// asynchronous synchronization of ghosts
virtual void
asynchronousSynchronizeImpl(const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/// wait end of asynchronous synchronization of ghosts
virtual void waitEndSynchronizeImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/// compute all buffer sizes
virtual void
computeAllBufferSizes(const DataAccessor<Entity> & data_accessor);
/// compute buffer size for a given tag and data accessor
virtual void computeBufferSizeImpl(const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
virtual void synchronizeImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
this->asynchronousSynchronizeImpl(data_accessor, tag);
this->waitEndSynchronizeImpl(data_accessor, tag);
}
/* ------------------------------------------------------------------------ */
/// reset send and recv element lists
void reset();
/// extract the elements that have a true predicate from in_synchronizer and
/// store them in the current synchronizer
template <typename Pred>
void split(SynchronizerImpl & in_synchronizer, Pred && pred);
/// update schemes in a synchronizer
template <typename Updater> void updateSchemes(Updater && scheme_updater);
/// filter the send scheme and let the other processor now about iterate
template <typename Pred> void filterScheme(Pred && pred);
/// flip send and receive schemes
void swapSendRecv();
/// copy the schemes of an other communicator.
SynchronizerImpl & operator=(const SynchronizerImpl & other);
/// gather data on the predefined root process (master version)
template <typename T>
void gather(const Array<T> & to_gather, Array<T> & gathered);
/// gather data on the predefined root process (slave version)
template <typename T> void gather(const Array<T> & to_gather);
/// scatter data from the predefined root process (master version)
template <typename T>
void scatter(Array<T> & scattered, const Array<T> & to_scatter);
/// scatter data from the predefined root process (slave version)
template <typename T> void scatter(Array<T> & scattered);
template <typename T>
void synchronizeArray(Array<T> & array) const;
/// Uses the synchronizer to perform a reduction on the vector
template <template <class> class Op, typename T>
void reduceSynchronizeArray(Array<T> & array) const;
protected:
/// copy schemes
void copySchemes(const SynchronizerImpl & other);
/// check if dof changed set on at least one processor
inline bool hasChanged();
/// init the scheme for scatter and gather operation, need extra memory
inline void initScatterGatherCommunicationScheme();
/// list the entities to send to root process
virtual void fillEntityToSend(Array<Entity> & /*entities_to_send*/) {
AKANTU_TO_IMPLEMENT();
}
virtual Entity localToGlobalEntity(const Entity & /*local*/) {
AKANTU_TO_IMPLEMENT();
}
virtual UInt canScatterSize() {
AKANTU_TO_IMPLEMENT();
}
virtual UInt gatheredSize() {
AKANTU_TO_IMPLEMENT();
}
public:
/* ------------------------------------------------------------------------ */
virtual UInt sanityCheckDataSize(const Array<Entity> & elements,
const SynchronizationTag & tag,
- bool from_comm_desc = true) const;
+ bool is_comm_desc = true) const;
virtual void
packSanityCheckData(CommunicationDescriptor<Entity> & comm_desc) const;
virtual void
unpackSanityCheckData(CommunicationDescriptor<Entity> & comm_desc) const;
virtual void packSanityCheckData(CommunicationBuffer & /*buffer*/,
const Array<Entity> & /*elements*/,
const SynchronizationTag & /*tag*/) const {}
virtual void unpackSanityCheckData(CommunicationBuffer & /*buffer*/,
const Array<Entity> & /*elements*/,
const SynchronizationTag & /*tag*/,
UInt /*proc*/, UInt /*rank*/) const {}
public:
AKANTU_GET_MACRO(Communications, communications,
const Communications<Entity> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(Communications, communications,
Communications<Entity> &);
virtual Int getRank(const Entity & entity) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// information on the communications
Communications<Entity> communications;
/// did the scheme change, this is to recreate the scatter/gather data if
/// needed
bool entities_changed{true};
/// Root processor for scatter/gather operations
Int root{0};
/// entities coming/going from/to root
Array<Entity> entities_from_root;
/// entities received from slaves proc (only on master)
std::map<UInt, Array<Entity>> master_receive_entities;
};
} // namespace akantu
#include "synchronizer_impl_tmpl.hh"
-#endif /* __AKANTU_SYNCHRONIZER_IMPL_HH__ */
+#endif /* AKANTU_SYNCHRONIZER_IMPL_HH_ */
diff --git a/src/synchronizer/synchronizer_impl_tmpl.hh b/src/synchronizer/synchronizer_impl_tmpl.hh
index 4e424d1c8..36e37152f 100644
--- a/src/synchronizer/synchronizer_impl_tmpl.hh
+++ b/src/synchronizer/synchronizer_impl_tmpl.hh
@@ -1,851 +1,867 @@
/**
* @file synchronizer_impl_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 07 2016
* @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the SynchronizerImpl
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity>
SynchronizerImpl<Entity>::SynchronizerImpl(const Communicator & comm,
const ID & id, MemoryID memory_id)
: Synchronizer(comm, id, memory_id), communications(comm) {}
/* -------------------------------------------------------------------------- */
template <class Entity>
SynchronizerImpl<Entity>::SynchronizerImpl(const SynchronizerImpl & other,
const ID & id)
: Synchronizer(other), communications(other.communications) {
this->id = id;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::communicateOnce(
const std::tuple<CommunicationSendRecv, CommunicationSendRecv> &
send_recv_schemes,
const Tag::CommTags & comm_tag, DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const {
// no need to synchronize
- if (this->nb_proc == 1)
+ if (this->nb_proc == 1) {
return;
+ }
- CommunicationSendRecv send_dir, recv_dir;
+ CommunicationSendRecv send_dir;
+ CommunicationSendRecv recv_dir;
std::tie(send_dir, recv_dir) = send_recv_schemes;
using CommunicationRequests = std::vector<CommunicationRequest>;
using CommunicationBuffers = std::map<UInt, CommunicationBuffer>;
- CommunicationRequests send_requests, recv_requests;
- CommunicationBuffers send_buffers, recv_buffers;
+ CommunicationRequests send_requests;
+ CommunicationRequests recv_requests;
+ CommunicationBuffers send_buffers;
+ CommunicationBuffers recv_buffers;
auto postComm = [&](const auto & sr, auto & buffers,
auto & requests) -> void {
for (auto && pair : communications.iterateSchemes(sr)) {
auto & proc = pair.first;
const auto & scheme = pair.second;
- if (scheme.size() == 0)
+ if (scheme.empty()) {
continue;
+ }
auto & buffer = buffers[proc];
auto buffer_size = data_accessor.getNbData(scheme, tag);
- if (buffer_size == 0)
+ if (buffer_size == 0) {
continue;
+ }
#ifndef AKANTU_NDEBUG
buffer_size += this->sanityCheckDataSize(scheme, tag, false);
#endif
buffer.resize(buffer_size);
if (sr == recv_dir) {
requests.push_back(communicator.asyncReceive(
buffer, proc,
Tag::genTag(this->rank, UInt(tag), comm_tag, this->hash_id)));
} else {
#ifndef AKANTU_NDEBUG
this->packSanityCheckData(buffer, scheme, tag);
#endif
data_accessor.packData(buffer, scheme, tag);
AKANTU_DEBUG_ASSERT(
buffer.getPackedSize() == buffer.size(),
"The data accessor did not pack all the data it "
"promised in communication with tag "
<< tag << " (Promised: " << buffer.size()
<< "bytes, packed: " << buffer.getPackedSize() << "bytes [avg: "
<< Real(buffer.size() - buffer.getPackedSize()) / scheme.size()
<< "bytes per entity missing])");
send_requests.push_back(communicator.asyncSend(
buffer, proc,
Tag::genTag(proc, UInt(tag), comm_tag, this->hash_id)));
}
}
};
// post the receive requests
postComm(recv_dir, recv_buffers, recv_requests);
// post the send data requests
postComm(send_dir, send_buffers, send_requests);
// treat the receive requests
UInt request_ready;
- while ((request_ready = communicator.waitAny(recv_requests)) != UInt(-1)) {
+ while ((request_ready = Communicator::waitAny(recv_requests)) != UInt(-1)) {
auto & req = recv_requests[request_ready];
auto proc = req.getSource();
auto & buffer = recv_buffers[proc];
const auto & scheme = this->communications.getScheme(proc, recv_dir);
#ifndef AKANTU_NDEBUG
this->unpackSanityCheckData(buffer, scheme, tag, proc, this->rank);
#endif
data_accessor.unpackData(buffer, scheme, tag);
AKANTU_DEBUG_ASSERT(
buffer.getLeftToUnpack() == 0,
"The data accessor ignored some data in communication with tag "
<< tag);
req.free();
recv_requests.erase(recv_requests.begin() + request_ready);
}
- communicator.waitAll(send_requests);
- communicator.freeCommunicationRequest(send_requests);
+ Communicator::waitAll(send_requests);
+ Communicator::freeCommunicationRequest(send_requests);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::slaveReductionOnceImpl(
DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const {
- communicateOnce(std::make_tuple(_recv, _send), Tag::_REDUCE, data_accessor,
+ communicateOnce(std::make_tuple(_recv, _send), Tag::_reduce, data_accessor,
tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::synchronizeOnceImpl(
DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const {
- communicateOnce(std::make_tuple(_send, _recv), Tag::_SYNCHRONIZE,
+ communicateOnce(std::make_tuple(_send, _recv), Tag::_synchronize,
data_accessor, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::asynchronousSynchronizeImpl(
const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
- if (not this->communications.hasCommunicationSize(tag))
+ if (not this->communications.hasCommunicationSize(tag)) {
this->computeBufferSize(data_accessor, tag);
+ }
this->communications.incrementCounter(tag);
// Posting the receive -------------------------------------------------------
if (this->communications.hasPendingRecv(tag)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"There must still be some pending receive communications."
<< " Tag is " << tag << " Cannot start new ones");
}
for (auto && comm_desc : this->communications.iterateRecv(tag)) {
comm_desc.postRecv(this->hash_id);
}
// Posting the sends -------------------------------------------------------
if (communications.hasPendingSend(tag)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"There must be some pending sending communications."
<< " Tag is " << tag);
}
for (auto && comm_desc : this->communications.iterateSend(tag)) {
comm_desc.resetBuffer();
#ifndef AKANTU_NDEBUG
this->packSanityCheckData(comm_desc);
#endif
comm_desc.packData(data_accessor);
comm_desc.postSend(this->hash_id);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::waitEndSynchronizeImpl(
DataAccessor<Entity> & data_accessor, const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
if (this->communications.begin(tag, _recv) !=
this->communications.end(tag, _recv) &&
- !this->communications.hasPendingRecv(tag))
+ !this->communications.hasPendingRecv(tag)) {
AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
"No pending communication with the tag \""
<< tag);
+ }
#endif
auto recv_end = this->communications.end(tag, _recv);
decltype(recv_end) recv_it;
while ((recv_it = this->communications.waitAnyRecv(tag)) != recv_end) {
auto && comm_desc = *recv_it;
#ifndef AKANTU_NDEBUG
this->unpackSanityCheckData(comm_desc);
#endif
comm_desc.unpackData(data_accessor);
comm_desc.resetBuffer();
comm_desc.freeRequest();
}
this->communications.waitAllSend(tag);
this->communications.freeSendRequests(tag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::computeAllBufferSizes(
const DataAccessor<Entity> & data_accessor) {
for (auto && tag : this->communications.iterateTags()) {
this->computeBufferSize(data_accessor, tag);
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::computeBufferSizeImpl(
const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (not this->communications.hasCommunication(tag)) {
this->communications.initializeCommunications(tag);
AKANTU_DEBUG_ASSERT(communications.hasCommunication(tag) == true,
"Communications where not properly initialized");
}
for (auto sr : iterate_send_recv) {
for (auto && pair : this->communications.iterateSchemes(sr)) {
auto proc = pair.first;
const auto & scheme = pair.second;
UInt size = 0;
#ifndef AKANTU_NDEBUG
size += this->sanityCheckDataSize(scheme, tag);
#endif
size += data_accessor.getNbData(scheme, tag);
AKANTU_DEBUG_INFO("I have "
<< size << "(" << printMemorySize<char>(size) << " - "
<< scheme.size() << " element(s)) data to "
<< std::string(sr == _recv ? "receive from" : "send to")
<< proc << " for tag " << tag);
this->communications.setCommunicationSize(tag, proc, size, sr);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Entity> void SynchronizerImpl<Entity>::reset() {
AKANTU_DEBUG_IN();
communications.resetSchemes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Entity>
template <typename Pred>
void SynchronizerImpl<Entity>::split(SynchronizerImpl<Entity> & in_synchronizer,
Pred && pred) {
AKANTU_DEBUG_IN();
auto filter_list = [&](auto & list, auto & new_list) {
auto copy = list;
list.resize(0);
new_list.resize(0);
for (auto && entity : copy) {
if (std::forward<Pred>(pred)(entity)) {
new_list.push_back(entity);
} else {
list.push_back(entity);
}
}
};
for (auto sr : iterate_send_recv) {
for (auto & scheme_pair :
in_synchronizer.communications.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
auto & new_scheme = communications.createScheme(proc, sr);
filter_list(scheme, new_scheme);
}
}
in_synchronizer.communications.invalidateSizes();
communications.invalidateSizes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Entity>
template <typename Updater>
void SynchronizerImpl<Entity>::updateSchemes(Updater && scheme_updater) {
for (auto sr : iterate_send_recv) {
for (auto & scheme_pair : communications.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
std::forward<Updater>(scheme_updater)(scheme, proc, sr);
}
}
communications.invalidateSizes();
}
/* -------------------------------------------------------------------------- */
template <typename Entity>
template <typename Pred>
void SynchronizerImpl<Entity>::filterScheme(Pred && pred) {
std::vector<CommunicationRequest> requests;
std::unordered_map<UInt, Array<UInt>> keep_entities;
auto filter_list = [](const auto & keep, auto & list) {
Array<Entity> new_list;
for (const auto & keep_entity : keep) {
const Entity & entity = list(keep_entity);
new_list.push_back(entity);
}
list.copy(new_list);
};
// loop over send_schemes
for (auto & scheme_pair : communications.iterateSchemes(_recv)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
auto & keep_entity = keep_entities[proc];
for (auto && entity : enumerate(scheme)) {
if (pred(std::get<1>(entity))) {
keep_entity.push_back(std::get<0>(entity));
}
}
- auto tag = Tag::genTag(this->rank, 0, Tag::_MODIFY_SCHEME);
+ auto tag = Tag::genTag(this->rank, 0, Tag::_modify_scheme);
AKANTU_DEBUG_INFO("I have " << keep_entity.size()
<< " elements to still receive from processor "
<< proc << " (communication tag : " << tag
<< ")");
filter_list(keep_entity, scheme);
requests.push_back(communicator.asyncSend(keep_entity, proc, tag));
}
// clean the receive scheme
for (auto & scheme_pair : communications.iterateSchemes(_send)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
- auto tag = Tag::genTag(proc, 0, Tag::_MODIFY_SCHEME);
+ auto tag = Tag::genTag(proc, 0, Tag::_modify_scheme);
AKANTU_DEBUG_INFO("Waiting list of elements to keep from processor "
<< proc << " (communication tag : " << tag << ")");
CommunicationStatus status;
communicator.probe<UInt>(proc, tag, status);
Array<UInt> keep_entity(status.size(), 1, "keep_element");
AKANTU_DEBUG_INFO("I have "
<< keep_entity.size()
<< " elements to keep in my send list to processor "
<< proc << " (communication tag : " << tag << ")");
communicator.receive(keep_entity, proc, tag);
filter_list(keep_entity, scheme);
}
- communicator.waitAll(requests);
- communicator.freeCommunicationRequest(requests);
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
communications.invalidateSizes();
}
/* -------------------------------------------------------------------------- */
template <class Entity> void SynchronizerImpl<Entity>::swapSendRecv() {
communications.swapSendRecv();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::copySchemes(const SynchronizerImpl & other) {
reset();
for (auto sr : iterate_send_recv) {
for (auto & scheme_pair : other.communications.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & other_scheme = scheme_pair.second;
auto & scheme = communications.createScheme(proc, sr);
scheme.copy(other_scheme);
}
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
-SynchronizerImpl<Entity> & SynchronizerImpl<Entity>::
-operator=(const SynchronizerImpl & other) {
+SynchronizerImpl<Entity> &
+SynchronizerImpl<Entity>::operator=(const SynchronizerImpl & other) {
copySchemes(other);
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
-UInt SynchronizerImpl<Entity>::sanityCheckDataSize(const Array<Entity> &,
- const SynchronizationTag &,
- bool is_comm_desc) const {
+UInt SynchronizerImpl<Entity>::sanityCheckDataSize(
+ const Array<Entity> & /*unused*/, const SynchronizationTag & /*unused*/,
+ bool is_comm_desc) const {
if (not is_comm_desc) {
return 0;
}
UInt size = 0;
size += sizeof(SynchronizationTag); // tag
size += sizeof(UInt); // comm_desc.getNbData();
size += sizeof(UInt); // comm_desc.getProc();
size += sizeof(this->rank); // mesh.getCommunicator().whoAmI();
return size;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::packSanityCheckData(
CommunicationDescriptor<Entity> & comm_desc) const {
auto & buffer = comm_desc.getBuffer();
buffer << comm_desc.getTag();
buffer << comm_desc.getNbData();
buffer << comm_desc.getProc();
buffer << this->rank;
const auto & tag = comm_desc.getTag();
const auto & send_element = comm_desc.getScheme();
this->packSanityCheckData(buffer, send_element, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::unpackSanityCheckData(
CommunicationDescriptor<Entity> & comm_desc) const {
auto & buffer = comm_desc.getBuffer();
const auto & tag = comm_desc.getTag();
auto nb_data = comm_desc.getNbData();
auto proc = comm_desc.getProc();
auto rank = this->rank;
decltype(nb_data) recv_nb_data;
decltype(proc) recv_proc;
decltype(rank) recv_rank;
SynchronizationTag t;
buffer >> t;
buffer >> recv_nb_data;
buffer >> recv_proc;
buffer >> recv_rank;
AKANTU_DEBUG_ASSERT(
t == tag, "The tag received does not correspond to the tag expected");
AKANTU_DEBUG_ASSERT(
nb_data == recv_nb_data,
"The nb_data received does not correspond to the nb_data expected");
AKANTU_DEBUG_ASSERT(UInt(recv_rank) == proc,
"The rank received does not correspond to the proc");
AKANTU_DEBUG_ASSERT(recv_proc == UInt(rank),
"The proc received does not correspond to the rank");
auto & recv_element = comm_desc.getScheme();
this->unpackSanityCheckData(buffer, recv_element, tag, proc, rank);
}
/* -------------------------------------------------------------------------- */
template <class Entity> bool SynchronizerImpl<Entity>::hasChanged() {
communicator.allReduce(entities_changed, SynchronizerOperation::_lor);
return entities_changed;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::initScatterGatherCommunicationScheme() {
if (this->nb_proc == 1) {
entities_changed = false;
AKANTU_DEBUG_OUT();
return;
}
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
inline void SynchronizerImpl<UInt>::initScatterGatherCommunicationScheme() {
AKANTU_DEBUG_IN();
if (this->nb_proc == 1) {
entities_changed = false;
AKANTU_DEBUG_OUT();
return;
}
this->entities_from_root.clear();
this->master_receive_entities.clear();
Array<UInt> entities_to_send;
fillEntityToSend(entities_to_send);
std::vector<CommunicationRequest> requests;
if (this->rank == UInt(this->root)) {
master_receive_entities[this->root].copy(entities_to_send);
Array<UInt> nb_entities_per_proc(this->nb_proc);
communicator.gather(entities_to_send.size(), nb_entities_per_proc);
for (UInt p = 0; p < nb_proc; ++p) {
- if (p == UInt(this->root))
+ if (p == UInt(this->root)) {
continue;
+ }
auto & receive_per_proc = master_receive_entities[p];
receive_per_proc.resize(nb_entities_per_proc(p));
- if (nb_entities_per_proc(p) == 0)
+ if (nb_entities_per_proc(p) == 0) {
continue;
+ }
requests.push_back(communicator.asyncReceive(
receive_per_proc, p,
- Tag::genTag(p, 0, Tag::_GATHER_INITIALIZATION, this->hash_id)));
+ Tag::genTag(p, 0, Tag::_gather_initialization, this->hash_id)));
}
} else {
communicator.gather(entities_to_send.size(), this->root);
AKANTU_DEBUG(dblDebug, "I have " << entities_to_send.size()
<< " entities to send to master proc");
- if (entities_to_send.size() != 0) {
+ if (not entities_to_send.empty()) {
requests.push_back(communicator.asyncSend(
entities_to_send, this->root,
- Tag::genTag(this->rank, 0, Tag::_GATHER_INITIALIZATION,
+ Tag::genTag(this->rank, 0, Tag::_gather_initialization,
this->hash_id)));
}
}
entities_changed = false;
- communicator.waitAll(requests);
- communicator.freeCommunicationRequest(requests);
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::gather(const Array<T> & to_gather,
Array<T> & gathered) {
- if (this->hasChanged())
+ if (this->hasChanged()) {
initScatterGatherCommunicationScheme();
+ }
AKANTU_DEBUG_ASSERT(this->rank == UInt(this->root),
"This function cannot be called on a slave processor");
AKANTU_DEBUG_ASSERT(to_gather.size() == this->canScatterSize(),
"The array to gather does not have the correct size");
AKANTU_DEBUG_ASSERT(gathered.size() == this->gatheredSize(),
"The gathered array does not have the correct size");
if (this->nb_proc == 1) {
gathered.copy(to_gather, true);
AKANTU_DEBUG_OUT();
return;
}
std::map<UInt, CommunicationBuffer> buffers;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
- if (p == UInt(this->root))
+ if (p == UInt(this->root)) {
continue;
+ }
auto receive_it = this->master_receive_entities.find(p);
AKANTU_DEBUG_ASSERT(receive_it != this->master_receive_entities.end(),
"Could not find the receive list for dofs of proc "
<< p);
const auto & receive_entities = receive_it->second;
- if (receive_entities.size() == 0)
+ if (receive_entities.empty()) {
continue;
+ }
CommunicationBuffer & buffer = buffers[p];
buffer.resize(receive_entities.size() * to_gather.getNbComponent() *
sizeof(T));
AKANTU_DEBUG_INFO(
"Preparing to receive data for "
<< receive_entities.size() << " entities from processor " << p << " "
- << Tag::genTag(p, this->root, Tag::_GATHER, this->hash_id));
+ << Tag::genTag(p, this->root, Tag::_gather, this->hash_id));
requests.push_back(communicator.asyncReceive(
- buffer, p, Tag::genTag(p, this->root, Tag::_GATHER, this->hash_id)));
+ buffer, p, Tag::genTag(p, this->root, Tag::_gather, this->hash_id)));
}
auto data_gathered_it = gathered.begin(to_gather.getNbComponent());
{ // copy master data
auto data_to_gather_it = to_gather.begin(to_gather.getNbComponent());
for (auto local_entity : entities_from_root) {
UInt global_entity = localToGlobalEntity(local_entity);
Vector<T> entity_data_gathered = data_gathered_it[global_entity];
Vector<T> entity_data_to_gather = data_to_gather_it[local_entity];
entity_data_gathered = entity_data_to_gather;
}
}
auto rr = UInt(-1);
- while ((rr = communicator.waitAny(requests)) != UInt(-1)) {
+ while ((rr = Communicator::waitAny(requests)) != UInt(-1)) {
auto & request = requests[rr];
auto sender = request.getSource();
AKANTU_DEBUG_ASSERT(this->master_receive_entities.find(sender) !=
this->master_receive_entities.end() &&
buffers.find(sender) != buffers.end(),
"Missing infos concerning proc " << sender);
const auto & receive_entities =
this->master_receive_entities.find(sender)->second;
auto & buffer = buffers[sender];
for (auto global_entity : receive_entities) {
Vector<T> entity_data = data_gathered_it[global_entity];
buffer >> entity_data;
}
requests.erase(requests.begin() + rr);
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::gather(const Array<T> & to_gather) {
AKANTU_DEBUG_IN();
- if (this->hasChanged())
+ if (this->hasChanged()) {
initScatterGatherCommunicationScheme();
+ }
AKANTU_DEBUG_ASSERT(this->rank != UInt(this->root),
"This function cannot be called on the root processor");
AKANTU_DEBUG_ASSERT(to_gather.size() == this->canScatterSize(),
"The array to gather does not have the correct size");
- if (this->entities_from_root.size() == 0) {
+ if (this->entities_from_root.empty()) {
AKANTU_DEBUG_OUT();
return;
}
CommunicationBuffer buffer(this->entities_from_root.size() *
to_gather.getNbComponent() * sizeof(T));
auto data_it = to_gather.begin(to_gather.getNbComponent());
for (auto entity : this->entities_from_root) {
Vector<T> data = data_it[entity];
buffer << data;
}
AKANTU_DEBUG_INFO("Gathering data for "
<< to_gather.size() << " dofs on processor " << this->root
<< " "
- << Tag::genTag(this->rank, 0, Tag::_GATHER, this->hash_id));
+ << Tag::genTag(this->rank, 0, Tag::_gather, this->hash_id));
communicator.send(buffer, this->root,
- Tag::genTag(this->rank, 0, Tag::_GATHER, this->hash_id));
+ Tag::genTag(this->rank, 0, Tag::_gather, this->hash_id));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::scatter(Array<T> & scattered,
const Array<T> & to_scatter) {
AKANTU_DEBUG_IN();
- if (this->hasChanged())
+ if (this->hasChanged()) {
initScatterGatherCommunicationScheme();
+ }
AKANTU_DEBUG_ASSERT(this->rank == UInt(this->root),
"This function cannot be called on a slave processor");
AKANTU_DEBUG_ASSERT(scattered.size() == this->canScatterSize(),
"The scattered array does not have the correct size");
AKANTU_DEBUG_ASSERT(to_scatter.size() == this->gatheredSize(),
"The array to scatter does not have the correct size");
if (this->nb_proc == 1) {
scattered.copy(to_scatter, true);
AKANTU_DEBUG_OUT();
return;
}
std::map<UInt, CommunicationBuffer> buffers;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
auto data_to_scatter_it = to_scatter.begin(to_scatter.getNbComponent());
if (p == this->rank) {
auto data_scattered_it = scattered.begin(to_scatter.getNbComponent());
// copy the data for the local processor
for (auto local_entity : entities_from_root) {
auto global_entity = localToGlobalEntity(local_entity);
Vector<T> entity_data_to_scatter = data_to_scatter_it[global_entity];
Vector<T> entity_data_scattered = data_scattered_it[local_entity];
entity_data_scattered = entity_data_to_scatter;
}
continue;
}
const auto & receive_entities =
this->master_receive_entities.find(p)->second;
// prepare the send buffer
CommunicationBuffer & buffer = buffers[p];
buffer.resize(receive_entities.size() * scattered.getNbComponent() *
sizeof(T));
// pack the data
for (auto global_entity : receive_entities) {
Vector<T> entity_data_to_scatter = data_to_scatter_it[global_entity];
buffer << entity_data_to_scatter;
}
// send the data
requests.push_back(communicator.asyncSend(
- buffer, p, Tag::genTag(p, 0, Tag::_SCATTER, this->hash_id)));
+ buffer, p, Tag::genTag(p, 0, Tag::_scatter, this->hash_id)));
}
// wait a clean communications
- communicator.waitAll(requests);
- communicator.freeCommunicationRequest(requests);
+ Communicator::waitAll(requests);
+ Communicator::freeCommunicationRequest(requests);
// synchronize slave and ghost nodes
synchronizeArray(scattered);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::scatter(Array<T> & scattered) {
AKANTU_DEBUG_IN();
- if (this->hasChanged())
+ if (this->hasChanged()) {
this->initScatterGatherCommunicationScheme();
+ }
AKANTU_DEBUG_ASSERT(this->rank != UInt(this->root),
"This function cannot be called on the root processor");
AKANTU_DEBUG_ASSERT(scattered.size() == this->canScatterSize(),
"The scattered array does not have the correct size");
// prepare the data
auto data_scattered_it = scattered.begin(scattered.getNbComponent());
CommunicationBuffer buffer(this->entities_from_root.size() *
scattered.getNbComponent() * sizeof(T));
// receive the data
communicator.receive(
buffer, this->root,
- Tag::genTag(this->rank, 0, Tag::_SCATTER, this->hash_id));
+ Tag::genTag(this->rank, 0, Tag::_scatter, this->hash_id));
// unpack the data
for (auto local_entity : entities_from_root) {
Vector<T> data_scattered(data_scattered_it[local_entity]);
buffer >> data_scattered;
}
// synchronize the ghosts
synchronizeArray(scattered);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::synchronizeArray(Array<T> & array) const {
static_assert(std::is_same<Entity, UInt>::value,
"Not implemented for other type than UInt");
SimpleUIntDataAccessor<T> data_accessor(array, SynchronizationTag::_whatever);
this->synchronizeOnce(data_accessor, SynchronizationTag::_whatever);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <template <class> class Op, typename T>
void SynchronizerImpl<Entity>::reduceSynchronizeArray(Array<T> & array) const {
static_assert(std::is_same<Entity, UInt>::value,
"Not implemented for other type than UInt");
ReduceDataAccessor<UInt, Op, T> data_accessor(array,
SynchronizationTag::_whatever);
this->slaveReductionOnceImpl(data_accessor, SynchronizationTag::_whatever);
this->synchronizeArray(array);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/synchronizer_registry.hh b/src/synchronizer/synchronizer_registry.hh
index 0dd1e420f..0a6bd2424 100644
--- a/src/synchronizer/synchronizer_registry.hh
+++ b/src/synchronizer/synchronizer_registry.hh
@@ -1,89 +1,89 @@
/**
* @file synchronizer_registry.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Dec 03 2017
*
* @brief Registry of synchronizers
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SYNCHRONIZER_REGISTRY_HH__
-#define __AKANTU_SYNCHRONIZER_REGISTRY_HH__
+#ifndef AKANTU_SYNCHRONIZER_REGISTRY_HH_
+#define AKANTU_SYNCHRONIZER_REGISTRY_HH_
namespace akantu {
class DataAccessorBase;
class Synchronizer;
} // namespace akantu
namespace akantu {
class SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SynchronizerRegistry();
virtual ~SynchronizerRegistry();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronize operation
void synchronize(SynchronizationTag tag);
/// asynchronous synchronization
void asynchronousSynchronize(SynchronizationTag tag);
/// wait end of asynchronous synchronization
void waitEndSynchronize(SynchronizationTag tag);
/// register a new synchronization
void registerSynchronizer(Synchronizer & synchronizer,
SynchronizationTag tag);
/// Register a different data accessor.
void registerDataAccessor(DataAccessorBase & data_accessor);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using Tag2Sync = std::multimap<SynchronizationTag, Synchronizer *>;
/// list of registered synchronization
Tag2Sync synchronizers;
/// data accessor that will permit to do the pack/unpack things
DataAccessorBase * data_accessor{nullptr};
};
} // namespace akantu
-#endif /* __AKANTU_SYNCHRONIZER_REGISTRY_HH__ */
+#endif /* AKANTU_SYNCHRONIZER_REGISTRY_HH_ */
diff --git a/src/synchronizer/synchronizer_tmpl.hh b/src/synchronizer/synchronizer_tmpl.hh
index 1a173065d..1dc55d4cd 100644
--- a/src/synchronizer/synchronizer_tmpl.hh
+++ b/src/synchronizer/synchronizer_tmpl.hh
@@ -1,136 +1,136 @@
/**
* @file synchronizer_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 07 2016
* @date last modification: Thu May 11 2017
*
* @brief Implementation of the helper classes for the synchronizer
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "data_accessor.hh"
#include "synchronizer.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_SYNCHRONIZER_TMPL_HH__
-#define __AKANTU_SYNCHRONIZER_TMPL_HH__
+#ifndef AKANTU_SYNCHRONIZER_TMPL_HH_
+#define AKANTU_SYNCHRONIZER_TMPL_HH_
namespace akantu {
template <class DataAccessorT>
void Synchronizer::slaveReductionOnce(DataAccessorT & data_accessor,
const SynchronizationTag & tag) const {
if (const auto * synch_el =
dynamic_cast<const SynchronizerImpl<Element> *>(this)) {
synch_el->slaveReductionOnceImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (const auto * synch_dof =
dynamic_cast<const SynchronizerImpl<UInt> *>(this)) {
synch_dof->slaveReductionOnceImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
template <class DataAccessorT>
void Synchronizer::synchronizeOnce(DataAccessorT & data_accessor,
const SynchronizationTag & tag) const {
if (const auto * synch_el =
dynamic_cast<const SynchronizerImpl<Element> *>(this)) {
synch_el->synchronizeOnceImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (const auto * synch_dof =
dynamic_cast<const SynchronizerImpl<UInt> *>(this)) {
synch_dof->synchronizeOnceImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/// synchronize ghosts
template <class DataAccessorT>
void Synchronizer::synchronize(DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->synchronizeImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->synchronizeImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/* -------------------------------------------------------------------------- */
template <class DataAccessorT>
void Synchronizer::asynchronousSynchronize(const DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->asynchronousSynchronizeImpl(
dynamic_cast<const DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->asynchronousSynchronizeImpl(
dynamic_cast<const DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/* -------------------------------------------------------------------------- */
template <class DataAccessorT>
void Synchronizer::waitEndSynchronize(DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->waitEndSynchronizeImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->waitEndSynchronizeImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/// compute buffer size for a given tag and data accessor
template <class DataAccessorT>
void Synchronizer::computeBufferSize(const DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->computeBufferSizeImpl(
dynamic_cast<const DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->computeBufferSizeImpl(
dynamic_cast<const DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
} // namespace akantu
-#endif /* __AKANTU_SYNCHRONIZER_TMPL_HH__ */
+#endif /* AKANTU_SYNCHRONIZER_TMPL_HH_ */
diff --git a/test/test_common/test_tensors.cc b/test/test_common/test_tensors.cc
index 3580345f9..c219aa4ef 100644
--- a/test/test_common/test_tensors.cc
+++ b/test/test_common/test_tensors.cc
@@ -1,592 +1,592 @@
/**
* @file test_tensors.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
* @date last modification: Mon Jan 22 2018
*
* @brief test the tensors types
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_iterators.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#include <cstdlib>
#include <gtest/gtest.h>
#include <memory>
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
/* -------------------------------------------------------------------------- */
class TensorConstructorFixture : public ::testing::Test {
public:
void SetUp() override {
for (auto & r : reference) {
r = rand(); // google-test seeds srand()
}
}
void TearDown() override {}
template <typename V> void compareToRef(const V & v) {
for (int i = 0; i < size_; ++i) {
EXPECT_DOUBLE_EQ(reference[i], v.storage()[i]);
}
}
protected:
const int size_{24};
const std::array<int, 2> mat_size{{4, 6}};
// const std::array<int, 3> tens3_size{{4, 2, 3}};
std::array<double, 24> reference;
};
/* -------------------------------------------------------------------------- */
class TensorFixture : public TensorConstructorFixture {
public:
TensorFixture()
: vref(reference.data(), size_),
mref(reference.data(), mat_size[0], mat_size[1]) {}
protected:
Vector<double> vref;
Matrix<double> mref;
};
/* -------------------------------------------------------------------------- */
// Vector ----------------------------------------------------------------------
TEST_F(TensorConstructorFixture, VectorDefaultConstruct) {
Vector<double> v;
EXPECT_EQ(0, v.size());
EXPECT_EQ(nullptr, v.storage());
EXPECT_EQ(false, v.isWrapped());
}
TEST_F(TensorConstructorFixture, VectorConstruct1) {
double r = rand();
Vector<double> v(size_, r);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(false, v.isWrapped());
for (int i = 0; i < size_; ++i) {
EXPECT_DOUBLE_EQ(r, v(i));
EXPECT_DOUBLE_EQ(r, v[i]);
}
}
TEST_F(TensorConstructorFixture, VectorConstructWrapped) {
Vector<double> v(reference.data(), size_);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(true, v.isWrapped());
for (int i = 0; i < size_; ++i) {
EXPECT_DOUBLE_EQ(reference[i], v(i));
EXPECT_DOUBLE_EQ(reference[i], v[i]);
}
}
TEST_F(TensorConstructorFixture, VectorConstructInitializer) {
Vector<double> v{0., 1., 2., 3., 4., 5.};
EXPECT_EQ(6, v.size());
EXPECT_EQ(false, v.isWrapped());
for (int i = 0; i < 6; ++i) {
EXPECT_DOUBLE_EQ(i, v(i));
}
}
TEST_F(TensorConstructorFixture, VectorConstructCopy1) {
Vector<double> vref(reference.data(), reference.size());
Vector<double> v(vref);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(false, v.isWrapped());
compareToRef(v);
}
TEST_F(TensorConstructorFixture, VectorConstructCopy2) {
Vector<double> vref(reference.data(), reference.size());
Vector<double> v(vref, false);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(true, v.isWrapped());
compareToRef(v);
}
TEST_F(TensorConstructorFixture, VectorConstructProxy1) {
VectorProxy<double> vref(reference.data(), reference.size());
EXPECT_EQ(size_, vref.size());
compareToRef(vref);
Vector<double> v(vref);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(true, v.isWrapped());
compareToRef(v);
}
TEST_F(TensorConstructorFixture, VectorConstructProxy2) {
Vector<double> vref(reference.data(), reference.size());
VectorProxy<double> v(vref);
EXPECT_EQ(size_, v.size());
compareToRef(v);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, VectorEqual) {
Vector<double> v;
v = vref;
compareToRef(v);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(false, v.isWrapped());
}
TEST_F(TensorFixture, VectorEqualProxy) {
VectorProxy<double> vref_proxy(vref);
Vector<double> v;
v = vref;
compareToRef(v);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(false, v.isWrapped());
}
TEST_F(TensorFixture, VectorEqualProxy2) {
Vector<double> v_store(size_, 0.);
VectorProxy<double> v(v_store);
v = vref;
compareToRef(v);
compareToRef(v_store);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, VectorSet) {
Vector<double> v(vref);
compareToRef(v);
double r = rand();
v.set(r);
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(r, v[i]);
}
TEST_F(TensorFixture, VectorClear) {
Vector<double> v(vref);
compareToRef(v);
- v.clear();
+ v.zero();
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0, v[i]);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, VectorDivide) {
Vector<double> v;
double r = rand();
v = vref / r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] / r, v[i]);
}
TEST_F(TensorFixture, VectorMultiply1) {
Vector<double> v;
double r = rand();
v = vref * r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, v[i]);
}
TEST_F(TensorFixture, VectorMultiply2) {
Vector<double> v;
double r = rand();
v = r * vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, v[i]);
}
TEST_F(TensorFixture, VectorAddition) {
Vector<double> v;
v = vref + vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * 2., v[i]);
}
TEST_F(TensorFixture, VectorSubstract) {
Vector<double> v;
v = vref - vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0., v[i]);
}
TEST_F(TensorFixture, VectorDivideEqual) {
Vector<double> v(vref);
double r = rand();
v /= r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] / r, v[i]);
}
TEST_F(TensorFixture, VectorMultiplyEqual1) {
Vector<double> v(vref);
double r = rand();
v *= r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, v[i]);
}
TEST_F(TensorFixture, VectorMultiplyEqual2) {
Vector<double> v(vref);
v *= v;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * reference[i], v[i]);
}
TEST_F(TensorFixture, VectorAdditionEqual) {
Vector<double> v(vref);
v += vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * 2., v[i]);
}
TEST_F(TensorFixture, VectorSubstractEqual) {
Vector<double> v(vref);
v -= vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0., v[i]);
}
/* -------------------------------------------------------------------------- */
// Matrix ----------------------------------------------------------------------
TEST_F(TensorConstructorFixture, MatrixDefaultConstruct) {
Matrix<double> m;
EXPECT_EQ(0, m.size());
EXPECT_EQ(0, m.rows());
EXPECT_EQ(0, m.cols());
EXPECT_EQ(nullptr, m.storage());
EXPECT_EQ(false, m.isWrapped());
}
TEST_F(TensorConstructorFixture, MatrixConstruct1) {
double r = rand();
Matrix<double> m(mat_size[0], mat_size[1], r);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
for (int i = 0; i < mat_size[0]; ++i) {
for (int j = 0; j < mat_size[1]; ++j) {
EXPECT_EQ(r, m(i, j));
EXPECT_EQ(r, m[i + j * mat_size[0]]);
}
}
}
TEST_F(TensorConstructorFixture, MatrixConstructWrapped) {
Matrix<double> m(reference.data(), mat_size[0], mat_size[1]);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(true, m.isWrapped());
for (int i = 0; i < mat_size[0]; ++i) {
for (int j = 0; j < mat_size[1]; ++j) {
EXPECT_DOUBLE_EQ(reference[i + j * mat_size[0]], m(i, j));
}
}
compareToRef(m);
}
TEST_F(TensorConstructorFixture, MatrixConstructInitializer) {
Matrix<double> m{{0., 1., 2.}, {3., 4., 5.}};
EXPECT_EQ(6, m.size());
EXPECT_EQ(2, m.rows());
EXPECT_EQ(3, m.cols());
EXPECT_EQ(false, m.isWrapped());
int c = 0;
for (int i = 0; i < 2; ++i) {
for (int j = 0; j < 3; ++j, ++c) {
EXPECT_DOUBLE_EQ(c, m(i, j));
}
}
}
TEST_F(TensorConstructorFixture, MatrixConstructCopy1) {
Matrix<double> mref(reference.data(), mat_size[0], mat_size[1]);
Matrix<double> m(mref);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
compareToRef(m);
}
TEST_F(TensorConstructorFixture, MatrixConstructCopy2) {
Matrix<double> mref(reference.data(), mat_size[0], mat_size[1]);
Matrix<double> m(mref);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
compareToRef(m);
}
TEST_F(TensorConstructorFixture, MatrixConstructProxy1) {
MatrixProxy<double> mref(reference.data(), mat_size[0], mat_size[1]);
EXPECT_EQ(size_, mref.size());
EXPECT_EQ(mat_size[0], mref.size(0));
EXPECT_EQ(mat_size[1], mref.size(1));
compareToRef(mref);
Matrix<double> m(mref);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(true, m.isWrapped());
compareToRef(m);
}
TEST_F(TensorConstructorFixture, MatrixConstructProxy2) {
Matrix<double> mref(reference.data(), mat_size[0], mat_size[1]);
MatrixProxy<double> m(mref);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.size(0));
EXPECT_EQ(mat_size[1], m.size(1));
compareToRef(m);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, MatrixEqual) {
Matrix<double> m;
m = mref;
compareToRef(m);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
}
TEST_F(TensorFixture, MatrixEqualProxy1) {
MatrixProxy<double> mref_proxy(mref);
Matrix<double> m;
m = mref;
compareToRef(m);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
}
TEST_F(TensorFixture, MatrixEqualProxy2) {
Matrix<double> m_store(mat_size[0], mat_size[1], 0.);
MatrixProxy<double> m(m_store);
m = mref;
compareToRef(m);
compareToRef(m_store);
}
TEST_F(TensorFixture, MatrixEqualSlice) {
Matrix<double> m(mat_size[0], mat_size[1], 0.);
for (unsigned int i = 0; i < m.cols(); ++i)
m(i) = Vector<Real>(mref(i));
compareToRef(m);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, MatrixSet) {
Matrix<double> m(mref);
compareToRef(m);
double r = rand();
m.set(r);
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(r, m[i]);
}
TEST_F(TensorFixture, MatrixClear) {
Matrix<double> m(mref);
compareToRef(m);
- m.clear();
+ m.zero();
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0, m[i]);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, MatrixDivide) {
Matrix<double> m;
double r = rand();
m = mref / r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] / r, m[i]);
}
TEST_F(TensorFixture, MatrixMultiply1) {
Matrix<double> m;
double r = rand();
m = mref * r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, m[i]);
}
TEST_F(TensorFixture, MatrixMultiply2) {
Matrix<double> m;
double r = rand();
m = r * mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, m[i]);
}
TEST_F(TensorFixture, MatrixAddition) {
Matrix<double> m;
m = mref + mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * 2., m[i]);
}
TEST_F(TensorFixture, MatrixSubstract) {
Matrix<double> m;
m = mref - mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0., m[i]);
}
TEST_F(TensorFixture, MatrixDivideEqual) {
Matrix<double> m(mref);
double r = rand();
m /= r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] / r, m[i]);
}
TEST_F(TensorFixture, MatrixMultiplyEqual1) {
Matrix<double> m(mref);
double r = rand();
m *= r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, m[i]);
}
TEST_F(TensorFixture, MatrixAdditionEqual) {
Matrix<double> m(mref);
m += mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * 2., m[i]);
}
TEST_F(TensorFixture, MatrixSubstractEqual) {
Matrix<double> m(mref);
m -= mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0., m[i]);
}
TEST_F(TensorFixture, MatrixIterator) {
Matrix<double> m(mref);
UInt col_count = 0;
for (auto && col : m) {
Vector<Real> col_hand(m.storage() + col_count * m.rows(), m.rows());
Vector<Real> col_wrap(col);
auto comp = (col_wrap - col_hand).norm<L_inf>();
EXPECT_DOUBLE_EQ(0., comp);
++col_count;
}
}
TEST_F(TensorFixture, MatrixIteratorZip) {
Matrix<double> m1(mref);
Matrix<double> m2(mref);
UInt col_count = 0;
for (auto && col : zip(m1, m2)) {
Vector<Real> col1(std::get<0>(col));
Vector<Real> col2(std::get<1>(col));
auto comp = (col1 - col2).norm<L_inf>();
EXPECT_DOUBLE_EQ(0., comp);
++col_count;
}
}
#if defined(AKANTU_USE_LAPACK)
TEST_F(TensorFixture, MatrixEigs) {
Matrix<double> m{{0, 1, 0, 0}, {1., 0, 0, 0}, {0, 1, 0, 1}, {0, 0, 4, 0}};
Matrix<double> eig_vects(4, 4);
Vector<double> eigs(4);
m.eig(eigs, eig_vects);
Vector<double> eigs_ref{2, 1., -1., -2};
auto lambda_v = m * eig_vects;
for (int i = 0; i < 4; ++i) {
EXPECT_NEAR(eigs_ref(i), eigs(i), 1e-14);
for (int j = 0; j < 4; ++j) {
EXPECT_NEAR(lambda_v(i)(j), eigs(i) * eig_vects(i)(j), 1e-14);
}
}
}
#endif
/* -------------------------------------------------------------------------- */
} // namespace
diff --git a/test/test_fe_engine/test_fe_engine_fixture.hh b/test/test_fe_engine/test_fe_engine_fixture.hh
index 0fe2442ed..700d72b85 100644
--- a/test/test_fe_engine/test_fe_engine_fixture.hh
+++ b/test/test_fe_engine/test_fe_engine_fixture.hh
@@ -1,111 +1,111 @@
/**
* @file test_fe_engine_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
* @date last modification: Mon Feb 19 2018
*
* @brief Fixture for feengine tests
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <element_class.hh>
#include <fe_engine.hh>
#include <integrator_gauss.hh>
#include <shape_lagrange.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TEST_FE_ENGINE_FIXTURE_HH__
-#define __AKANTU_TEST_FE_ENGINE_FIXTURE_HH__
+#ifndef AKANTU_TEST_FE_ENGINE_FIXTURE_HH_
+#define AKANTU_TEST_FE_ENGINE_FIXTURE_HH_
using namespace akantu;
/// Generic class for FEEngine tests
template <typename type_, template <ElementKind> class shape_t,
ElementKind kind = _ek_regular>
class TestFEMBaseFixture : public ::testing::Test {
public:
static constexpr const ElementType type = type_::value;
static constexpr const size_t dim = ElementClass<type>::getSpatialDimension();
using FEM = FEEngineTemplate<IntegratorGauss, shape_t, kind>;
/// Setup reads mesh corresponding to element type and initializes an FEEngine
void SetUp() override {
const auto dim = this->dim;
mesh = std::make_unique<Mesh>(dim);
std::stringstream meshfilename;
meshfilename << type << ".msh";
this->readMesh(meshfilename.str());
lower = mesh->getLowerBounds();
upper = mesh->getUpperBounds();
nb_element = this->mesh->getNbElement(type);
fem = std::make_unique<FEM>(*mesh, dim, "my_fem");
nb_quadrature_points_total =
GaussIntegrationElement<type>::getNbQuadraturePoints() * nb_element;
SCOPED_TRACE(std::to_string(type));
}
void TearDown() override {
fem.reset(nullptr);
mesh.reset(nullptr);
}
/// Should be reimplemented if further treatment of the mesh is needed
virtual void readMesh(std::string file_name) { mesh->read(file_name); }
protected:
std::unique_ptr<FEM> fem;
std::unique_ptr<Mesh> mesh;
UInt nb_element;
UInt nb_quadrature_points_total;
Vector<Real> lower;
Vector<Real> upper;
};
template <typename type_, template <ElementKind> class shape_t,
ElementKind kind>
constexpr const ElementType TestFEMBaseFixture<type_, shape_t, kind>::type;
template <typename type_, template <ElementKind> class shape_t,
ElementKind kind>
constexpr const size_t TestFEMBaseFixture<type_, shape_t, kind>::dim;
/* -------------------------------------------------------------------------- */
/// Base class for test with Lagrange FEEngine and regular elements
template <typename type_>
using TestFEMFixture = TestFEMBaseFixture<type_, ShapeLagrange, _ek_regular>;
/* -------------------------------------------------------------------------- */
using fe_engine_types = gtest_list_t<TestElementTypes>;
TYPED_TEST_SUITE(TestFEMFixture, fe_engine_types);
-#endif /* __AKANTU_TEST_FE_ENGINE_FIXTURE_HH__ */
+#endif /* AKANTU_TEST_FE_ENGINE_FIXTURE_HH_ */
diff --git a/test/test_fe_engine/test_fe_engine_structural_fixture.hh b/test/test_fe_engine/test_fe_engine_structural_fixture.hh
index faa5697fd..6dcd943ff 100644
--- a/test/test_fe_engine/test_fe_engine_structural_fixture.hh
+++ b/test/test_fe_engine/test_fe_engine_structural_fixture.hh
@@ -1,63 +1,63 @@
/**
* @file test_fe_engine_structural_fixture.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Aug 20 2010
* @date last modification: Fri Jan 26 2018
*
* @brief test of the fem class
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_io_msh_struct.hh"
#include "test_fe_engine_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TEST_FE_ENGINE_STRUCTURAL_FIXTURE_HH__
-#define __AKANTU_TEST_FE_ENGINE_STRUCTURAL_FIXTURE_HH__
+#ifndef AKANTU_TEST_FE_ENGINE_STRUCTURAL_FIXTURE_HH_
+#define AKANTU_TEST_FE_ENGINE_STRUCTURAL_FIXTURE_HH_
using namespace akantu;
/// Base class for structural FEEngine tests with structural elements
template <typename type_>
class TestFEMStructuralFixture
: public TestFEMBaseFixture<type_, ShapeStructural, _ek_structural> {
using parent = TestFEMBaseFixture<type_, ShapeStructural, _ek_structural>;
public:
static const UInt ndof = ElementClass<parent::type>::getNbDegreeOfFreedom();
/// Need to tell the mesh to load structural elements
void readMesh(std::string file_name) override {
this->mesh->read(file_name, _miot_gmsh_struct);
}
};
template <typename type_> const UInt TestFEMStructuralFixture<type_>::ndof;
// using types = gtest_list_t<TestElementTypes>;
// TYPED_TEST_SUITE(TestFEMFixture, types);
-#endif /* __AKANTU_TEST_FE_ENGINE_STRUCTURAL_FIXTURE_HH__ */
+#endif /* AKANTU_TEST_FE_ENGINE_STRUCTURAL_FIXTURE_HH_ */
diff --git a/test/test_gtest_utils.hh b/test/test_gtest_utils.hh
index 762540c52..6a1f51c18 100644
--- a/test/test_gtest_utils.hh
+++ b/test/test_gtest_utils.hh
@@ -1,258 +1,258 @@
/**
* @file test_gtest_utils.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
* @date last modification: Wed Feb 21 2018
*
* @brief Utils to help write tests
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_iterators.hh"
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TEST_GTEST_UTILS_HH__
-#define __AKANTU_TEST_GTEST_UTILS_HH__
+#ifndef AKANTU_TEST_GTEST_UTILS_HH_
+#define AKANTU_TEST_GTEST_UTILS_HH_
#if !defined(TYPED_TEST_SUITE)
#define TYPED_TEST_SUITE(...) TYPED_TEST_CASE(__VA_ARGS__)
#endif
#if !defined(TYPED_TEST_SUITE_P)
#define TYPED_TEST_SUITE_P(...) TYPED_TEST_CASE_P(__VA_ARGS__)
#endif
#if !defined(REGISTER_TYPED_TEST_SUITE_P)
#define REGISTER_TYPED_TEST_SUITE_P(...) REGISTER_TYPED_TEST_CASE_P(__VA_ARGS__)
#endif
#if !defined(INSTANTIATE_TYPED_TEST_SUITE_P)
#define INSTANTIATE_TYPED_TEST_SUITE_P(...) \
INSTANTIATE_TYPED_TEST_CASE_P(__VA_ARGS__)
#endif
namespace {
/* -------------------------------------------------------------------------- */
template <::akantu::ElementType t>
using element_type_t = std::integral_constant<::akantu::ElementType, t>;
/* -------------------------------------------------------------------------- */
template <typename... T> struct gtest_list {};
template <typename... Ts> struct gtest_list<std::tuple<Ts...>> {
using type = ::testing::Types<Ts...>;
};
template <typename... T> using gtest_list_t = typename gtest_list<T...>::type;
/* -------------------------------------------------------------------------- */
//template <typename... T> struct tuple_concat {};
template <typename... Ts>
struct tuple_concat {
using type = decltype(std::tuple_cat(std::declval<Ts>()...));
};
template <typename... T>
using tuple_concat_t = typename tuple_concat<T...>::type;
/* -------------------------------------------------------------------------- */
template <template <typename> class Pred, typename... Ts>
struct tuple_filter {};
template <template <typename> class Pred, typename T>
struct tuple_filter<Pred, std::tuple<T>> {
using type = std::conditional_t<Pred<T>::value, std::tuple<T>, std::tuple<>>;
};
template <template <typename> class Pred, typename T, typename... Ts>
struct tuple_filter<Pred, std::tuple<T, Ts...>> {
using type =
tuple_concat_t<typename tuple_filter<Pred, std::tuple<T>>::type,
typename tuple_filter<Pred, std::tuple<Ts...>>::type>;
};
template <template <typename> class Pred, typename... Ts>
using tuple_filter_t = typename tuple_filter<Pred, Ts...>::type;
/* -------------------------------------------------------------------------- */
template <size_t N, typename... Ts> struct tuple_split {};
template <size_t N, typename T, typename... Ts>
struct tuple_split<N, std::tuple<T, Ts...>> {
protected:
using split = tuple_split<N - 1, std::tuple<Ts...>>;
public:
using type = tuple_concat_t<std::tuple<T>, typename split::type>;
using type_tail = typename split::type_tail;
};
template <typename T, typename... Ts>
struct tuple_split<1, std::tuple<T, Ts...>> {
using type = std::tuple<T>;
using type_tail = std::tuple<Ts...>;
};
template <size_t N, typename... T>
using tuple_split_t = typename tuple_split<N, T...>::type;
template <size_t N, typename... T>
using tuple_split_tail_t = typename tuple_split<N, T...>::type_tail;
/* -------------------------------------------------------------------------- */
template <typename... T> struct cross_product {};
template <typename... T2s>
struct cross_product<std::tuple<>, std::tuple<T2s...>> {
using type = std::tuple<>;
};
template <typename T1, typename... T1s, typename... T2s>
struct cross_product<std::tuple<T1, T1s...>, std::tuple<T2s...>> {
using type = tuple_concat_t<
std::tuple<std::tuple<T1, T2s>...>,
typename cross_product<std::tuple<T1s...>, std::tuple<T2s...>>::type>;
};
template <typename... T>
using cross_product_t = typename cross_product<T...>::type;
/* -------------------------------------------------------------------------- */
} // namespace
#define OP_CAT(s, data, elem) BOOST_PP_CAT(_element_type, elem)
// creating a type instead of a using helps to debug
#define AKANTU_DECLARE_ELEMENT_TYPE_STRUCT(r, data, elem) \
struct BOOST_PP_CAT(_element_type, elem) \
: public element_type_t<::akantu::elem> {};
BOOST_PP_SEQ_FOR_EACH(AKANTU_DECLARE_ELEMENT_TYPE_STRUCT, _,
AKANTU_ALL_ELEMENT_TYPE)
#undef AKANTU_DECLARE_ELEMENT_TYPE_STRUCT
using TestElementTypesAll = std::tuple<BOOST_PP_SEQ_ENUM(
BOOST_PP_SEQ_TRANSFORM(OP_CAT, _, AKANTU_ek_regular_ELEMENT_TYPE))>;
#if defined(AKANTU_COHESIVE_ELEMENT)
using TestCohesiveElementTypes = std::tuple<BOOST_PP_SEQ_ENUM(
BOOST_PP_SEQ_TRANSFORM(OP_CAT, _, AKANTU_ek_cohesive_ELEMENT_TYPE))>;
#endif
#if defined(AKANTU_STRUCTURAL_MECHANICS)
using TestElementTypesStructural = std::tuple<BOOST_PP_SEQ_ENUM(
BOOST_PP_SEQ_TRANSFORM(OP_CAT, _, AKANTU_ek_structural_ELEMENT_TYPE))>;
#endif
using TestAllDimensions = std::tuple<std::integral_constant<unsigned int, 1>,
std::integral_constant<unsigned int, 2>,
std::integral_constant<unsigned int, 3>>;
template <typename T, ::akantu::ElementType type>
using is_element = aka::bool_constant<T::value == type>;
template <typename T>
using not_is_point_1 = aka::negation<is_element<T, ::akantu::_point_1>>;
using TestElementTypes = tuple_filter_t<not_is_point_1, TestElementTypesAll>;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
using StructuralTestElementTypes =
tuple_filter_t<not_is_point_1, TestElementTypesStructural>;
#endif
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <size_t degree> class Polynomial {
public:
Polynomial() = default;
Polynomial(std::initializer_list<double> && init) {
for (auto && pair : akantu::zip(init, constants))
std::get<1>(pair) = std::get<0>(pair);
}
double operator()(double x) {
double res = 0.;
for (auto && vals : akantu::enumerate(constants)) {
double a;
int k;
std::tie(k, a) = vals;
res += a * std::pow(x, k);
}
return res;
}
Polynomial extract(size_t pdegree) {
Polynomial<degree> extract(*this);
for (size_t d = pdegree + 1; d < degree + 1; ++d)
extract.constants[d] = 0;
return extract;
}
auto integral() {
Polynomial<degree + 1> integral_;
integral_.set(0, 0.);
;
for (size_t d = 0; d < degree + 1; ++d) {
integral_.set(1 + d, get(d) / double(d + 1));
}
return integral_;
}
auto integrate(double a, double b) {
auto primitive = integral();
return (primitive(b) - primitive(a));
}
double get(int i) const { return constants[i]; }
void set(int i, double a) { constants[i] = a; }
protected:
std::array<double, degree + 1> constants;
};
template <size_t degree>
std::ostream & operator<<(std::ostream & stream, const Polynomial<degree> & p) {
for (size_t d = 0; d < degree + 1; ++d) {
if (d != 0)
stream << " + ";
stream << p.get(degree - d);
if (d != degree)
stream << "x ^ " << degree - d;
}
return stream;
}
/* -------------------------------------------------------------------------- */
-#endif /* __AKANTU_TEST_GTEST_UTILS_HH__ */
+#endif /* AKANTU_TEST_GTEST_UTILS_HH_ */
diff --git a/test/test_model/patch_tests/patch_test_linear_fixture.hh b/test/test_model/patch_tests/patch_test_linear_fixture.hh
index 3f67deb72..fbdb13a3c 100644
--- a/test/test_model/patch_tests/patch_test_linear_fixture.hh
+++ b/test/test_model/patch_tests/patch_test_linear_fixture.hh
@@ -1,182 +1,182 @@
/**
* @file patch_test_linear_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
* @date last modification: Wed Jan 31 2018
*
* @brief Fixture for linear patch tests
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_utils.hh"
#include "model.hh"
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PATCH_TEST_LINEAR_FIXTURE_HH__
-#define __AKANTU_PATCH_TEST_LINEAR_FIXTURE_HH__
+#ifndef AKANTU_PATCH_TEST_LINEAR_FIXTURE_HH_
+#define AKANTU_PATCH_TEST_LINEAR_FIXTURE_HH_
//#define DEBUG_TEST
using namespace akantu;
template <typename type_, typename M>
class TestPatchTestLinear : public ::testing::Test {
public:
static constexpr ElementType type = type_::value;
static constexpr size_t dim = ElementClass<type>::getSpatialDimension();
virtual void SetUp() {
mesh = std::make_unique<Mesh>(dim);
mesh->read(std::to_string(type) + ".msh");
MeshUtils::buildFacets(*mesh);
mesh->createBoundaryGroupFromGeometry();
model = std::make_unique<M>(*mesh);
}
virtual void TearDown() {
model.reset(nullptr);
mesh.reset(nullptr);
}
virtual void initModel(const AnalysisMethod & method,
const std::string & material_file) {
debug::setDebugLevel(dblError);
getStaticParser().parse(material_file);
this->model->initFull(_analysis_method = method);
this->applyBC();
if (method != _static)
this->model->setTimeStep(0.8 * this->model->getStableTimeStep());
}
virtual void applyBC() {
auto & boundary = this->model->getBlockedDOFs();
for (auto & eg : mesh->iterateElementGroups()) {
for (const auto & node : eg.getNodeGroup()) {
for (UInt s = 0; s < boundary.getNbComponent(); ++s) {
boundary(node, s) = true;
}
}
}
}
virtual void applyBConDOFs(const Array<Real> & dofs) {
const auto & coordinates = this->mesh->getNodes();
for (auto & eg : this->mesh->iterateElementGroups()) {
for (const auto & node : eg.getNodeGroup()) {
this->setLinearDOF(dofs.begin(dofs.getNbComponent())[node],
coordinates.begin(this->dim)[node]);
}
}
}
template <typename V> Matrix<Real> prescribed_gradient(const V & dof) {
Matrix<Real> gradient(dof.getNbComponent(), dim);
for (UInt i = 0; i < gradient.rows(); ++i) {
for (UInt j = 0; j < gradient.cols(); ++j) {
gradient(i, j) = alpha(i, j + 1);
}
}
return gradient;
}
template <typename Gradient, typename DOFs>
void checkGradient(const Gradient & gradient, const DOFs & dofs) {
auto pgrad = prescribed_gradient(dofs);
for (auto & grad :
make_view(gradient, gradient.getNbComponent() / dim, dim)) {
auto diff = grad - pgrad;
auto gradient_error =
diff.template norm<L_inf>() / grad.template norm<L_inf>();
EXPECT_NEAR(0, gradient_error, gradient_tolerance);
}
}
template <typename presult_func_t, typename Result, typename DOFs>
void checkResults(presult_func_t && presult_func, const Result & results,
const DOFs & dofs) {
auto presult = presult_func(prescribed_gradient(dofs));
for (auto & result :
make_view(results, results.getNbComponent() / dim, dim)) {
auto diff = result - presult;
auto result_error =
diff.template norm<L_inf>() / presult.template norm<L_inf>();
EXPECT_NEAR(0, result_error, result_tolerance);
}
}
template <typename V1, typename V2>
void setLinearDOF(V1 && dof, V2 && coord) {
for (UInt i = 0; i < dof.size(); ++i) {
dof(i) = this->alpha(i, 0);
for (UInt j = 0; j < coord.size(); ++j) {
dof(i) += this->alpha(i, j + 1) * coord(j);
}
}
}
template <typename V> void checkDOFs(V && dofs) {
const auto & coordinates = mesh->getNodes();
Vector<Real> ref_dof(dofs.getNbComponent());
for (auto && tuple : zip(make_view(coordinates, dim),
make_view(dofs, dofs.getNbComponent()))) {
setLinearDOF(ref_dof, std::get<0>(tuple));
auto diff = std::get<1>(tuple) - ref_dof;
auto dofs_error = diff.template norm<L_inf>();
EXPECT_NEAR(0, dofs_error, dofs_tolerance);
}
}
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<M> model;
Matrix<Real> alpha{{0.01, 0.02, 0.03, 0.04},
{0.05, 0.06, 0.07, 0.08},
{0.09, 0.10, 0.11, 0.12}};
Real gradient_tolerance{1e-13};
Real result_tolerance{1e-13};
Real dofs_tolerance{1e-15};
};
template <typename type_, typename M>
constexpr ElementType TestPatchTestLinear<type_, M>::type;
template <typename tuple_, typename M>
constexpr size_t TestPatchTestLinear<tuple_, M>::dim;
-#endif /* __AKANTU_PATCH_TEST_LINEAR_FIXTURE_HH__ */
+#endif /* AKANTU_PATCH_TEST_LINEAR_FIXTURE_HH_ */
diff --git a/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.hh b/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.hh
index f3a7a04dd..449544034 100644
--- a/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.hh
+++ b/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.hh
@@ -1,76 +1,76 @@
/**
* @file patch_test_linear_heat_transfer_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
* @date last modification: Wed Jan 31 2018
*
* @brief HeatTransfer patch tests fixture
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model.hh"
/* -------------------------------------------------------------------------- */
#include "patch_test_linear_fixture.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PATCH_TEST_LINEAR_HEAT_TRANSFER_FIXTURE_HH__
-#define __AKANTU_PATCH_TEST_LINEAR_HEAT_TRANSFER_FIXTURE_HH__
+#ifndef AKANTU_PATCH_TEST_LINEAR_HEAT_TRANSFER_FIXTURE_HH_
+#define AKANTU_PATCH_TEST_LINEAR_HEAT_TRANSFER_FIXTURE_HH_
/* -------------------------------------------------------------------------- */
template <typename type>
class TestPatchTestHTMLinear
: public TestPatchTestLinear<type, HeatTransferModel> {
using parent = TestPatchTestLinear<type, HeatTransferModel>;
public:
void applyBC() override {
parent::applyBC();
auto & temperature = this->model->getTemperature();
this->applyBConDOFs(temperature);
}
void initModel(const AnalysisMethod & method,
const std::string & material_file) override {
TestPatchTestLinear<type, HeatTransferModel>::initModel(method,
material_file);
if (method != _static)
this->model->setTimeStep(0.5 * this->model->getStableTimeStep());
}
void checkAll() {
auto & temperature = this->model->getTemperature();
Matrix<Real> C = this->model->get("conductivity");
this->checkDOFs(temperature);
this->checkGradient(this->model->getTemperatureGradient(this->type),
temperature);
this->checkResults(
[&](const Matrix<Real> & grad_T) { return C * grad_T.transpose(); },
this->model->getKgradT(this->type), temperature);
}
};
using htm_types = gtest_list_t<TestElementTypes>;
TYPED_TEST_SUITE(TestPatchTestHTMLinear, htm_types);
-#endif /* __AKANTU_PATCH_TEST_LINEAR_HEAT_TRANSFER_FIXTURE_HH__ */
+#endif /* AKANTU_PATCH_TEST_LINEAR_HEAT_TRANSFER_FIXTURE_HH_ */
diff --git a/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.hh b/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.hh
index 21d7d4c59..1ac362d9c 100644
--- a/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.hh
+++ b/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.hh
@@ -1,153 +1,153 @@
/**
* @file patch_test_linear_solid_mechanics_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
*
* @brief SolidMechanics patch tests fixture
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "patch_test_linear_fixture.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_PATCH_TEST_LINEAR_SOLID_MECHANICS_FIXTURE_HH__
-#define __AKANTU_PATCH_TEST_LINEAR_SOLID_MECHANICS_FIXTURE_HH__
+#ifndef AKANTU_PATCH_TEST_LINEAR_SOLID_MECHANICS_FIXTURE_HH_
+#define AKANTU_PATCH_TEST_LINEAR_SOLID_MECHANICS_FIXTURE_HH_
/* -------------------------------------------------------------------------- */
template <typename tuple_>
class TestPatchTestSMMLinear
: public TestPatchTestLinear<std::tuple_element_t<0, tuple_>,
SolidMechanicsModel> {
using parent =
TestPatchTestLinear<std::tuple_element_t<0, tuple_>, SolidMechanicsModel>;
public:
static constexpr bool plane_strain = std::tuple_element_t<1, tuple_>::value;
void applyBC() override {
parent::applyBC();
auto & displacement = this->model->getDisplacement();
this->applyBConDOFs(displacement);
}
void checkForces() {
auto & mat = this->model->getMaterial(0);
auto & internal_forces = this->model->getInternalForce();
auto & external_forces = this->model->getExternalForce();
auto dim = this->dim;
Matrix<Real> sigma =
make_view(mat.getStress(this->type), dim, dim).begin()[0];
- external_forces.clear();
+ external_forces.zero();
if (dim > 1) {
for (auto & eg : this->mesh->iterateElementGroups()) {
this->model->applyBC(BC::Neumann::FromHigherDim(sigma), eg.getName());
}
} else {
external_forces(0) = -sigma(0, 0);
external_forces(1) = sigma(0, 0);
}
Real force_norm_inf = -std::numeric_limits<Real>::max();
Vector<Real> total_force(dim);
- total_force.clear();
+ total_force.zero();
for (auto && f : make_view(internal_forces, dim)) {
total_force += f;
force_norm_inf = std::max(force_norm_inf, f.template norm<L_inf>());
}
EXPECT_NEAR(0, total_force.template norm<L_inf>() / force_norm_inf, 1e-9);
for (auto && tuple : zip(make_view(internal_forces, dim),
make_view(external_forces, dim))) {
auto && f_int = std::get<0>(tuple);
auto && f_ext = std::get<1>(tuple);
auto f = f_int + f_ext;
EXPECT_NEAR(0, f.template norm<L_inf>() / force_norm_inf, 1e-9);
}
}
void checkAll() {
auto & displacement = this->model->getDisplacement();
auto & mat = this->model->getMaterial(0);
this->checkDOFs(displacement);
this->checkGradient(mat.getGradU(this->type), displacement);
this->checkResults(
[&](const Matrix<Real> & pstrain) {
Real nu = this->model->getMaterial(0).get("nu");
Real E = this->model->getMaterial(0).get("E");
auto strain = (pstrain + pstrain.transpose()) / 2.;
auto trace = strain.trace();
auto lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
auto mu = E / (2 * (1 + nu));
if (not this->plane_strain) {
lambda = nu * E / (1 - nu * nu);
}
decltype(strain) stress(this->dim, this->dim);
if (this->dim == 1) {
stress(0, 0) = E * strain(0, 0);
} else {
for (UInt i = 0; i < this->dim; ++i)
for (UInt j = 0; j < this->dim; ++j)
stress(i, j) =
(i == j) * lambda * trace + 2 * mu * strain(i, j);
}
return stress;
},
mat.getStress(this->type), displacement);
this->checkForces();
}
};
template <typename tuple_>
constexpr bool TestPatchTestSMMLinear<tuple_>::plane_strain;
template <typename T> struct invalid_plan_stress : std::true_type {};
template <typename type, typename bool_c>
struct invalid_plan_stress<std::tuple<type, bool_c>>
: aka::bool_constant<ElementClass<type::value>::getSpatialDimension() !=
2 and
not bool_c::value> {};
using true_false =
std::tuple<aka::bool_constant<true>, aka::bool_constant<false>>;
template <typename T> using valid_types = aka::negation<invalid_plan_stress<T>>;
using model_types = gtest_list_t<
tuple_filter_t<valid_types, cross_product_t<TestElementTypes, true_false>>>;
TYPED_TEST_SUITE(TestPatchTestSMMLinear, model_types);
-#endif /* __AKANTU_PATCH_TEST_LINEAR_SOLID_MECHANICS_FIXTURE_HH__ */
+#endif /* AKANTU_PATCH_TEST_LINEAR_SOLID_MECHANICS_FIXTURE_HH_ */
diff --git a/test/test_model/test_common/test_dof_manager.cc b/test/test_model/test_common/test_dof_manager.cc
index 74931c92f..a17f2c96a 100644
--- a/test/test_model/test_common/test_dof_manager.cc
+++ b/test/test_model/test_common/test_dof_manager.cc
@@ -1,298 +1,298 @@
/**
* @file test_dof_manager.cc
*
* @author Nicolas Richart
*
* @date creation Wed Jan 30 2019
*
* @brief test the dof managers
*
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <dof_manager.hh>
#include <mesh_partition_scotch.hh>
#include <mesh_utils.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <numeric>
#include <string>
#include <type_traits>
/* -------------------------------------------------------------------------- */
namespace akantu {
enum DOFManagerType { _dmt_default, _dmt_petsc };
}
AKANTU_ENUM_HASH(DOFManagerType)
using namespace akantu;
// defined as struct to get there names in gtest outputs
struct _dof_manager_default
: public std::integral_constant<DOFManagerType, _dmt_default> {};
struct _dof_manager_petsc
: public std::integral_constant<DOFManagerType, _dmt_petsc> {};
using dof_manager_types = ::testing::Types<
#ifdef AKANTU_USE_PETSC
_dof_manager_petsc,
#endif
_dof_manager_default>;
namespace std {
std::string to_string(const DOFManagerType & type) {
std::unordered_map<DOFManagerType, std::string> map{
#ifdef AKANTU_USE_PETSC
{_dmt_petsc, "petsc"},
#endif
{_dmt_default, "default"},
};
return map.at(type);
}
} // namespace std
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManagerTester {
public:
DOFManagerTester(std::unique_ptr<DOFManager> dof_manager)
: dof_manager(std::move(dof_manager)) {}
DOFManager & operator*() { return *dof_manager; }
DOFManager * operator->() { return dof_manager.get(); }
void getArrayPerDOFs(const ID & id, SolverVector & vector,
Array<Real> & array) {
dof_manager->getArrayPerDOFs(id, vector, array);
}
SolverVector & residual() { return *dof_manager->residual; }
private:
std::unique_ptr<DOFManager> dof_manager;
};
} // namespace akantu
template <class T> class DOFManagerFixture : public ::testing::Test {
public:
constexpr static DOFManagerType type = T::value;
constexpr static UInt dim = 3;
void SetUp() override {
mesh = std::make_unique<Mesh>(this->dim);
auto & communicator = Communicator::getStaticCommunicator();
if (communicator.whoAmI() == 0) {
mesh->read("mesh.msh");
}
mesh->distribute();
nb_nodes = this->mesh->getNbNodes();
nb_total_nodes = this->mesh->getNbGlobalNodes();
auto && range_nodes = arange(nb_nodes);
nb_pure_local =
std::accumulate(range_nodes.begin(), range_nodes.end(), 0,
[&](auto && init, auto && val) {
return init + mesh->isLocalOrMasterNode(val);
});
}
void TearDown() override {
mesh.reset();
dof1.reset();
dof2.reset();
}
decltype(auto) alloc() {
std::unordered_map<DOFManagerType, std::string> types{
{_dmt_default, "default"}, {_dmt_petsc, "petsc"}};
return DOFManagerTester(DOFManagerFactory::getInstance().allocate(
types[T::value], *mesh, "dof_manager", 0));
}
decltype(auto) registerDOFs(DOFSupportType dst1, DOFSupportType dst2) {
auto dof_manager = DOFManagerTester(this->alloc());
auto n1 = dst1 == _dst_nodal ? nb_nodes : nb_pure_local;
this->dof1 = std::make_unique<Array<Real>>(n1, 3);
dof_manager->registerDOFs("dofs1", *this->dof1, dst1);
EXPECT_EQ(dof_manager.residual().size(), nb_total_nodes * 3);
auto n2 = dst2 == _dst_nodal ? nb_nodes : nb_pure_local;
this->dof2 = std::make_unique<Array<Real>>(n2, 5);
dof_manager->registerDOFs("dofs2", *this->dof2, dst2);
EXPECT_EQ(dof_manager.residual().size(), nb_total_nodes * 8);
return dof_manager;
}
protected:
Int nb_nodes{0}, nb_total_nodes{0}, nb_pure_local{0};
std::unique_ptr<Mesh> mesh;
std::unique_ptr<Array<Real>> dof1;
std::unique_ptr<Array<Real>> dof2;
};
template <class T> constexpr DOFManagerType DOFManagerFixture<T>::type;
template <class T> constexpr UInt DOFManagerFixture<T>::dim;
TYPED_TEST_SUITE(DOFManagerFixture, dof_manager_types);
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, Construction) {
auto dof_manager = this->alloc();
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, DoubleConstruction) {
auto dof_manager = this->alloc();
dof_manager = this->alloc();
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterGenericDOF1) {
auto dof_manager = this->alloc();
Array<Real> dofs(this->nb_pure_local, 3);
dof_manager->registerDOFs("dofs1", dofs, _dst_generic);
EXPECT_GE(dof_manager.residual().size(), this->nb_total_nodes * 3);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterNodalDOF1) {
auto dof_manager = this->alloc();
Array<Real> dofs(this->nb_nodes, 3);
dof_manager->registerDOFs("dofs1", dofs, _dst_nodal);
EXPECT_GE(dof_manager.residual().size(), this->nb_total_nodes * 3);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterGenericDOF2) {
this->registerDOFs(_dst_generic, _dst_generic);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterNodalDOF2) {
this->registerDOFs(_dst_nodal, _dst_nodal);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterMixedDOF) {
auto dof_manager = this->registerDOFs(_dst_nodal, _dst_generic);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, AssembleVector) {
auto dof_manager = this->registerDOFs(_dst_nodal, _dst_generic);
- dof_manager.residual().clear();
+ dof_manager.residual().zero();
for (auto && data :
enumerate(make_view(*this->dof1, this->dof1->getNbComponent()))) {
auto n = std::get<0>(data);
auto & l = std::get<1>(data);
l.set(1. * this->mesh->isLocalOrMasterNode(n));
}
this->dof2->set(2.);
dof_manager->assembleToResidual("dofs1", *this->dof1);
dof_manager->assembleToResidual("dofs2", *this->dof2);
this->dof1->set(0.);
this->dof2->set(0.);
dof_manager.getArrayPerDOFs("dofs1", dof_manager.residual(), *this->dof1);
for (auto && data :
enumerate(make_view(*this->dof1, this->dof1->getNbComponent()))) {
if (this->mesh->isLocalOrMasterNode(std::get<0>(data))) {
const auto & l = std::get<1>(data);
auto e = (l - Vector<Real>{1., 1., 1.}).norm();
ASSERT_EQ(e, 0.);
}
}
dof_manager.getArrayPerDOFs("dofs2", dof_manager.residual(), *this->dof2);
for (auto && l : make_view(*this->dof2, this->dof2->getNbComponent())) {
auto e = (l - Vector<Real>{2., 2., 2., 2., 2.}).norm();
ASSERT_EQ(e, 0.);
}
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, AssembleMatrixNodal) {
auto dof_manager = this->registerDOFs(_dst_nodal, _dst_nodal);
auto && K = dof_manager->getNewMatrix("K", _symmetric);
- K.clear();
+ K.zero();
auto && elemental_matrix = std::make_unique<Array<Real>>(
this->mesh->getNbElement(this->dim), 8 * 3 * 8 * 3);
for (auto && m : make_view(*elemental_matrix, 8 * 3, 8 * 3)) {
m.set(1.);
}
dof_manager->assembleElementalMatricesToMatrix(
"K", "dofs1", *elemental_matrix, _hexahedron_8);
elemental_matrix = std::make_unique<Array<Real>>(
this->mesh->getNbElement(this->dim), 8 * 5 * 8 * 5);
for (auto && m : make_view(*elemental_matrix, 8 * 5, 8 * 5)) {
m.set(1.);
}
dof_manager->assembleElementalMatricesToMatrix(
"K", "dofs2", *elemental_matrix, _hexahedron_8);
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(*this->mesh, node_to_elem, this->dim);
- dof_manager.residual().clear();
+ dof_manager.residual().zero();
for (auto && data :
enumerate(zip(make_view(*this->dof1, this->dof1->getNbComponent()),
make_view(*this->dof2, this->dof2->getNbComponent())))) {
auto n = std::get<0>(data);
auto & l1 = std::get<0>(std::get<1>(data));
auto & l2 = std::get<1>(std::get<1>(data));
auto v = 1. * this->mesh->isLocalOrMasterNode(n);
l1.set(v);
l2.set(v);
}
dof_manager->assembleToResidual("dofs1", *this->dof1);
dof_manager->assembleToResidual("dofs2", *this->dof2);
for (auto && n : arange(this->nb_nodes)) {
if (not this->mesh->isLocalOrMasterNode(n)) {
}
}
}
diff --git a/test/test_model/test_common/test_model_solver/test_dof_manager_default.cc b/test/test_model/test_common/test_model_solver/test_dof_manager_default.cc
index a8f7fb29d..09354c24b 100644
--- a/test/test_model/test_common/test_model_solver/test_dof_manager_default.cc
+++ b/test/test_model/test_common/test_model_solver/test_dof_manager_default.cc
@@ -1,129 +1,129 @@
/**
* @file test_dof_manager_default.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 26 2016
* @date last modification: Thu Feb 01 2018
*
* @brief Test default dof manager
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "sparse_matrix_aij.hh"
#include "time_step_solver.hh"
using namespace akantu;
/**
* =\o-----o-----o-> F
* | |
* |---- L ----|
*/
class MySolverCallback : public SolverCallback {
public:
MySolverCallback(Real F, DOFManagerDefault & dof_manager, UInt nb_dofs = 3)
: dof_manager(dof_manager), dispacement(nb_dofs, 1, "disp"),
blocked(nb_dofs, 1), forces(nb_dofs, 1), nb_dofs(nb_dofs) {
dof_manager.registerDOFs("disp", dispacement, _dst_generic);
dof_manager.registerBlockedDOFs("disp", blocked);
dispacement.set(0.);
forces.set(0.);
blocked.set(false);
forces(nb_dofs - 1, _x) = F;
blocked(0, _x) = true;
}
void assembleMatrix(const ID & matrix_id) {
if (matrix_id != "K")
return;
auto & K = dynamic_cast<SparseMatrixAIJ &>(dof_manager.getMatrix("K"));
- K.clear();
+ K.zero();
for (UInt i = 1; i < nb_dofs - 1; ++i)
K.add(i, i, 2.);
for (UInt i = 0; i < nb_dofs - 1; ++i)
K.add(i, i + 1, -1.);
K.add(0, 0, 1);
K.add(nb_dofs - 1, nb_dofs - 1, 1);
// K *= 1 / L_{el}
K *= nb_dofs - 1;
}
MatrixType getMatrixType(const ID & matrix_id) {
if (matrix_id == "K")
return _symmetric;
return _mt_not_defined;
}
void assembleLumpedMatrix(const ID &) {}
void assembleResidual() { dof_manager.assembleToResidual("disp", forces); }
void predictor() {}
void corrector() {}
DOFManagerDefault & dof_manager;
Array<Real> dispacement;
Array<bool> blocked;
Array<Real> forces;
UInt nb_dofs;
};
int main(int argc, char * argv[]) {
initialize(argc, argv);
DOFManagerDefault dof_manager("test_dof_manager");
MySolverCallback callback(10., dof_manager, 11);
NonLinearSolver & nls =
dof_manager.getNewNonLinearSolver("my_nls", NonLinearSolverType::_linear);
TimeStepSolver & tss = dof_manager.getNewTimeStepSolver(
"my_tss", TimeStepSolverType::_static, nls, callback);
tss.setIntegrationScheme("disp", IntegrationSchemeType::_pseudo_time);
tss.solveStep(callback);
dof_manager.getMatrix("K").saveMatrix("K_dof_manager_default.mtx");
Array<Real>::const_scalar_iterator disp_it = callback.dispacement.begin();
Array<Real>::const_scalar_iterator force_it = callback.forces.begin();
Array<bool>::const_scalar_iterator blocked_it = callback.blocked.begin();
std::cout << std::setw(8) << "disp"
<< " " << std::setw(8) << "force"
<< " " << std::setw(8) << "blocked" << std::endl;
for (; disp_it != callback.dispacement.end();
++disp_it, ++force_it, ++blocked_it) {
std::cout << std::setw(8) << *disp_it << " " << std::setw(8) << *force_it
<< " " << std::setw(8) << std::boolalpha << *blocked_it
<< std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.cc b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.cc
index f7d30409d..3a4247ffd 100644
--- a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.cc
+++ b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.cc
@@ -1,245 +1,245 @@
/**
* @file test_model_solver_dynamic.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 13 2016
* @date last modification: Tue Feb 20 2018
*
* @brief Test default dof manager
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#include "dumpable_inline_impl.hh"
#include "dumper_element_partition.hh"
#include "dumper_iohelper_paraview.hh"
/* -------------------------------------------------------------------------- */
#include "test_model_solver_my_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#ifndef EXPLICIT
#define EXPLICIT true
#endif
using namespace akantu;
class Sinusoidal : public BC::Dirichlet::DirichletFunctor {
public:
Sinusoidal(MyModel & model, Real amplitude, Real pulse_width, Real t)
: model(model), A(amplitude), k(2 * M_PI / pulse_width),
t(t), v{std::sqrt(model.E / model.rho)} {}
void operator()(UInt n, Vector<bool> & /*flags*/, Vector<Real> & disp,
const Vector<Real> & coord) const {
auto x = coord(_x);
model.velocity(n, _x) = k * v * A * sin(k * (x - v * t));
disp(_x) = A * cos(k * (x - v * t));
}
private:
MyModel & model;
Real A{1.};
Real k{2 * M_PI};
Real t{1.};
Real v{1.};
};
static void genMesh(Mesh & mesh, UInt nb_nodes);
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt prank = Communicator::getStaticCommunicator().whoAmI();
UInt global_nb_nodes = 201;
UInt max_steps = 400;
Real time_step = 0.001;
Mesh mesh(1);
Real F = -9.81;
bool _explicit = EXPLICIT;
const Real pulse_width = 0.2;
const Real A = 0.01;
ID dof_manager_type = "default";
#if defined(DOF_MANAGER_TYPE)
dof_manager_type = DOF_MANAGER_TYPE;
#endif
if (prank == 0)
genMesh(mesh, global_nb_nodes);
mesh.distribute();
// mesh.makePeriodic(_x);
MyModel model(F, mesh, _explicit, dof_manager_type);
- model.forces.clear();
- model.blocked.clear();
+ model.forces.zero();
+ model.blocked.zero();
model.applyBC(Sinusoidal(model, A, pulse_width, 0.), "all");
model.applyBC(BC::Dirichlet::FlagOnly(_x), "border");
if (!_explicit) {
model.getNewSolver("dynamic", TimeStepSolverType::_dynamic,
NonLinearSolverType::_newton_raphson);
model.setIntegrationScheme("dynamic", "disp",
IntegrationSchemeType::_trapezoidal_rule_2,
IntegrationScheme::_displacement);
} else {
model.getNewSolver("dynamic", TimeStepSolverType::_dynamic_lumped,
NonLinearSolverType::_lumped);
model.setIntegrationScheme("dynamic", "disp",
IntegrationSchemeType::_central_difference,
IntegrationScheme::_acceleration);
}
model.setTimeStep(time_step);
if (prank == 0) {
std::cout << std::scientific;
std::cout << std::setw(14) << "time"
<< "," << std::setw(14) << "wext"
<< "," << std::setw(14) << "epot"
<< "," << std::setw(14) << "ekin"
<< "," << std::setw(14) << "total"
<< "," << std::setw(14) << "max_disp"
<< "," << std::setw(14) << "min_disp" << std::endl;
}
Real wext = 0.;
- model.getDOFManager().clearResidual();
+ model.getDOFManager().zeroResidual();
model.assembleResidual();
Real epot = 0; // model.getPotentialEnergy();
Real ekin = 0; // model.getKineticEnergy();
Real einit = ekin + epot;
Real etot = ekin + epot - wext - einit;
Real max_disp = 0., min_disp = 0.;
for (auto && disp : model.displacement) {
max_disp = std::max(max_disp, disp);
min_disp = std::min(min_disp, disp);
}
if (prank == 0) {
std::cout << std::setw(14) << 0. << "," << std::setw(14) << wext << ","
<< std::setw(14) << epot << "," << std::setw(14) << ekin << ","
<< std::setw(14) << etot << "," << std::setw(14) << max_disp
<< "," << std::setw(14) << min_disp << std::endl;
}
#if EXPLICIT == false
NonLinearSolver & solver =
model.getDOFManager().getNonLinearSolver("dynamic");
solver.set("max_iterations", 20);
#endif
auto && dumper = std::make_shared<DumperParaview>("dynamic", "./paraview");
mesh.registerExternalDumper(dumper, "dynamic", true);
mesh.addDumpMesh(mesh);
mesh.addDumpFieldExternalToDumper("dynamic", "displacement",
model.displacement);
mesh.addDumpFieldExternalToDumper("dynamic", "velocity", model.velocity);
mesh.addDumpFieldExternalToDumper("dynamic", "forces", model.forces);
mesh.addDumpFieldExternalToDumper("dynamic", "internal_forces",
model.internal_forces);
mesh.addDumpFieldExternalToDumper("dynamic", "acceleration",
model.acceleration);
mesh.dump();
for (UInt i = 1; i < max_steps + 1; ++i) {
model.applyBC(Sinusoidal(model, A, pulse_width, time_step * (i - 1)),
"border");
model.solveStep("dynamic");
mesh.dump();
epot = model.getPotentialEnergy();
ekin = model.getKineticEnergy();
wext += model.getExternalWorkIncrement();
etot = ekin + epot - wext - einit;
Real max_disp = 0., min_disp = 0.;
for (auto && disp : model.displacement) {
max_disp = std::max(max_disp, disp);
min_disp = std::min(min_disp, disp);
}
if (prank == 0) {
std::cout << std::setw(14) << time_step * i << "," << std::setw(14)
<< wext << "," << std::setw(14) << epot << "," << std::setw(14)
<< ekin << "," << std::setw(14) << etot << "," << std::setw(14)
<< max_disp << "," << std::setw(14) << min_disp << std::endl;
}
}
// output.close();
finalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void genMesh(Mesh & mesh, UInt nb_nodes) {
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
Array<UInt> & conn = mesh_accessor.getConnectivity(_segment_2);
nodes.resize(nb_nodes);
auto & all = mesh.createNodeGroup("all_nodes");
for (UInt n = 0; n < nb_nodes; ++n) {
nodes(n, _x) = n * (1. / (nb_nodes - 1));
all.add(n);
}
mesh.createElementGroupFromNodeGroup("all", "all_nodes");
conn.resize(nb_nodes - 1);
for (UInt n = 0; n < nb_nodes - 1; ++n) {
conn(n, 0) = n;
conn(n, 1) = n + 1;
}
Array<UInt> & conn_points = mesh_accessor.getConnectivity(_point_1);
conn_points.resize(2);
conn_points(0, 0) = 0;
conn_points(1, 0) = nb_nodes - 1;
auto & border = mesh.createElementGroup("border", 0);
border.add({_point_1, 0, _not_ghost}, true);
border.add({_point_1, 1, _not_ghost}, true);
mesh_accessor.makeReady();
}
diff --git a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.cc b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.cc
index 5c39c1779..725148a1b 100644
--- a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.cc
+++ b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.cc
@@ -1,837 +1,837 @@
/**
* @file test_model_solver_dynamic.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 13 2016
* @date last modification: Tue Feb 20 2018
*
* @brief Test default dof manager
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#include "boundary_condition_functor.hh"
#include "mpi_communicator_data.hh"
/* -------------------------------------------------------------------------- */
#include "dumpable_inline_impl.hh"
#include "dumper_element_partition.hh"
#include "dumper_iohelper_paraview.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#include <petscmat.h>
#include <petscsnes.h>
#include <petscvec.h>
/* -------------------------------------------------------------------------- */
#ifndef EXPLICIT
#define EXPLICIT true
#endif
template <typename func>
void CHECK_ERR_CXX(func && func_, PetscErrorCode ierr) {
if (PetscUnlikely(ierr != 0)) {
const char * desc;
PetscErrorMessage(ierr, &desc, nullptr);
AKANTU_EXCEPTION("Error in PETSc call to \'" << func_ << "\': " << desc);
}
}
using namespace akantu;
static void genMesh(Mesh & mesh, UInt nb_nodes);
class MyModel {
public:
MyModel(Real F, Mesh & mesh, bool lumped)
: nb_dofs(mesh.getNbNodes()), nb_elements(mesh.getNbElement(_segment_2)),
lumped(lumped), E(1.), A(1.), rho(1.), mesh(mesh),
displacement(nb_dofs, 1, "disp"), velocity(nb_dofs, 1, "velo"),
acceleration(nb_dofs, 1, "accel"), blocked(nb_dofs, 1, "blocked"),
forces(nb_dofs, 1, "force_ext"),
internal_forces(nb_dofs, 1, "force_int"),
stresses(nb_elements, 1, "stress"), strains(nb_elements, 1, "strain"),
initial_lengths(nb_elements, 1, "L0") {
auto n_global = mesh.getNbGlobalNodes();
int n_local = 0;
std::vector<PetscInt> nodes_global_ids(nb_dofs);
for (auto && data : enumerate(nodes_global_ids)) {
auto n = std::get<0>(data);
n_local += mesh.isLocalOrMasterNode(n);
std::get<1>(data) = mesh.getNodeGlobalId(n);
}
mpi_comm = dynamic_cast<MPICommunicatorData &>(
mesh.getCommunicator().getCommunicatorData())
.getMPICommunicator();
MeshAccessor mesh_accessor(mesh);
ierr = ISLocalToGlobalMappingCreate(
mpi_comm, 1, mesh.getNbNodes(), nodes_global_ids.data(),
PETSC_COPY_VALUES, &petsc_local_to_global);
CHECK_ERR_CXX("ISLocalToGlobalMappingCreate", ierr);
auto setName = [](auto && Obj, auto && name) {
PetscObjectSetName(reinterpret_cast<PetscObject>(Obj), name);
};
ierr = VecCreate(mpi_comm, &rhs);
ierr = VecSetSizes(rhs, n_local, n_global);
ierr = VecSetFromOptions(rhs);
ierr = VecSetLocalToGlobalMapping(rhs, petsc_local_to_global);
setName(rhs, "rhs");
ierr = VecDuplicate(rhs, &x);
ierr = VecDuplicate(rhs, &x_save);
ierr = VecDuplicate(rhs, &dx);
ierr = VecDuplicate(rhs, &f_int);
ierr = VecDuplicate(rhs, &f_dirichlet);
setName(x, "x");
setName(x_save, "x save");
setName(dx, "dx");
setName(f_int, "f_int");
setName(f_dirichlet, "f_dirichlet");
ierr = MatCreate(mpi_comm, &M);
ierr = MatSetSizes(M, n_local, n_local, n_global, n_global);
ierr = MatSetFromOptions(M);
ierr = MatSetOption(M, MAT_SYMMETRIC, PETSC_TRUE);
ierr = MatSetOption(M, MAT_ROW_ORIENTED, PETSC_TRUE);
ierr = MatSetUp(M);
ierr = MatSetLocalToGlobalMapping(M, petsc_local_to_global,
petsc_local_to_global);
setName(M, "M");
assembleMass();
ierr = MatDuplicate(M, MAT_DO_NOT_COPY_VALUES, &K);
setName(K, "K");
ierr = MatDuplicate(M, MAT_DO_NOT_COPY_VALUES, &J);
setName(J, "J");
ierr = SNESCreate(mpi_comm, &snes);
ierr = SNESSetFromOptions(snes);
ierr = SNESSetFunction(snes, rhs, MyModel::FormFunction, this);
ierr = SNESSetJacobian(snes, J, J, MyModel::FormJacobian, this);
PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_INDEX);
displacement.set(0.);
velocity.set(0.);
acceleration.set(0.);
forces.set(0.);
blocked.set(false);
blocked(0, 0) = true;
blocked(nb_dofs - 1, 0) = true;
displacement(0, 0) = 0;
displacement(nb_dofs - 1, 0) = 1;
for (auto && data :
zip(make_view(this->mesh.getConnectivity(_segment_2), 2),
make_view(this->initial_lengths))) {
const auto & conn = std::get<0>(data);
auto & L = std::get<1>(data);
auto p1 = this->mesh.getNodes()(conn(0), _x);
auto p2 = this->mesh.getNodes()(conn(1), _x);
L = std::abs(p2 - p1);
}
}
// static PetscErrorCode SNESMonitor(SNES snes,PetscInt its,PetscReal
// fnorm,void *ctx) {
// auto & _this = *reinterpret_cast<MyModel *>(ctx);
// //SNESMonitorDefault(snes, its, fnorm, PETSC_VIEWER_STDOUT_WORLD);
// }
static PetscErrorCode FormFunction(SNES /*snes*/, Vec /*dx*/, Vec /*f*/,
void * ctx) {
auto & _this = *reinterpret_cast<MyModel *>(ctx);
_this.assembleResidual();
return 0;
}
static PetscErrorCode FormJacobian(SNES /*snes*/, Vec /*dx*/, Mat /*J*/,
Mat /*P*/, void * ctx) {
auto & _this = *reinterpret_cast<MyModel *>(ctx);
_this.assembleJacobian();
return 0;
}
~MyModel() {
ierr = MatDestroy(&M);
ierr = MatDestroy(&K);
ierr = MatDestroy(&J);
ierr = VecDestroy(&rhs);
ierr = VecDestroy(&x);
ierr = VecDestroy(&dx);
ierr = VecDestroy(&x_save);
ierr = VecDestroy(&f_int);
PetscFinalize();
}
void solveStep() {
std::cout << "solveStep" << std::endl;
copy(x_save, displacement);
ierr = SNESSolve(snes, NULL, dx);
CHECK_ERR_CXX("SNESSolve", ierr);
setSolutionToDisplacement();
assembleResidual();
}
void applyBC() {
std::vector<PetscInt> rows;
for (auto && data : enumerate(blocked)) {
if (std::get<1>(data)) {
rows.push_back(std::get<0>(data));
}
}
copy(x, displacement);
ierr = MatZeroRowsColumnsLocal(J, rows.size(), rows.data(), 1., x,
f_dirichlet);
VecView(f_dirichlet, PETSC_VIEWER_STDOUT_WORLD);
CHECK_ERR_CXX("MatZeroRowsColumnsLocal", ierr);
}
void setSolutionToDisplacement() {
std::cout << "setSolutionToDisplacement" << std::endl;
ierr = VecWAXPY(x, 1, x_save, dx);
copy(displacement, x);
}
void assembleJacobian() {
std::cout << "assembleJacobian" << std::endl;
setSolutionToDisplacement();
assembleStiffness();
ierr = MatZeroEntries(J);
CHECK_ERR_CXX("MatZeroEntries", ierr);
ierr = MatAXPY(J, 1., K, SAME_NONZERO_PATTERN);
CHECK_ERR_CXX("MatAXPY", ierr);
MatView(J, PETSC_VIEWER_STDOUT_WORLD);
applyBC();
MatView(J, PETSC_VIEWER_STDOUT_WORLD);
}
void assembleMass() {
std::cout << "assembleMass" << std::endl;
ierr = MatZeroEntries(M);
CHECK_ERR_CXX("MatZeroEntries", ierr);
Array<Real> m_all_el(this->nb_elements, 4);
Matrix<Real> m(2, 2);
m(0, 0) = m(1, 1) = 2;
m(0, 1) = m(1, 0) = 1;
// under integrated
// m(0, 0) = m(1, 1) = 3./2.;
// m(0, 1) = m(1, 0) = 3./2.;
// lumping the mass matrix
// m(0, 0) += m(0, 1);
// m(1, 1) += m(1, 0);
// m(0, 1) = m(1, 0) = 0;
for (auto && data :
zip(make_view(this->mesh.getConnectivity(_segment_2), 2),
make_view(m_all_el, 2, 2))) {
const auto & conn = std::get<0>(data);
auto & m_el = std::get<1>(data);
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
m_el = m;
m_el *= rho * A * L / 6.;
Vector<Int> conn_int(conn.size());
for (auto && data : zip(conn_int, conn)) {
std::get<0>(data) = std::get<1>(data);
}
ierr = MatSetValuesLocal(M, conn_int.size(), conn_int.storage(),
conn_int.size(), conn_int.storage(), m.storage(),
ADD_VALUES);
}
ierr = MatAssemblyBegin(M, MAT_FINAL_ASSEMBLY);
ierr = MatAssemblyEnd(M, MAT_FINAL_ASSEMBLY);
ierr = MatSetOption(M, MAT_NEW_NONZERO_LOCATIONS, PETSC_FALSE);
PetscViewer viewer;
ierr = PetscViewerASCIIOpen(mpi_comm, "M.mtx", &viewer);
PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_MATRIXMARKET);
ierr = MatView(M, viewer);
PetscViewerPopFormat(viewer);
ierr = PetscViewerDestroy(&viewer);
// this->getDOFManager().assembleElementalMatricesToMatrix(
// "M", "disp", m_all_el, _segment_2);
is_mass_assembled = true;
}
// MatrixType getMatrixType(const ID &) { return _symmetric; }
// void assembleMatrix(const ID & matrix_id) {
// if (matrix_id == "K") {
// if (not is_stiffness_assembled)
// this->assembleStiffness();
// } else if (matrix_id == "M") {
// if (not is_mass_assembled)
// this->assembleMass();
// } else if (matrix_id == "C") {
// // pass, no damping matrix
// } else {
// AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
// << matrix_id);
// }
// }
void assembleLumpedMatrix(const ID & matrix_id) {
std::cout << "assembleLumpedMatrix" << std::endl;
AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
<< matrix_id);
}
void assembleStiffness() {
std::cout << "assembleStiffness" << std::endl;
// SparseMatrix & K = this->getDOFManager().getMatrix("K");
- // K.clear();
+ // K.zero();
ierr = MatZeroEntries(K);
CHECK_ERR_CXX("MatZeroEntries", ierr);
Matrix<Real> k(2, 2);
k(0, 0) = k(1, 1) = 1;
k(0, 1) = k(1, 0) = -1;
Array<Real> k_all_el(this->nb_elements, 4);
auto k_it = k_all_el.begin(2, 2);
auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2).end(2);
for (; cit != cend; ++cit, ++k_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
auto & k_el = *k_it;
k_el = k;
k_el *= E * A / L;
Vector<Int> conn_int(conn.size());
for (auto && data : zip(conn_int, conn)) {
std::get<0>(data) = std::get<1>(data);
}
ierr = MatSetValuesLocal(K, conn_int.size(), conn_int.storage(),
conn_int.size(), conn_int.storage(),
k_el.storage(), ADD_VALUES);
}
ierr = MatAssemblyBegin(K, MAT_FINAL_ASSEMBLY);
CHECK_ERR_CXX("MatAssemblyBegin", ierr);
ierr = MatAssemblyEnd(K, MAT_FINAL_ASSEMBLY);
CHECK_ERR_CXX("MatAssemblyEnd", ierr);
ierr = MatSetOption(K, MAT_NEW_NONZERO_LOCATIONS, PETSC_FALSE);
CHECK_ERR_CXX("MatSetOption", ierr);
PetscViewer viewer;
ierr = PetscViewerASCIIOpen(mpi_comm, "K.mtx", &viewer);
CHECK_ERR_CXX("PetscViewerASCIIOpen", ierr);
PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_MATRIXMARKET);
ierr = MatView(K, viewer);
CHECK_ERR_CXX("MatView", ierr);
PetscViewerPopFormat(viewer);
ierr = PetscViewerDestroy(&viewer);
CHECK_ERR_CXX("PetscViewerDestroy", ierr);
// this->getDOFManager().assembleElementalMatricesToMatrix(
// "K", "disp", k_all_el, _segment_2);
is_stiffness_assembled = true;
}
void copy(Array<Real> & y, Vec x) {
std::cout << "copy <-" << std::endl;
const PetscScalar * x_local;
ierr = VecGetArrayRead(x, &x_local);
for (auto && data : zip(y, range(x_local + 0, x_local + y.size()))) {
std::get<0>(data) = std::get<1>(data);
}
ierr = VecRestoreArrayRead(x, &x_local);
// VecView(x, PETSC_VIEWER_STDOUT_WORLD);
// std::cout << y.getID() << " " << Vector<Real>(y.storage(), y.size())
// << std::endl;
}
void print(const Array<Real> & x) const {
std::cout << x.getID() << " " << Vector<Real>(x.storage(), x.size())
<< std::endl;
}
void copy(Vec x, const Array<Real> & y) {
std::cout << "copy ->" << std::endl;
PetscScalar * x_local;
ierr = VecGetArray(x, &x_local);
for (auto && data : zip(y, range(x_local + 0, x_local + y.size()))) {
std::get<1>(data) = std::get<0>(data);
}
ierr = VecRestoreArray(x, &x_local);
// std::cout << y.getID() << " " << Vector<Real>(y.storage(), y.size())
// << std::endl;
// VecView(x, PETSC_VIEWER_STDOUT_WORLD);
}
void assembleResidual() {
std::cout << "assembleResidual" << std::endl;
// this->getDOFManager().assembleToResidual("disp", forces);
setSolutionToDisplacement();
copy(rhs, forces);
// VecAXPY(rhs, -1., f_dirichlet);
print(displacement);
this->assembleResidual(_not_ghost);
// this->synchronize(SynchronizationTag::_user_1);
// this->getDOFManager().assembleToResidual("disp", internal_forces, -1.);
VecAXPY(rhs, 1., f_int);
for (auto && data : enumerate(blocked)) {
if (std::get<1>(data)) {
VecSetValueLocal(rhs, std::get<0>(data), 0., INSERT_VALUES);
}
}
VecAssemblyBegin(rhs);
VecAssemblyEnd(rhs);
VecView(rhs, PETSC_VIEWER_STDOUT_WORLD);
}
- void assembleResidual(const GhostType & ghost_type) {
+ void assembleResidual(GhostType ghost_type) {
std::cout << "assembleResidual" << std::endl;
VecZeroEntries(f_int);
auto cit = this->mesh.getConnectivity(_segment_2, ghost_type).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2, ghost_type).end(2);
auto strain_it = this->strains.begin();
auto stress_it = this->stresses.begin();
auto L_it = this->initial_lengths.begin();
for (; cit != cend; ++cit, ++strain_it, ++stress_it, ++L_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real u1 = this->displacement(n1, _x);
Real u2 = this->displacement(n2, _x);
*strain_it = (u2 - u1) / *L_it;
*stress_it = E * *strain_it;
Real f_n = A * *stress_it;
std::cout << n1 << "[" << u1 << "]"
<< " <-> " << n2 << "[" << u2 << "]"
<< " : " << f_n << std::endl;
ierr = VecSetValueLocal(f_int, n1, -f_n, ADD_VALUES);
ierr = VecSetValueLocal(f_int, n2, f_n, ADD_VALUES);
}
ierr = VecAssemblyBegin(f_int);
ierr = VecAssemblyEnd(f_int);
// this->getDOFManager().assembleElementalArrayLocalArray(
// forces_internal_el, internal_forces, _segment_2, ghost_type);
}
Real getPotentialEnergy() {
std::cout << "getPotentialEnergy" << std::endl;
copy(x, displacement);
Vec Ax;
ierr = VecDuplicate(x, &Ax);
ierr = MatMult(K, x, Ax);
PetscScalar res;
ierr = VecDot(x, Ax, &res);
return res / 2.;
}
Real getKineticEnergy() {
std::cout << "getKineticEnergy" << std::endl;
return 0;
}
// Real getExternalWorkIncrement() {
// Real res = 0;
// auto it = velocity.begin();
// auto end = velocity.end();
// auto if_it = internal_forces.begin();
// auto ef_it = forces.begin();
// auto b_it = blocked.begin();
// for (UInt node = 0; it != end; ++it, ++if_it, ++ef_it, ++b_it, ++node) {
// if (mesh.isLocalOrMasterNode(node))
// res += (*b_it ? -*if_it : *ef_it) * *it;
// }
// mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
// return res * this->getTimeStep();
// }
// void predictor() {}
// void corrector() {}
// /* ------------------------------------------------------------------------
// */ UInt getNbData(const Array<Element> & elements,
// const SynchronizationTag &) const {
// return elements.size() * sizeof(Real);
// }
// void packData(CommunicationBuffer & buffer, const Array<Element> &
// elements,
// const SynchronizationTag & tag) const {
// if (tag == SynchronizationTag::_user_1) {
// for (const auto & el : elements) {
// buffer << this->stresses(el.element);
// }
// }
// }
// void unpackData(CommunicationBuffer & buffer, const Array<Element> &
// elements,
// const SynchronizationTag & tag) {
// if (tag == SynchronizationTag::_user_1) {
// auto cit = this->mesh.getConnectivity(_segment_2, _ghost).begin(2);
// for (const auto & el : elements) {
// Real stress;
// buffer >> stress;
// Real f = A * stress;
// Vector<UInt> conn = cit[el.element];
// this->internal_forces(conn(0), _x) += -f;
// this->internal_forces(conn(1), _x) += f;
// }
// }
// }
Real getExternalWorkIncrement() {
std::cout << "getExternalWorkIncrement" << std::endl;
return 0.;
}
template <class Functor> void applyBC(Functor && func, const ID & group_id) {
auto & group = mesh.getElementGroup(group_id).getNodeGroup().getNodes();
auto blocked_dofs = make_view(blocked, 1).begin();
auto disps = make_view(displacement, 1).begin();
auto poss = make_view(mesh.getNodes(), 1).begin();
for (auto && node : group) {
auto disp = Vector<Real>(disps[node]);
auto pos = Vector<Real>(poss[node]);
auto flags = Vector<bool>(blocked_dofs[node]);
func(node, flags, disp, pos);
}
}
const Mesh & getMesh() const { return mesh; }
UInt getSpatialDimension() const { return 1; }
auto & getBlockedDOFs() { return blocked; }
void setTimeStep(Real dt) {
std::cout << "setTimeStep" << std::endl;
this->dt = dt;
}
private:
PetscErrorCode ierr{0};
MPI_Comm mpi_comm;
ISLocalToGlobalMapping petsc_local_to_global;
UInt nb_dofs;
UInt nb_elements;
bool lumped;
bool is_stiffness_assembled{false};
bool is_mass_assembled{false};
bool is_lumped_mass_assembled{false};
Mat K{nullptr}, J{nullptr}, M{nullptr};
Vec rhs{nullptr}, x{nullptr}, x_save{nullptr}, dx{nullptr}, f_int{nullptr},
f_dirichlet{nullptr};
SNES snes;
Real dt{0};
Array<Real> save_displacement;
public:
Real E, A, rho;
Mesh & mesh;
Array<Real> displacement;
Array<Real> velocity;
Array<Real> acceleration;
Array<bool> blocked;
Array<Real> forces;
Array<Real> internal_forces;
Array<Real> stresses;
Array<Real> strains;
Array<Real> initial_lengths;
};
/* -------------------------------------------------------------------------- */
class Sinusoidal : public BC::Dirichlet::DirichletFunctor {
public:
Sinusoidal(MyModel & model, Real amplitude, Real pulse_width, Real t)
: model(model), A(amplitude), k(2 * M_PI / pulse_width),
t(t), v{std::sqrt(model.E / model.rho)} {}
void operator()(UInt n, Vector<bool> & /*flags*/, Vector<Real> & disp,
const Vector<Real> & coord) const {
auto x = coord(_x);
model.velocity(n, _x) = k * v * A * sin(k * (x - v * t));
disp(_x) = A * cos(k * (x - v * t));
}
private:
MyModel & model;
Real A{1.};
Real k{2 * M_PI};
Real t{1.};
Real v{1.};
};
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
PetscInitialize(&argc, &argv, nullptr, nullptr);
UInt prank = Communicator::getStaticCommunicator().whoAmI();
UInt global_nb_nodes = 3;
UInt max_steps = 400;
Real time_step = 0.001;
Mesh mesh(1);
Real F = -9.81;
bool _explicit = EXPLICIT;
// const Real pulse_width = 0.2;
const Real A = 0.01;
if (prank == 0)
genMesh(mesh, global_nb_nodes);
mesh.distribute();
// mesh.makePeriodic(_x);
MyModel model(F, mesh, _explicit);
- // model.forces.clear();
- // model.blocked.clear();
+ // model.forces.zero();
+ // model.blocked.zero();
// model.applyBC(Sinusoidal(model, A, pulse_width, 0.), "all");
// model.applyBC(BC::Dirichlet::FlagOnly(_x), "border");
// if (!_explicit) {
// model.getNewSolver("dynamic", TimeStepSolverType::_dynamic,
// NonLinearSolverType::_newton_raphson);
// model.setIntegrationScheme("dynamic", "disp",
// IntegrationSchemeType::_trapezoidal_rule_2,
// IntegrationScheme::_displacement);
// } else {
// model.getNewSolver("dynamic", TimeStepSolverType::_dynamic_lumped,
// NonLinearSolverType::_lumped);
// model.setIntegrationScheme("dynamic", "disp",
// IntegrationSchemeType::_central_difference,
// IntegrationScheme::_acceleration);
// }
model.setTimeStep(time_step);
if (prank == 0) {
std::cout << std::scientific;
std::cout << std::setw(14) << "time"
<< "," << std::setw(14) << "wext"
<< "," << std::setw(14) << "epot"
<< "," << std::setw(14) << "ekin"
<< "," << std::setw(14) << "total"
<< "," << std::setw(14) << "max_disp"
<< "," << std::setw(14) << "min_disp" << std::endl;
}
Real wext = 0.;
// model.getDOFManager().clearResidual();
// model.assembleResidual();
Real epot = 0; // model.getPotentialEnergy();
Real ekin = 0; // model.getKineticEnergy();
Real einit = ekin + epot;
Real etot = ekin + epot - wext - einit;
Real max_disp = 0., min_disp = 0.;
for (auto && disp : model.displacement) {
max_disp = std::max(max_disp, disp);
min_disp = std::min(min_disp, disp);
}
if (prank == 0) {
std::cout << std::setw(14) << 0. << "," << std::setw(14) << wext << ","
<< std::setw(14) << epot << "," << std::setw(14) << ekin << ","
<< std::setw(14) << etot << "," << std::setw(14) << max_disp
<< "," << std::setw(14) << min_disp << std::endl;
}
// #if EXPLICIT == false
// NonLinearSolver & solver =
// model.getDOFManager().getNonLinearSolver("dynamic");
// solver.set("max_iterations", 20);
// #endif
auto * dumper = new DumperParaview("dynamic", "./paraview");
mesh.registerExternalDumper(*dumper, "dynamic", true);
mesh.addDumpMesh(mesh);
mesh.addDumpFieldExternalToDumper("dynamic", "displacement",
model.displacement);
mesh.addDumpFieldExternalToDumper("dynamic", "velocity", model.velocity);
mesh.addDumpFieldExternalToDumper("dynamic", "forces", model.forces);
mesh.addDumpFieldExternalToDumper("dynamic", "acceleration",
model.acceleration);
mesh.dump();
max_steps = 1;
for (UInt i = 1; i < max_steps + 1; ++i) {
// model.applyBC(Sinusoidal(model, A, pulse_width, time_step * (i - 1)),
// "border");
model.solveStep();
mesh.dump();
epot = model.getPotentialEnergy();
ekin = model.getKineticEnergy();
wext += model.getExternalWorkIncrement();
etot = ekin + epot - wext - einit;
Real max_disp = 0., min_disp = 0.;
for (auto && disp : model.displacement) {
max_disp = std::max(max_disp, disp);
min_disp = std::min(min_disp, disp);
}
if (prank == 0) {
std::cout << std::setw(14) << time_step * i << "," << std::setw(14)
<< wext << "," << std::setw(14) << epot << "," << std::setw(14)
<< ekin << "," << std::setw(14) << etot << "," << std::setw(14)
<< max_disp << "," << std::setw(14) << min_disp << std::endl;
}
}
// output.close();
// finalize();
// PetscFinalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void genMesh(Mesh & mesh, UInt nb_nodes) {
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
Array<UInt> & conn = mesh_accessor.getConnectivity(_segment_2);
nodes.resize(nb_nodes);
// auto & all = mesh.createNodeGroup("all_nodes");
for (UInt n = 0; n < nb_nodes; ++n) {
nodes(n, _x) = n * (1. / (nb_nodes - 1));
// all.add(n);
}
// mesh.createElementGroupFromNodeGroup("all", "all_nodes");
conn.resize(nb_nodes - 1);
for (UInt n = 0; n < nb_nodes - 1; ++n) {
conn(n, 0) = n;
conn(n, 1) = n + 1;
}
// Array<UInt> & conn_points = mesh_accessor.getConnectivity(_point_1);
// conn_points.resize(2);
// conn_points(0, 0) = 0;
// conn_points(1, 0) = nb_nodes - 1;
// auto & border = mesh.createElementGroup("border", 0);
// border.add({_point_1, 0, _not_ghost}, true);
// border.add({_point_1, 1, _not_ghost}, true);
mesh_accessor.makeReady();
}
diff --git a/test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh b/test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh
index 990063fce..c9dcd224d 100644
--- a/test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh
+++ b/test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh
@@ -1,448 +1,448 @@
/**
* @file test_model_solver_my_model.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 13 2016
* @date last modification: Tue Feb 20 2018
*
* @brief Test default dof manager
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "boundary_condition.hh"
#include "communicator.hh"
#include "data_accessor.hh"
#include "dof_manager_default.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "model_solver.hh"
#include "periodic_node_synchronizer.hh"
#include "solver_vector_default.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
-#ifndef __AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH__
-#define __AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH__
+#ifndef AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH_
+#define AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH_
/**
* =\o-----o-----o-> F
* | |
* |---- L ----|
*/
class MyModel : public ModelSolver,
public BoundaryCondition<MyModel>,
public DataAccessor<Element> {
public:
MyModel(Real F, Mesh & mesh, bool lumped,
const ID & dof_manager_type = "default")
: ModelSolver(mesh, ModelType::_model, "model_solver", 0),
nb_dofs(mesh.getNbNodes()), nb_elements(mesh.getNbElement(_segment_2)),
lumped(lumped), E(1.), A(1.), rho(1.), mesh(mesh),
displacement(nb_dofs, 1, "disp"), velocity(nb_dofs, 1, "velo"),
acceleration(nb_dofs, 1, "accel"), blocked(nb_dofs, 1, "blocked"),
forces(nb_dofs, 1, "force_ext"),
internal_forces(nb_dofs, 1, "force_int"),
stresses(nb_elements, 1, "stress"), strains(nb_elements, 1, "strain"),
initial_lengths(nb_elements, 1, "L0") {
this->initBC(*this, displacement, forces);
this->initDOFManager(dof_manager_type);
this->getDOFManager().registerDOFs("disp", displacement, _dst_nodal);
this->getDOFManager().registerDOFsDerivative("disp", 1, velocity);
this->getDOFManager().registerDOFsDerivative("disp", 2, acceleration);
this->getDOFManager().registerBlockedDOFs("disp", blocked);
displacement.set(0.);
velocity.set(0.);
acceleration.set(0.);
forces.set(0.);
blocked.set(false);
UInt global_nb_nodes = mesh.getNbGlobalNodes();
for (auto && n : arange(nb_dofs)) {
auto global_id = mesh.getNodeGlobalId(n);
if (global_id == (global_nb_nodes - 1))
forces(n, _x) = F;
if (global_id == 0)
blocked(n, _x) = true;
}
auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2).end(2);
auto L_it = this->initial_lengths.begin();
for (; cit != cend; ++cit, ++L_it) {
const Vector<UInt> & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
*L_it = std::abs(p2 - p1);
}
this->registerDataAccessor(*this);
this->registerSynchronizer(
const_cast<ElementSynchronizer &>(this->mesh.getElementSynchronizer()),
SynchronizationTag::_user_1);
}
void assembleLumpedMass() {
auto & M = this->getDOFManager().getLumpedMatrix("M");
- M.clear();
+ M.zero();
this->assembleLumpedMass(_not_ghost);
if (this->mesh.getNbElement(_segment_2, _ghost) > 0)
this->assembleLumpedMass(_ghost);
is_lumped_mass_assembled = true;
}
- void assembleLumpedMass(const GhostType & ghost_type) {
+ void assembleLumpedMass(GhostType ghost_type) {
Array<Real> M(nb_dofs, 1, 0.);
Array<Real> m_all_el(this->mesh.getNbElement(_segment_2, ghost_type), 2);
for (auto && data :
zip(make_view(this->mesh.getConnectivity(_segment_2), 2),
make_view(m_all_el, 2))) {
const auto & conn = std::get<0>(data);
auto & m_el = std::get<1>(data);
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
Real M_n = rho * A * L / 2;
m_el(0) = m_el(1) = M_n;
}
this->getDOFManager().assembleElementalArrayLocalArray(
m_all_el, M, _segment_2, ghost_type);
this->getDOFManager().assembleToLumpedMatrix("disp", M, "M");
}
void assembleMass() {
SparseMatrix & M = this->getDOFManager().getMatrix("M");
- M.clear();
+ M.zero();
Array<Real> m_all_el(this->nb_elements, 4);
Matrix<Real> m(2, 2);
m(0, 0) = m(1, 1) = 2;
m(0, 1) = m(1, 0) = 1;
// under integrated
// m(0, 0) = m(1, 1) = 3./2.;
// m(0, 1) = m(1, 0) = 3./2.;
// lumping the mass matrix
// m(0, 0) += m(0, 1);
// m(1, 1) += m(1, 0);
// m(0, 1) = m(1, 0) = 0;
for (auto && data :
zip(make_view(this->mesh.getConnectivity(_segment_2), 2),
make_view(m_all_el, 2, 2))) {
const auto & conn = std::get<0>(data);
auto & m_el = std::get<1>(data);
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
m_el = m;
m_el *= rho * A * L / 6.;
}
this->getDOFManager().assembleElementalMatricesToMatrix(
"M", "disp", m_all_el, _segment_2);
is_mass_assembled = true;
}
MatrixType getMatrixType(const ID &) override { return _symmetric; }
void assembleMatrix(const ID & matrix_id) override {
if (matrix_id == "K") {
if (not is_stiffness_assembled)
this->assembleStiffness();
} else if (matrix_id == "M") {
if (not is_mass_assembled)
this->assembleMass();
} else if (matrix_id == "C") {
// pass, no damping matrix
} else {
AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
<< matrix_id);
}
}
void assembleLumpedMatrix(const ID & matrix_id) override {
if (matrix_id == "M") {
if (not is_lumped_mass_assembled)
this->assembleLumpedMass();
} else {
AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
<< matrix_id);
}
}
void assembleStiffness() {
SparseMatrix & K = this->getDOFManager().getMatrix("K");
- K.clear();
+ K.zero();
Matrix<Real> k(2, 2);
k(0, 0) = k(1, 1) = 1;
k(0, 1) = k(1, 0) = -1;
Array<Real> k_all_el(this->nb_elements, 4);
auto k_it = k_all_el.begin(2, 2);
auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2).end(2);
for (; cit != cend; ++cit, ++k_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
auto & k_el = *k_it;
k_el = k;
k_el *= E * A / L;
}
this->getDOFManager().assembleElementalMatricesToMatrix(
"K", "disp", k_all_el, _segment_2);
is_stiffness_assembled = true;
}
void assembleResidual() override {
this->getDOFManager().assembleToResidual("disp", forces);
- internal_forces.clear();
+ internal_forces.zero();
this->assembleResidualInternal(_not_ghost);
this->synchronize(SynchronizationTag::_user_1);
this->getDOFManager().assembleToResidual("disp", internal_forces, -1.);
}
- void assembleResidualInternal(const GhostType & ghost_type) {
+ void assembleResidualInternal(GhostType ghost_type) {
Array<Real> forces_internal_el(
this->mesh.getNbElement(_segment_2, ghost_type), 2);
auto cit = this->mesh.getConnectivity(_segment_2, ghost_type).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2, ghost_type).end(2);
auto f_it = forces_internal_el.begin(2);
auto strain_it = this->strains.begin();
auto stress_it = this->stresses.begin();
auto L_it = this->initial_lengths.begin();
for (; cit != cend; ++cit, ++f_it, ++strain_it, ++stress_it, ++L_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real u1 = this->displacement(n1, _x);
Real u2 = this->displacement(n2, _x);
*strain_it = (u2 - u1) / *L_it;
*stress_it = E * *strain_it;
Real f_n = A * *stress_it;
Vector<Real> & f = *f_it;
f(0) = -f_n;
f(1) = f_n;
}
this->getDOFManager().assembleElementalArrayLocalArray(
forces_internal_el, internal_forces, _segment_2, ghost_type);
}
Real getPotentialEnergy() {
Real res = 0;
if (not lumped) {
res = this->mulVectMatVect(this->displacement, "K", this->displacement);
} else {
auto strain_it = this->strains.begin();
auto stress_it = this->stresses.begin();
auto strain_end = this->strains.end();
auto L_it = this->initial_lengths.begin();
for (; strain_it != strain_end; ++strain_it, ++stress_it, ++L_it) {
res += *strain_it * *stress_it * A * *L_it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
}
return res / 2.;
}
Real getKineticEnergy() {
Real res = 0;
if (not lumped) {
res = this->mulVectMatVect(this->velocity, "M", this->velocity);
} else {
Array<Real> & m = dynamic_cast<SolverVectorDefault &>(
this->getDOFManager().getLumpedMatrix("M"));
auto it = velocity.begin();
auto end = velocity.end();
auto m_it = m.begin();
for (UInt node = 0; it != end; ++it, ++m_it, ++node) {
if (mesh.isLocalOrMasterNode(node))
res += *m_it * *it * *it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
}
return res / 2.;
}
Real getExternalWorkIncrement() {
Real res = 0;
auto it = velocity.begin();
auto end = velocity.end();
auto if_it = internal_forces.begin();
auto ef_it = forces.begin();
auto b_it = blocked.begin();
for (UInt node = 0; it != end; ++it, ++if_it, ++ef_it, ++b_it, ++node) {
if (mesh.isLocalOrMasterNode(node))
res += (*b_it ? -*if_it : *ef_it) * *it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
return res * this->getTimeStep();
}
Real mulVectMatVect(const Array<Real> & x, const ID & A_id,
const Array<Real> & y) {
Array<Real> Ay(nb_dofs);
this->getDOFManager().assembleMatMulVectToArray("disp", A_id, y, Ay);
Real res = 0.;
for (auto && data : zip(arange(nb_dofs), make_view(Ay), make_view(x))) {
res += std::get<2>(data) * std::get<1>(data) *
mesh.isLocalOrMasterNode(std::get<0>(data));
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
return res;
}
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag &) const override {
return elements.size() * sizeof(Real);
}
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_user_1) {
for (const auto & el : elements) {
buffer << this->stresses(el.element);
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override {
if (tag == SynchronizationTag::_user_1) {
auto cit = this->mesh.getConnectivity(_segment_2, _ghost).begin(2);
for (const auto & el : elements) {
Real stress;
buffer >> stress;
Real f = A * stress;
Vector<UInt> conn = cit[el.element];
this->internal_forces(conn(0), _x) += -f;
this->internal_forces(conn(1), _x) += f;
}
}
}
const Mesh & getMesh() const { return mesh; }
UInt getSpatialDimension() const { return 1; }
auto & getBlockedDOFs() { return blocked; }
private:
UInt nb_dofs;
UInt nb_elements;
bool lumped;
bool is_stiffness_assembled{false};
bool is_mass_assembled{false};
bool is_lumped_mass_assembled{false};
public:
Real E, A, rho;
Mesh & mesh;
Array<Real> displacement;
Array<Real> velocity;
Array<Real> acceleration;
Array<bool> blocked;
Array<Real> forces;
Array<Real> internal_forces;
Array<Real> stresses;
Array<Real> strains;
Array<Real> initial_lengths;
};
-#endif /* __AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH__ */
+#endif /* AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH_ */
} // namespace akantu
diff --git a/test/test_model/test_common/test_non_local_toolbox/my_model.hh b/test/test_model/test_common/test_non_local_toolbox/my_model.hh
index ab8b82fe2..46908a634 100644
--- a/test/test_model/test_common/test_non_local_toolbox/my_model.hh
+++ b/test/test_model/test_common/test_non_local_toolbox/my_model.hh
@@ -1,123 +1,123 @@
/**
* @file my_model.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 11 2017
* @date last modification: Sat Feb 03 2018
*
* @brief A Documented file.
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "model.hh"
#include "non_local_manager.hh"
#include "non_local_manager_callback.hh"
#include "non_local_neighborhood_base.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
class MyModel : public Model, public NonLocalManagerCallback {
using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
public:
MyModel(Mesh & mesh, UInt spatial_dimension)
: Model(mesh, ModelType::_model, spatial_dimension),
manager(*this, *this) {
registerFEEngineObject<MyFEEngineType>("FEEngine", mesh, spatial_dimension);
manager.registerNeighborhood("test_region", "test_region");
getFEEngine().initShapeFunctions();
manager.initialize();
}
void initModel() override {}
MatrixType getMatrixType(const ID &) override { return _mt_not_defined; }
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & /*method*/) override {
return std::make_tuple("test", TimeStepSolverType::_static);
}
void assembleMatrix(const ID &) override {}
void assembleLumpedMatrix(const ID &) override {}
void assembleResidual() override {}
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override {}
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) override {}
void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) override {}
void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) override {}
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override {}
void insertIntegrationPointsInNeighborhoods(
- const GhostType & ghost_type) override {
+ GhostType ghost_type) override {
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_tmp_nl", this->id, this->memory_id);
quadrature_points_coordinates.initialize(this->getFEEngine(),
_nb_component = spatial_dimension,
_ghost_type = ghost_type);
IntegrationPoint q;
q.ghost_type = ghost_type;
q.global_num = 0;
auto & neighborhood = manager.getNeighborhood("test_region");
for (auto & type : quadrature_points_coordinates.elementTypes(
spatial_dimension, ghost_type)) {
q.type = type;
auto & quads = quadrature_points_coordinates(type, ghost_type);
this->getFEEngine().computeIntegrationPointsCoordinates(quads, type,
ghost_type);
auto quad_it = quads.begin(quads.getNbComponent());
auto quad_end = quads.end(quads.getNbComponent());
q.num_point = 0;
for (; quad_it != quad_end; ++quad_it) {
neighborhood.insertIntegrationPoint(q, *quad_it);
++q.num_point;
++q.global_num;
}
}
}
- void computeNonLocalStresses(const GhostType &) override {}
+ void computeNonLocalStresses(GhostType) override {}
- void updateLocalInternal(ElementTypeMapReal &, const GhostType &,
- const ElementKind &) override {}
+ void updateLocalInternal(ElementTypeMapReal &, GhostType,
+ ElementKind) override {}
- void updateNonLocalInternal(ElementTypeMapReal &, const GhostType &,
- const ElementKind &) override {}
+ void updateNonLocalInternal(ElementTypeMapReal &, GhostType,
+ ElementKind) override {}
const auto & getNonLocalManager() const { return manager; }
private:
NonLocalManager manager;
};
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_build_neighborhood_parallel.cc b/test/test_model/test_common/test_non_local_toolbox/test_build_neighborhood_parallel.cc
index 2a0f7da51..e401abce2 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_build_neighborhood_parallel.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_build_neighborhood_parallel.cc
@@ -1,188 +1,188 @@
/**
* @file test_build_neighborhood_parallel.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Tue Feb 20 2018
*
* @brief test in parallel for the class NonLocalNeighborhood
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper_paraview.hh"
#include "non_local_neighborhood_base.hh"
#include "solid_mechanics_model.hh"
#include "test_material.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_parallel_test.dat", argc, argv);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
// some configuration variables
const UInt spatial_dimension = 2;
// mesh creation and read
Mesh mesh(spatial_dimension);
if (prank == 0) {
mesh.read("parallel_test.msh");
}
mesh.distribute();
/// model creation
SolidMechanicsModel model(mesh);
/// dump the ghost elements before the non-local part is intialized
DumperParaview dumper_ghost("ghost_elements");
dumper_ghost.registerMesh(mesh, spatial_dimension, _ghost);
if (psize > 1) {
dumper_ghost.dump();
}
/// creation of material selector
auto && mat_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
model.setMaterialSelector(mat_selector);
/// dump material index in paraview
model.addDumpField("partitions");
model.dump();
/// model initialization changed to use our material
model.initFull();
/// dump the ghost elements after ghosts for non-local have been added
if (psize > 1)
dumper_ghost.dump();
model.addDumpField("grad_u");
model.addDumpField("grad_u non local");
model.addDumpField("material_index");
/// apply constant strain field everywhere in the plate
Matrix<Real> applied_strain(spatial_dimension, spatial_dimension);
- applied_strain.clear();
+ applied_strain.zero();
for (UInt i = 0; i < spatial_dimension; ++i)
applied_strain(i, i) = 2.;
ElementType element_type = _triangle_3;
GhostType ghost_type = _not_ghost;
/// apply constant grad_u field in all elements
for (UInt m = 0; m < model.getNbMaterials(); ++m) {
auto & mat = model.getMaterial(m);
auto & grad_u = const_cast<Array<Real> &>(
mat.getInternal<Real>("grad_u")(element_type, ghost_type));
auto grad_u_it = grad_u.begin(spatial_dimension, spatial_dimension);
auto grad_u_end = grad_u.end(spatial_dimension, spatial_dimension);
for (; grad_u_it != grad_u_end; ++grad_u_it)
(*grad_u_it) = -1. * applied_strain;
}
/// double the strain in the center: find the closed gauss point to the center
/// compute the quadrature points
ElementTypeMapReal quad_coords("quad_coords");
quad_coords.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_with_nb_element = true);
model.getFEEngine().computeIntegrationPointsCoordinates(quad_coords);
Vector<Real> center(spatial_dimension, 0.);
Real min_distance = 2;
IntegrationPoint q_min;
for (auto type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_elements = mesh.getNbElement(type, _not_ghost);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(type);
Array<Real> & coords = quad_coords(type, _not_ghost);
auto coord_it = coords.begin(spatial_dimension);
for (UInt e = 0; e < nb_elements; ++e) {
for (UInt q = 0; q < nb_quads; ++q, ++coord_it) {
Real dist = center.distance(*coord_it);
if (dist < min_distance) {
min_distance = dist;
q_min.element = e;
q_min.num_point = q;
q_min.global_num = nb_elements * nb_quads + q;
q_min.type = type;
}
}
}
}
Real global_min = min_distance;
comm.allReduce(global_min, SynchronizerOperation::_min);
if (Math::are_float_equal(global_min, min_distance)) {
UInt mat_index = model.getMaterialByElement(q_min.type, _not_ghost)
.begin()[q_min.element];
Material & mat = model.getMaterial(mat_index);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(q_min.type);
UInt local_el_index =
model.getMaterialLocalNumbering(q_min.type, _not_ghost)
.begin()[q_min.element];
UInt local_num = (local_el_index * nb_quads) + q_min.num_point;
Array<Real> & grad_u = const_cast<Array<Real> &>(
mat.getInternal<Real>("grad_u")(q_min.type, _not_ghost));
Array<Real>::iterator<Matrix<Real>> grad_u_it =
grad_u.begin(spatial_dimension, spatial_dimension);
grad_u_it += local_num;
Matrix<Real> & g_u = *grad_u_it;
g_u += applied_strain;
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
/// damage the element with higher grad_u completely, so that it is
/// not taken into account for the averaging
if (Math::are_float_equal(global_min, min_distance)) {
UInt mat_index = model.getMaterialByElement(q_min.type, _not_ghost)
.begin()[q_min.element];
Material & mat = model.getMaterial(mat_index);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(q_min.type);
UInt local_el_index =
model.getMaterialLocalNumbering(q_min.type, _not_ghost)
.begin()[q_min.element];
UInt local_num = (local_el_index * nb_quads) + q_min.num_point;
Array<Real> & damage = const_cast<Array<Real> &>(
mat.getInternal<Real>("damage")(q_min.type, _not_ghost));
Real * dam_ptr = damage.storage();
dam_ptr += local_num;
*dam_ptr = 0.9;
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_material.hh b/test/test_model/test_common/test_non_local_toolbox/test_material.hh
index 30488d09f..1d5e79fc1 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_material.hh
+++ b/test/test_model/test_common/test_non_local_toolbox/test_material.hh
@@ -1,71 +1,71 @@
/**
* @file test_material.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Sep 11 2017
*
* @brief test material for the non-local neighborhood base test
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage.hh"
#include "material_damage_non_local.hh"
-#ifndef __TEST_MATERIAL_HH__
-#define __TEST_MATERIAL_HH__
+#ifndef TEST_MATERIAL_HH_
+#define TEST_MATERIAL_HH_
using namespace akantu;
template <UInt dim>
class TestMaterial
: public MaterialDamageNonLocal<dim, MaterialDamage<dim, MaterialElastic>> {
/* ------------------------------------------------------------------------ */
/* Constructor/Destructor */
/* ------------------------------------------------------------------------ */
public:
using Parent =
MaterialDamageNonLocal<dim, MaterialDamage<dim, MaterialElastic>>;
TestMaterial(SolidMechanicsModel & model, const ID & id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void registerNonLocalVariables() override final;
void computeNonLocalStress(ElementType, GhostType) override final{};
void computeNonLocalStresses(GhostType) override final{};
protected:
ID getNeighborhoodName() override { return "test_region"; }
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> grad_u_nl;
};
-#endif /* __TEST_MATERIAL_HH__ */
+#endif /* TEST_MATERIAL_HH_ */
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_material_damage.hh b/test/test_model/test_common/test_non_local_toolbox/test_material_damage.hh
index 9f1fcd7ce..df0f12c6b 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_material_damage.hh
+++ b/test/test_model/test_common/test_non_local_toolbox/test_material_damage.hh
@@ -1,73 +1,73 @@
/**
* @file test_material_damage.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Sep 19 2017
*
* @brief test material damage for the non-local remove damage test
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage.hh"
#include "material_damage_non_local.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __TEST_MATERIAL_DAMAGE_HH__
-#define __TEST_MATERIAL_DAMAGE_HH__
+#ifndef TEST_MATERIAL_DAMAGE_HH_
+#define TEST_MATERIAL_DAMAGE_HH_
using namespace akantu;
template <UInt dim>
class TestMaterialDamage
: public MaterialDamageNonLocal<dim, MaterialDamage<dim, MaterialElastic>> {
using Parent =
MaterialDamageNonLocal<dim, MaterialDamage<dim, MaterialElastic>>;
/* ------------------------------------------------------------------------ */
/* Constructor/Destructor */
/* ------------------------------------------------------------------------ */
public:
TestMaterialDamage(SolidMechanicsModel & model, const ID & id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void registerNonLocalVariables() override final;
void computeNonLocalStress(ElementType, GhostType) override final{};
void insertQuadsInNeighborhoods(GhostType ghost_type);
protected:
// ID getNeighborhoodName() override { return "test_region"; }
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> grad_u_nl;
};
-#endif /* __TEST_MATERIAL_DAMAGE_HH__ */
+#endif /* TEST_MATERIAL_DAMAGE_HH_ */
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_non_local_averaging.cc b/test/test_model/test_common/test_non_local_toolbox/test_non_local_averaging.cc
index a54755496..17099789a 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_non_local_averaging.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_non_local_averaging.cc
@@ -1,110 +1,110 @@
/**
* @file test_non_local_averaging.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Tue Dec 05 2017
*
* @brief test for non-local averaging of strain
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_paraview.hh"
#include "non_local_manager.hh"
#include "non_local_neighborhood.hh"
#include "solid_mechanics_model.hh"
#include "test_material.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_avg.dat", argc, argv);
// some configuration variables
const UInt spatial_dimension = 2;
ElementType element_type = _quadrangle_4;
GhostType ghost_type = _not_ghost;
// mesh creation and read
Mesh mesh(spatial_dimension);
mesh.read("plate.msh");
/// model creation
SolidMechanicsModel model(mesh);
/// creation of material selector
auto && mat_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
model.setMaterialSelector(mat_selector);
/// model initialization changed to use our material
model.initFull();
/// dump material index in paraview
model.addDumpField("material_index");
model.addDumpField("grad_u");
model.addDumpField("grad_u non local");
model.dump();
/// apply constant strain field everywhere in the plate
Matrix<Real> applied_strain(spatial_dimension, spatial_dimension);
- applied_strain.clear();
+ applied_strain.zero();
for (UInt i = 0; i < spatial_dimension; ++i)
applied_strain(i, i) = 2.;
/// apply constant grad_u field in all elements
for (auto & mat : model.getMaterials()) {
auto & grad_us =
mat.getInternal<Real>("eigen_grad_u")(element_type, ghost_type);
for (auto & grad_u :
make_view(grad_us, spatial_dimension, spatial_dimension)) {
grad_u = -1. * applied_strain;
}
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
/// verify the result: non-local averaging over constant field must
/// yield same constant field
Real test_result = 0.;
Matrix<Real> difference(spatial_dimension, spatial_dimension, 0.);
for (auto & mat : model.getMaterials()) {
auto & grad_us_nl =
mat.getInternal<Real>("grad_u non local")(element_type, ghost_type);
for (auto & grad_u_nl :
make_view(grad_us_nl, spatial_dimension, spatial_dimension)) {
difference = grad_u_nl - applied_strain;
test_result += difference.norm<L_2>();
}
}
if (test_result > 10.e-13) {
AKANTU_EXCEPTION("the total norm is: " << test_result);
}
return 0;
}
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_remove_damage_weight_function.cc b/test/test_model/test_common/test_non_local_toolbox/test_remove_damage_weight_function.cc
index 736b833a0..fff5be6a4 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_remove_damage_weight_function.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_remove_damage_weight_function.cc
@@ -1,190 +1,190 @@
/**
* @file test_remove_damage_weight_function.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 07 2015
* @date last modification: Tue Dec 05 2017
*
* @brief Test the damage weight funcion for non local computations
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_paraview.hh"
#include "non_local_manager.hh"
#include "non_local_neighborhood.hh"
#include "solid_mechanics_model.hh"
#include "test_material.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_remove_damage.dat", argc, argv);
// some configuration variables
const UInt spatial_dimension = 2;
ElementType element_type = _quadrangle_4;
GhostType ghost_type = _not_ghost;
// mesh creation and read
Mesh mesh(spatial_dimension);
mesh.read("plate.msh");
/// model creation
SolidMechanicsModel model(mesh);
/// creation of material selector
auto && mat_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
model.setMaterialSelector(mat_selector);
/// model initialization changed to use our material
model.initFull();
/// dump material index in paraview
model.addDumpField("material_index");
model.addDumpField("grad_u");
model.addDumpField("grad_u non local");
model.addDumpField("damage");
model.dump();
/// apply constant strain field in all elements except element 3 and 15
Matrix<Real> applied_strain(spatial_dimension, spatial_dimension);
- applied_strain.clear();
+ applied_strain.zero();
for (UInt i = 0; i < spatial_dimension; ++i)
applied_strain(i, i) = 2.;
/// apply different strain in element 3 and 15
Matrix<Real> modified_strain(spatial_dimension, spatial_dimension);
- modified_strain.clear();
+ modified_strain.zero();
for (UInt i = 0; i < spatial_dimension; ++i)
modified_strain(i, i) = 1.;
/// apply constant grad_u field in all elements
for (UInt m = 0; m < model.getNbMaterials(); ++m) {
Material & mat = model.getMaterial(m);
Array<Real> & grad_u = const_cast<Array<Real> &>(
mat.getInternal<Real>("eigen_grad_u")(element_type, ghost_type));
auto grad_u_it = grad_u.begin(spatial_dimension, spatial_dimension);
auto grad_u_end = grad_u.end(spatial_dimension, spatial_dimension);
UInt element_counter = 0;
for (; grad_u_it != grad_u_end; ++grad_u_it, ++element_counter)
if (element_counter == 12 || element_counter == 13 ||
element_counter == 14 || element_counter == 15)
(*grad_u_it) = -1. * modified_strain;
else
(*grad_u_it) = -1. * applied_strain;
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
/// save the weights in a file
auto & neighborhood_1 = model.getNonLocalManager().getNeighborhood("mat_1");
auto & neighborhood_2 = model.getNonLocalManager().getNeighborhood("mat_2");
neighborhood_1.saveWeights("before_0");
neighborhood_2.saveWeights("before_1");
for (UInt n = 0; n < 2; ++n) {
/// print results to screen for validation
std::stringstream sstr;
sstr << "before_" << n << ".0";
std::ifstream weights;
weights.open(sstr.str());
std::string current_line;
while (getline(weights, current_line))
std::cout << current_line << std::endl;
weights.close();
}
/// apply damage to not have the elements with lower strain impact the
/// averaging
for (UInt m = 0; m < model.getNbMaterials(); ++m) {
auto & mat =
dynamic_cast<MaterialDamage<spatial_dimension> &>(model.getMaterial(m));
auto & damage = const_cast<Array<Real> &>(
mat.getInternal<Real>("damage")(element_type, ghost_type));
auto dam_it = damage.begin();
auto dam_end = damage.end();
UInt element_counter = 0;
for (; dam_it != dam_end; ++dam_it, ++element_counter)
if (element_counter == 12 || element_counter == 13 ||
element_counter == 14 || element_counter == 15)
*dam_it = 0.9;
}
/// compute the non-local strains
model.assembleInternalForces();
neighborhood_1.saveWeights("after_0");
neighborhood_2.saveWeights("after_1");
for (UInt n = 0; n < 2; ++n) {
/// print results to screen for validation
std::stringstream sstr;
sstr << "after_" << n << ".0";
std::ifstream weights;
weights.open(sstr.str());
std::string current_line;
while (getline(weights, current_line))
std::cout << current_line << std::endl;
weights.close();
}
model.dump();
/// verify the result: non-local averaging over constant field must
/// yield same constant field
Real test_result = 0.;
Matrix<Real> difference(spatial_dimension, spatial_dimension, 0.);
Matrix<Real> difference_in_damaged_elements(spatial_dimension,
spatial_dimension, 0.);
for (UInt m = 0; m < model.getNbMaterials(); ++m) {
- difference_in_damaged_elements.clear();
+ difference_in_damaged_elements.zero();
auto & mat = model.getMaterial(m);
auto & grad_u_nl = const_cast<Array<Real> &>(
mat.getInternal<Real>("grad_u non local")(element_type, ghost_type));
auto grad_u_nl_it = grad_u_nl.begin(spatial_dimension, spatial_dimension);
auto grad_u_nl_end = grad_u_nl.end(spatial_dimension, spatial_dimension);
UInt element_counter = 0;
for (; grad_u_nl_it != grad_u_nl_end; ++grad_u_nl_it, ++element_counter) {
if (element_counter == 12 || element_counter == 13 ||
element_counter == 14 || element_counter == 15)
difference_in_damaged_elements += (*grad_u_nl_it);
else
difference = (*grad_u_nl_it) - applied_strain;
test_result += difference.norm<L_2>();
}
difference_in_damaged_elements *= (1 / 4.);
difference_in_damaged_elements -= (1.41142 * modified_strain);
test_result += difference_in_damaged_elements.norm<L_2>();
}
if (test_result > 10.e-5) {
std::cout << "the total norm is: " << test_result << std::endl;
return EXIT_FAILURE;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_fatigue.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_fatigue.cc
index 3d442838a..0b54fc97a 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_fatigue.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_fatigue.cc
@@ -1,242 +1,242 @@
/**
* @file test_cohesive_extrinsic_fatigue.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 20 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Test for the linear fatigue cohesive law
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_fatigue.hh"
#include "solid_mechanics_model_cohesive.hh"
#include <limits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
// the following class contains an implementation of the 1D linear
// fatigue cohesive law
class MaterialFatigue {
public:
MaterialFatigue(Real delta_f, Real sigma_c, Real delta_c)
: delta_f(delta_f), sigma_c(sigma_c), delta_c(delta_c), delta_prec(0),
traction(sigma_c), delta_max(0),
stiff_plus(std::numeric_limits<Real>::max()),
tolerance(Math::getTolerance()){};
Real computeTraction(Real delta) {
if (delta - delta_c > -tolerance)
traction = 0;
else if (delta_max < tolerance && delta < tolerance)
traction = sigma_c;
else {
Real delta_dot = delta - delta_prec;
if (delta_dot > -tolerance) {
stiff_plus *= 1 - delta_dot / delta_f;
traction += stiff_plus * delta_dot;
Real max_traction = sigma_c * (1 - delta / delta_c);
if (traction - max_traction > -tolerance || delta_max < tolerance) {
traction = max_traction;
stiff_plus = traction / delta;
}
} else {
Real stiff_minus = traction / delta_prec;
stiff_plus += (stiff_plus - stiff_minus) * delta_dot / delta_f;
traction += stiff_minus * delta_dot;
}
}
delta_prec = delta;
delta_max = std::max(delta, delta_max);
return traction;
}
private:
const Real delta_f;
const Real sigma_c;
const Real delta_c;
Real delta_prec;
Real traction;
Real delta_max;
Real stiff_plus;
const Real tolerance;
};
void imposeOpening(SolidMechanicsModelCohesive &, Real);
void arange(Array<Real> &, Real, Real, Real);
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material_fatigue.dat", argc, argv);
Math::setTolerance(1e-13);
const UInt spatial_dimension = 2;
const ElementType type = _quadrangle_4;
Mesh mesh(spatial_dimension);
mesh.read("fatigue.msh");
// init stuff
const ElementType type_facet = Mesh::getFacetType(type);
const ElementType type_cohesive =
FEEngine::getCohesiveElementType(type_facet);
SolidMechanicsModelCohesive model(mesh);
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
MaterialCohesiveLinearFatigue<2> & numerical_material =
dynamic_cast<MaterialCohesiveLinearFatigue<2> &>(
model.getMaterial("cohesive"));
Real delta_f = numerical_material.getParam("delta_f");
Real delta_c = numerical_material.getParam("delta_c");
Real sigma_c = 1;
const Array<Real> & traction_array =
numerical_material.getTraction(type_cohesive);
MaterialFatigue theoretical_material(delta_f, sigma_c, delta_c);
// model.setBaseName("fatigue");
// model.addDumpFieldVector("displacement");
// model.addDumpField("stress");
// model.dump();
// stretch material
Real strain = 1;
Array<Real> & displacement = model.getDisplacement();
const Array<Real> & position = mesh.getNodes();
for (UInt n = 0; n < mesh.getNbNodes(); ++n)
displacement(n, 0) = position(n, 0) * strain;
model.assembleInternalForces();
// model.dump();
// insert cohesive elements
model.checkCohesiveStress();
// create the displacement sequence
Real increment = 0.01;
Array<Real> openings;
arange(openings, 0, 0.5, increment);
arange(openings, 0.5, 0.1, increment);
arange(openings, 0.1, 0.7, increment);
arange(openings, 0.7, 0.3, increment);
arange(openings, 0.3, 0.6, increment);
arange(openings, 0.6, 0.3, increment);
arange(openings, 0.3, 0.7, increment);
arange(openings, 0.7, 1.3, increment);
const Array<UInt> & switches = numerical_material.getSwitches(type_cohesive);
// std::ofstream edis("fatigue_edis.txt");
// impose openings
for (UInt i = 0; i < openings.size(); ++i) {
// compute numerical traction
imposeOpening(model, openings(i));
model.assembleInternalForces();
// model.dump();
Real numerical_traction = traction_array(0, 0);
// compute theoretical traction
Real theoretical_traction =
theoretical_material.computeTraction(openings(i));
// test traction
if (std::abs(numerical_traction - theoretical_traction) > 1e-13)
AKANTU_ERROR("The numerical traction "
<< numerical_traction << " and theoretical traction "
<< theoretical_traction << " are not coincident");
// edis << model.getEnergy("dissipated") << std::endl;
}
if (switches(0) != 7)
AKANTU_ERROR("The number of switches is wrong");
std::cout << "OK: the test_cohesive_extrinsic_fatigue passed." << std::endl;
return 0;
}
/* -------------------------------------------------------------------------- */
void imposeOpening(SolidMechanicsModelCohesive & model, Real opening) {
UInt spatial_dimension = model.getSpatialDimension();
Mesh & mesh = model.getFEEngine().getMesh();
Array<Real> & position = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
UInt nb_nodes = mesh.getNbNodes();
Array<bool> update(nb_nodes);
- update.clear();
+ update.zero();
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator end = mesh.lastType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Vector<Real> barycenter(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, barycenter);
if (barycenter(0) > 1) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(el, n);
if (!update(node)) {
displacement(node, 0) = opening + position(node, 0);
update(node) = true;
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void arange(Array<Real> & openings, Real begin, Real end, Real increment) {
if (begin < end) {
for (Real opening = begin; opening < end - increment / 2.;
opening += increment)
openings.push_back(opening);
} else {
for (Real opening = begin; opening > end + increment / 2.;
opening -= increment)
openings.push_back(opening);
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh
index 2ae48fc21..e7c224b43 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh
@@ -1,342 +1,342 @@
/**
* @file test_cohesive_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Jan 10 2018
* @date last modification: Tue Feb 20 2018
*
* @brief Coehsive element test fixture
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TEST_COHESIVE_FIXTURE_HH__
-#define __AKANTU_TEST_COHESIVE_FIXTURE_HH__
+#ifndef AKANTU_TEST_COHESIVE_FIXTURE_HH_
+#define AKANTU_TEST_COHESIVE_FIXTURE_HH_
using namespace akantu;
template <::akantu::AnalysisMethod t>
using analysis_method_t = std::integral_constant<::akantu::AnalysisMethod, t>;
class StrainIncrement : public BC::Functor {
public:
StrainIncrement(const Matrix<Real> & strain, BC::Axis dir)
: strain_inc(strain), dir(dir) {}
void operator()(UInt /*node*/, Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const {
if (std::abs(coord(dir)) < 1e-8) {
return;
}
flags.set(true);
primal += strain_inc * coord;
}
static const BC::Functor::Type type = BC::Functor::_dirichlet;
private:
Matrix<Real> strain_inc;
BC::Axis dir;
};
template <typename param_> class TestSMMCFixture : public ::testing::Test {
public:
static constexpr ElementType cohesive_type =
std::tuple_element_t<0, param_>::value;
static constexpr ElementType type_1 = std::tuple_element_t<1, param_>::value;
static constexpr ElementType type_2 = std::tuple_element_t<2, param_>::value;
static constexpr size_t dim =
ElementClass<cohesive_type>::getSpatialDimension();
void SetUp() override {
mesh = std::make_unique<Mesh>(this->dim);
if (Communicator::getStaticCommunicator().whoAmI() == 0) {
ASSERT_NO_THROW({ mesh->read(this->mesh_name); });
}
mesh->distribute();
}
void TearDown() override {
model.reset(nullptr);
mesh.reset(nullptr);
}
void createModel() {
model = std::make_unique<SolidMechanicsModelCohesive>(*mesh);
model->initFull(_analysis_method = this->analysis_method,
_is_extrinsic = this->is_extrinsic);
auto time_step = this->model->getStableTimeStep() * 0.01;
this->model->setTimeStep(time_step);
if (dim == 1) {
surface = 1;
group_size = 1;
return;
}
auto facet_type = mesh->getFacetType(this->cohesive_type);
auto & fe_engine = model->getFEEngineBoundary();
auto & group = mesh->getElementGroup("insertion").getElements(facet_type);
Array<Real> ones(fe_engine.getNbIntegrationPoints(facet_type) *
group.size());
ones.set(1.);
surface = fe_engine.integrate(ones, facet_type, _not_ghost, group);
mesh->getCommunicator().allReduce(surface, SynchronizerOperation::_sum);
group_size = group.size();
mesh->getCommunicator().allReduce(group_size, SynchronizerOperation::_sum);
#define debug_ 0
#if debug_
this->model->addDumpFieldVector("displacement");
this->model->addDumpFieldVector("velocity");
this->model->addDumpFieldVector("internal_force");
this->model->addDumpFieldVector("external_force");
this->model->addDumpField("blocked_dofs");
this->model->addDumpField("stress");
this->model->addDumpField("strain");
this->model->assembleInternalForces();
this->model->setBaseNameToDumper("cohesive elements", "cohesive_elements");
this->model->addDumpFieldVectorToDumper("cohesive elements",
"displacement");
this->model->addDumpFieldToDumper("cohesive elements", "damage");
this->model->addDumpFieldToDumper("cohesive elements", "tractions");
this->model->addDumpFieldToDumper("cohesive elements", "opening");
this->model->dump();
this->model->dump("cohesive elements");
#endif
}
void setInitialCondition(const Matrix<Real> & strain) {
for (auto && data :
zip(make_view(this->mesh->getNodes(), this->dim),
make_view(this->model->getDisplacement(), this->dim))) {
const auto & pos = std::get<0>(data);
auto & disp = std::get<1>(data);
disp = strain * pos;
}
}
bool checkDamaged() {
UInt nb_damaged = 0;
auto & damage =
model->getMaterial("insertion").getArray<Real>("damage", cohesive_type);
for (auto d : damage) {
if (d >= .99)
++nb_damaged;
}
return (nb_damaged == group_size);
}
void steps(const Matrix<Real> & strain) {
StrainIncrement functor((1. / 300) * strain, this->dim == 1 ? _x : _y);
for (auto _ [[gnu::unused]] : arange(nb_steps)) {
this->model->applyBC(functor, "loading");
this->model->applyBC(functor, "fixed");
if (this->is_extrinsic)
this->model->checkCohesiveStress();
this->model->solveStep();
#if debug_
this->model->dump();
this->model->dump("cohesive elements");
#endif
}
}
void checkInsertion() {
auto nb_cohesive_element = this->mesh->getNbElement(cohesive_type);
mesh->getCommunicator().allReduce(nb_cohesive_element,
SynchronizerOperation::_sum);
EXPECT_EQ(nb_cohesive_element, group_size);
}
void checkDissipated(Real expected_density) {
Real edis = this->model->getEnergy("dissipated");
EXPECT_NEAR(this->surface * expected_density, edis, 5e-1);
}
void testModeI() {
this->createModel();
auto & mat_el = this->model->getMaterial("body");
auto speed = mat_el.getPushWaveSpeed(Element());
auto direction = _y;
if (dim == 1)
direction = _x;
auto length =
mesh->getUpperBounds()(direction) - mesh->getLowerBounds()(direction);
nb_steps = length / speed / model->getTimeStep();
SCOPED_TRACE(std::to_string(this->dim) + "D - " + std::to_string(type_1) +
":" + std::to_string(type_2));
auto & mat_co = this->model->getMaterial("insertion");
Real sigma_c = mat_co.get("sigma_c");
Real E = mat_el.get("E");
Real nu = mat_el.get("nu");
Matrix<Real> strain;
if (dim == 1) {
strain = {{1.}};
} else if (dim == 2) {
strain = {{-nu, 0.}, {0., 1. - nu}};
strain *= (1. + nu);
} else if (dim == 3) {
strain = {{-nu, 0., 0.}, {0., 1., 0.}, {0., 0., -nu}};
}
strain *= sigma_c / E;
this->setInitialCondition((1 - 1e-5) * strain);
this->steps(2e-2 * strain);
}
void testModeII() {
this->createModel();
auto & mat_el = this->model->getMaterial("body");
Real speed;
try {
speed =
mat_el.getShearWaveSpeed(Element()); // the slowest speed if exists
} catch (...) {
speed = mat_el.getPushWaveSpeed(Element());
}
auto direction = _y;
if (dim == 1)
direction = _x;
auto length =
mesh->getUpperBounds()(direction) - mesh->getLowerBounds()(direction);
nb_steps = 2 * length / 2. / speed / model->getTimeStep();
SCOPED_TRACE(std::to_string(this->dim) + "D - " + std::to_string(type_1) +
":" + std::to_string(type_2));
if (this->dim > 1)
this->model->applyBC(BC::Dirichlet::FlagOnly(_y), "sides");
if (this->dim > 2)
this->model->applyBC(BC::Dirichlet::FlagOnly(_z), "sides");
auto & mat_co = this->model->getMaterial("insertion");
Real sigma_c = mat_co.get("sigma_c");
Real beta = mat_co.get("beta");
// Real G_c = mat_co.get("G_c");
Real E = mat_el.get("E");
Real nu = mat_el.get("nu");
Matrix<Real> strain;
if (dim == 1) {
strain = {{1.}};
} else if (dim == 2) {
strain = {{0., 1.}, {0., 0.}};
strain *= (1. + nu);
} else if (dim == 3) {
strain = {{0., 1., 0.}, {0., 0., 0.}, {0., 0., 0.}};
strain *= (1. + nu);
}
strain *= 2 * beta * beta * sigma_c / E;
// nb_steps *= 5;
this->setInitialCondition((1. - 1e-5) * strain);
this->steps(0.005 * strain);
}
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<SolidMechanicsModelCohesive> model;
std::string mesh_name{std::to_string(cohesive_type) + std::to_string(type_1) +
(type_1 == type_2 ? "" : std::to_string(type_2)) +
".msh"};
bool is_extrinsic;
AnalysisMethod analysis_method;
Real surface{0};
UInt nb_steps{1000};
UInt group_size{10000};
};
/* -------------------------------------------------------------------------- */
template <typename param_>
constexpr ElementType TestSMMCFixture<param_>::cohesive_type;
template <typename param_>
constexpr ElementType TestSMMCFixture<param_>::type_1;
template <typename param_>
constexpr ElementType TestSMMCFixture<param_>::type_2;
template <typename param_> constexpr size_t TestSMMCFixture<param_>::dim;
/* -------------------------------------------------------------------------- */
using IsExtrinsicTypes = std::tuple<std::true_type, std::false_type>;
using AnalysisMethodTypes =
std::tuple<analysis_method_t<_explicit_lumped_mass>>;
using coh_types = gtest_list_t<std::tuple<
std::tuple<_element_type_cohesive_1d_2, _element_type_segment_2,
_element_type_segment_2>,
std::tuple<_element_type_cohesive_2d_4, _element_type_triangle_3,
_element_type_triangle_3>,
std::tuple<_element_type_cohesive_2d_4, _element_type_quadrangle_4,
_element_type_quadrangle_4>,
std::tuple<_element_type_cohesive_2d_4, _element_type_triangle_3,
_element_type_quadrangle_4>,
std::tuple<_element_type_cohesive_2d_6, _element_type_triangle_6,
_element_type_triangle_6>,
std::tuple<_element_type_cohesive_2d_6, _element_type_quadrangle_8,
_element_type_quadrangle_8>,
std::tuple<_element_type_cohesive_2d_6, _element_type_triangle_6,
_element_type_quadrangle_8>,
std::tuple<_element_type_cohesive_3d_6, _element_type_tetrahedron_4,
_element_type_tetrahedron_4>,
std::tuple<_element_type_cohesive_3d_12, _element_type_tetrahedron_10,
_element_type_tetrahedron_10> /*,
std::tuple<_element_type_cohesive_3d_8, _element_type_hexahedron_8,
_element_type_hexahedron_8>,
std::tuple<_element_type_cohesive_3d_16, _element_type_hexahedron_20,
_element_type_hexahedron_20>*/>>;
TYPED_TEST_SUITE(TestSMMCFixture, coh_types);
-#endif /* __AKANTU_TEST_COHESIVE_FIXTURE_HH__ */
+#endif /* AKANTU_TEST_COHESIVE_FIXTURE_HH_ */
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic.cc
index 51f72f56f..b2825f0ee 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic.cc
@@ -1,178 +1,178 @@
/**
* @file test_cohesive_intrinsic.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Mon Dec 18 2017
*
* @brief Test for cohesive elements
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "dumper_paraview.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
static void updateDisplacement(SolidMechanicsModelCohesive &, Array<UInt> &,
ElementType, Real);
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt spatial_dimension = 2;
const UInt max_steps = 350;
const ElementType type = _triangle_6;
Mesh mesh(spatial_dimension);
mesh.read("triangle.msh");
std::cout << mesh << std::endl;
SolidMechanicsModelCohesive model(mesh);
model.getElementInserter().setLimit(_x, -0.26, -0.24);
/// model initialization
model.initFull();
mesh.write("mesh_cohesive.msh");
Real time_step = model.getStableTimeStep() * 0.8;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
Array<bool> & boundary = model.getBlockedDOFs();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_element = mesh.getNbElement(type);
/// boundary conditions
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
for (UInt n = 0; n < nb_nodes; ++n) {
boundary(n, dim) = true;
}
}
model.assembleInternalForces();
model.setBaseName("intrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("strain");
model.addDumpField("external_force");
model.dump();
model.setBaseNameToDumper("cohesive elements", "cohesive_elements_triangle");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
/// update displacement
Array<UInt> elements;
Vector<Real> bary(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, bary);
if (bary(0) > -0.25)
elements.push_back(el);
}
Real increment = 0.01;
updateDisplacement(model, elements, type, increment);
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
updateDisplacement(model, elements, type, increment);
if (s % 1 == 0) {
model.dump();
model.dump("cohesive elements");
std::cout << "passing step " << s << "/" << max_steps
<< ", Ed = " << model.getEnergy("dissipated") << std::endl;
}
}
Real Ed = model.getEnergy("dissipated");
Real Edt = 2 * sqrt(2);
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_intrinsic was passed!" << std::endl;
return EXIT_SUCCESS;
}
static void updateDisplacement(SolidMechanicsModelCohesive & model,
Array<UInt> & elements, ElementType type,
Real increment) {
Mesh & mesh = model.getFEEngine().getMesh();
UInt nb_element = elements.size();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Array<Real> & displacement = model.getDisplacement();
Array<bool> update(nb_nodes);
- update.clear();
+ update.zero();
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(elements(el), n);
if (!update(node)) {
displacement(node, 0) += increment;
// displacement(node, 1) += increment;
update(node) = true;
}
}
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_quadrangle.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_quadrangle.cc
index 7fb24b1cf..4dd31e523 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_quadrangle.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_quadrangle.cc
@@ -1,205 +1,205 @@
/**
* @file test_cohesive_intrinsic_quadrangle.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Mon Dec 18 2017
*
* @brief Intrinsic cohesive elements' test for quadrangles
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
static void updateDisplacement(SolidMechanicsModelCohesive &, Array<UInt> &,
ElementType, Real);
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 2;
const UInt max_steps = 350;
const ElementType type = _quadrangle_4;
Mesh mesh(spatial_dimension);
mesh.read("quadrangle.msh");
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// debug::setDebugLevel(dblWarning);
SolidMechanicsModelCohesive model(mesh);
model.getElementInserter().setLimit(_x, -0.01, 0.01);
/// model initialization
model.initFull();
Real time_step = model.getStableTimeStep() * 0.8;
model.setTimeStep(time_step);
model.assembleMassLumped();
Array<bool> & boundary = model.getBlockedDOFs();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_element = mesh.getNbElement(type);
/// boundary conditions
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
for (UInt n = 0; n < nb_nodes; ++n) {
boundary(n, dim) = true;
}
}
model.assembleInternalForces();
model.setBaseName("intrinsic_quadrangle");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpField("external_force");
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_quadrangle");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump();
model.dump("cohesive elements");
/// update displacement
Array<UInt> elements;
Vector<Real> bary(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, bary);
if (bary(_x) > 0.)
elements.push_back(el);
}
Real increment = 0.01;
updateDisplacement(model, elements, type, increment);
// for (UInt n = 0; n < nb_nodes; ++n) {
// if (position(n, 1) + displacement(n, 1) > 0) {
// if (position(n, 0) == 0) {
// displacement(n, 1) -= 0.25;
// }
// if (position(n, 0) == 1) {
// displacement(n, 1) += 0.25;
// }
// }
// }
// std::ofstream edis("edis.txt");
// std::ofstream erev("erev.txt");
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
updateDisplacement(model, elements, type, increment);
if (s % 1 == 0) {
model.dump();
model.dump("cohesive elements");
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
// // update displacement
// for (UInt n = 0; n < nb_nodes; ++n) {
// if (position(n, 1) + displacement(n, 1) > 0) {
// displacement(n, 0) -= 0.01;
// }
// }
// Real Ed = dynamic_cast<MaterialCohesive&>
// (model.getMaterial(1)).getDissipatedEnergy();
// Real Er = dynamic_cast<MaterialCohesive&>
// (model.getMaterial(1)).getReversibleEnergy();
// edis << s << " "
// << Ed << std::endl;
// erev << s << " "
// << Er << std::endl;
}
// edis.close();
// erev.close();
Real Ed = model.getEnergy("dissipated");
Real Edt = 1;
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001) {
std::cout << "The dissipated energy is incorrect" << std::endl;
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_intrinsic_quadrangle was passed!"
<< std::endl;
return EXIT_SUCCESS;
}
static void updateDisplacement(SolidMechanicsModelCohesive & model,
Array<UInt> & elements, ElementType type,
Real increment) {
Mesh & mesh = model.getFEEngine().getMesh();
UInt nb_element = elements.size();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Array<Real> & displacement = model.getDisplacement();
Array<bool> update(nb_nodes);
- update.clear();
+ update.zero();
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(elements(el), n);
if (!update(node)) {
displacement(node, 0) += increment;
// displacement(node, 1) += increment;
update(node) = true;
}
}
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron.cc
index 7682ca5fe..f279a440e 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron.cc
@@ -1,353 +1,353 @@
/**
* @file test_cohesive_intrinsic_tetrahedron.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Aug 27 2013
* @date last modification: Mon Dec 18 2017
*
* @brief Test for cohesive elements
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
class Checker {
public:
Checker(const SolidMechanicsModelCohesive & model,
const Array<UInt> & elements, ElementType type);
void check(const Vector<Real> & opening, const Matrix<Real> & rotation) {
checkTractions(opening, rotation);
checkEquilibrium();
computeEnergy(opening);
}
void updateDisplacement(const Vector<Real> & increment);
protected:
void checkTractions(const Vector<Real> & opening,
const Matrix<Real> & rotation);
void checkEquilibrium();
void checkResidual(const Matrix<Real> & rotation);
void computeEnergy(const Vector<Real> & opening);
private:
std::set<UInt> nodes_to_check;
const SolidMechanicsModelCohesive & model;
ElementType type;
// const Array<UInt> & elements;
const Material & mat_cohesive;
Real sigma_c;
const Real beta;
const Real G_c;
const Real delta_0;
const Real kappa;
Real delta_c;
const UInt spatial_dimension;
const ElementType type_facet;
const ElementType type_cohesive;
const Array<Real> & traction;
const Array<Real> & damage;
const UInt nb_quad_per_el;
const UInt nb_element;
const Real beta2_kappa2;
const Real beta2_kappa;
Vector<Real> theoretical_traction;
Vector<Real> traction_old;
Vector<Real> opening_old;
Real Ed;
};
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material_tetrahedron.dat", argc, argv);
// debug::setDebugLevel(dblDump);
const UInt spatial_dimension = 3;
const UInt max_steps = 60;
const Real increment_constant = 0.01;
Math::setTolerance(1.e-12);
const ElementType type = _tetrahedron_10;
Mesh mesh(spatial_dimension);
mesh.read("tetrahedron.msh");
SolidMechanicsModelCohesive model(mesh);
model.getElementInserter().setLimit(_x, -0.01, 0.01);
/// model initialization
model.initFull();
Array<bool> & boundary = model.getBlockedDOFs();
boundary.set(true);
UInt nb_element = mesh.getNbElement(type);
model.setBaseName("intrinsic_tetrahedron");
model.addDumpFieldVector("displacement");
model.addDumpField("internal_force");
model.dump();
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_tetrahedron");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
/// find elements to displace
Array<UInt> elements;
Vector<Real> bary(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, bary);
if (bary(_x) > 0.01)
elements.push_back(el);
}
/// rotate mesh
Real angle = 1.;
// clang-format off
Matrix<Real> rotation{
{std::cos(angle), std::sin(angle) * -1., 0.},
{std::sin(angle), std::cos(angle), 0.},
{0., 0., 1.}};
// clang-format on
Vector<Real> increment_tmp{increment_constant, 2. * increment_constant,
3. * increment_constant};
Vector<Real> increment = rotation * increment_tmp;
auto & position = mesh.getNodes();
auto position_it = position.begin(spatial_dimension);
auto position_end = position.end(spatial_dimension);
for (; position_it != position_end; ++position_it) {
auto & pos = *position_it;
pos = rotation * pos;
}
model.dump();
model.dump("cohesive elements");
/// find nodes to check
Checker checker(model, elements, type);
checker.updateDisplacement(increment);
Real theoretical_Ed = 0;
Vector<Real> opening(spatial_dimension, 0.);
Vector<Real> opening_old(spatial_dimension, 0.);
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
model.dump();
model.dump("cohesive elements");
opening += increment_tmp;
checker.check(opening, rotation);
checker.updateDisplacement(increment);
}
model.dump();
model.dump("cohesive elements");
Real Ed = model.getEnergy("dissipated");
theoretical_Ed *= 4.;
std::cout << Ed << " " << theoretical_Ed << std::endl;
if (!Math::are_float_equal(Ed, theoretical_Ed) || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_intrinsic_tetrahedron was passed!"
<< std::endl;
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void Checker::updateDisplacement(const Vector<Real> & increment) {
Mesh & mesh = model.getFEEngine().getMesh();
const auto & connectivity = mesh.getConnectivity(type);
auto & displacement = model.getDisplacement();
Array<bool> update(displacement.size());
- update.clear();
+ update.zero();
auto conn_it = connectivity.begin(connectivity.getNbComponent());
auto conn_end = connectivity.begin(connectivity.getNbComponent());
for (; conn_it != conn_end; ++conn_it) {
const auto & conn = *conn_it;
for (UInt n = 0; n < conn.size(); ++n) {
UInt node = conn(n);
if (!update(node)) {
Vector<Real> node_disp(displacement.storage() +
node * spatial_dimension,
spatial_dimension);
node_disp += increment;
update(node) = true;
}
}
}
}
/* -------------------------------------------------------------------------- */
Checker::Checker(const SolidMechanicsModelCohesive & model,
const Array<UInt> & elements, ElementType type)
: model(model), type(std::move(type)), // elements(elements),
mat_cohesive(model.getMaterial(1)), sigma_c(mat_cohesive.get("sigma_c")),
beta(mat_cohesive.get("beta")), G_c(mat_cohesive.get("G_c")),
delta_0(mat_cohesive.get("delta_0")), kappa(mat_cohesive.get("kappa")),
spatial_dimension(model.getSpatialDimension()),
type_facet(Mesh::getFacetType(type)),
type_cohesive(FEEngine::getCohesiveElementType(type_facet)),
traction(mat_cohesive.getArray<Real>("tractions", type_cohesive)),
damage(mat_cohesive.getArray<Real>("damage", type_cohesive)),
nb_quad_per_el(model.getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(type_cohesive)),
nb_element(model.getMesh().getNbElement(type_cohesive)),
beta2_kappa2(beta * beta / kappa / kappa),
beta2_kappa(beta * beta / kappa) {
const Mesh & mesh = model.getMesh();
const auto & connectivity = mesh.getConnectivity(type);
const auto & position = mesh.getNodes();
auto conn_it = connectivity.begin(connectivity.getNbComponent());
for (const auto & element : elements) {
Vector<UInt> conn_el(conn_it[element]);
for (UInt n = 0; n < conn_el.size(); ++n) {
UInt node = conn_el(n);
if (Math::are_float_equal(position(node, _x), 0.))
nodes_to_check.insert(node);
}
}
delta_c = 2 * G_c / sigma_c;
sigma_c *= delta_c / (delta_c - delta_0);
}
/* -------------------------------------------------------------------------- */
void Checker::checkTractions(const Vector<Real> & opening,
const Matrix<Real> & rotation) {
auto normal_opening = opening * Vector<Real>{1., 0., 0.};
auto tangential_opening = opening - normal_opening;
const Real normal_opening_norm = normal_opening.norm();
const Real tangential_opening_norm = tangential_opening.norm();
const Real delta =
std::max(std::sqrt(tangential_opening_norm * tangential_opening_norm *
beta2_kappa2 +
normal_opening_norm * normal_opening_norm),
0.);
Real theoretical_damage = std::min(delta / delta_c, 1.);
theoretical_traction = (tangential_opening * beta2_kappa + normal_opening) *
sigma_c / delta * (1. - theoretical_damage);
// adjust damage
theoretical_damage = std::max((delta - delta_0) / (delta_c - delta_0), 0.);
theoretical_damage = std::min(theoretical_damage, 1.);
Vector<Real> theoretical_traction_rotated = rotation * theoretical_traction;
std::for_each(
traction.begin(spatial_dimension), traction.end(spatial_dimension),
[&theoretical_traction_rotated](auto && traction) {
Real diff =
Vector<Real>(theoretical_traction_rotated - traction).norm<L_inf>();
if (diff > 1e-14)
throw std::domain_error("Tractions are incorrect");
});
std::for_each(damage.begin(), damage.end(),
[&theoretical_damage](auto && damage) {
if (not Math::are_float_equal(theoretical_damage, damage))
throw std::domain_error("Damage is incorrect");
});
}
/* -------------------------------------------------------------------------- */
void Checker::computeEnergy(const Vector<Real> & opening) {
/// compute energy
auto Do = opening - opening_old;
auto Dt = traction_old + theoretical_traction;
Ed += .5 * Do.dot(Dt);
opening_old = opening;
traction_old = theoretical_traction;
}
/* -------------------------------------------------------------------------- */
void Checker::checkEquilibrium() {
Vector<Real> residual_sum(spatial_dimension, 0.);
const auto & residual = model.getInternalForce();
auto res_it = residual.begin(spatial_dimension);
auto res_end = residual.end(spatial_dimension);
for (; res_it != res_end; ++res_it)
residual_sum += *res_it;
if (!Math::are_float_equal(residual_sum.norm<L_inf>(), 0.))
throw std::domain_error("System is not in equilibrium!");
}
/* -------------------------------------------------------------------------- */
void Checker::checkResidual(const Matrix<Real> & rotation) {
Vector<Real> total_force(spatial_dimension, 0.);
const auto & residual = model.getInternalForce();
for (auto node : nodes_to_check) {
Vector<Real> res(residual.begin(spatial_dimension)[node]);
total_force += res;
}
Vector<Real> theoretical_total_force(spatial_dimension);
theoretical_total_force.mul<false>(rotation, theoretical_traction);
theoretical_total_force *= -1 * 2 * 2;
for (UInt s = 0; s < spatial_dimension; ++s) {
if (!Math::are_float_equal(total_force(s), theoretical_total_force(s))) {
std::cout << "Total force isn't correct!" << std::endl;
std::terminate();
}
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron_fragmentation.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron_fragmentation.cc
index df4ad6aae..33541f192 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron_fragmentation.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron_fragmentation.cc
@@ -1,125 +1,125 @@
/**
* @file test_cohesive_intrinsic_tetrahedron_fragmentation.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Oct 09 2013
* @date last modification: Mon Dec 18 2017
*
* @brief Test for cohesive elements
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
// debug::setDebugLevel(dblDump);
ElementType type = _tetrahedron_10;
const UInt spatial_dimension = 3;
const UInt max_steps = 100;
Mesh mesh(spatial_dimension);
mesh.read("tetrahedron_full.msh");
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initFull();
Real time_step = model.getStableTimeStep() * 0.8;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
model.assembleInternalForces();
model.setBaseName("intrinsic_tetrahedron_fragmentation");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_tetrahedron_fragmentation");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump();
model.dump("cohesive elements");
/// update displacement
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Vector<Real> bary(spatial_dimension);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Array<Real> & displacement = model.getDisplacement();
Array<bool> update(nb_nodes);
for (UInt s = 0; s < max_steps; ++s) {
Real increment = s / 10.;
- update.clear();
+ update.zero();
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, bary);
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(el, n);
if (!update(node)) {
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
displacement(node, dim) = increment * bary(dim);
update(node) = true;
}
}
}
}
if (s % 10 == 0) {
model.dump();
model.dump("cohesive elements");
}
}
if (nb_nodes != nb_element * Mesh::getNbNodesPerElement(type)) {
std::cout << "Wrong number of nodes" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_intrinsic_tetrahedron was passed!"
<< std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_fixture.hh b/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_fixture.hh
index 109205132..9bc4eac07 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_fixture.hh
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_fixture.hh
@@ -1,311 +1,311 @@
/**
* @file test_material_cohesive_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Feb 21 2018
*
* @brief Test the traction separations laws for cohesive elements
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
//#define debug_
/* -------------------------------------------------------------------------- */
template <template <UInt> class Mat, typename dim_>
class TestMaterialCohesiveFixture : public ::testing::Test {
public:
static constexpr UInt dim = dim_::value;
using Material = Mat<dim>;
void SetUp() override {
mesh = std::make_unique<Mesh>(dim);
model = std::make_unique<SolidMechanicsModelCohesive>(*mesh);
material = std::make_unique<Material>(*model);
material->SetUps();
openings = std::make_unique<Array<Real>>(0, dim);
tractions = std::make_unique<Array<Real>>(0, dim);
reset();
gen.seed(::testing::GTEST_FLAG(random_seed));
normal = getRandomNormal();
tangents = getRandomTangents();
}
void TearDown() override {
material.reset(nullptr);
model.reset(nullptr);
mesh.reset(nullptr);
openings.reset(nullptr);
tractions.reset(nullptr);
}
void reset() {
openings->resize(1);
tractions->resize(1);
- openings->clear();
- tractions->clear();
+ openings->zero();
+ tractions->zero();
}
/* ------------------------------------------------------------------------ */
void addOpening(const Vector<Real> & direction, Real start, Real stop,
UInt nb_steps) {
for (auto s : arange(nb_steps)) {
auto opening =
direction * (start + (stop - start) / Real(nb_steps) * Real(s + 1));
openings->push_back(opening);
}
tractions->resize(openings->size());
}
/* ------------------------------------------------------------------------ */
Vector<Real> getRandomVector() {
std::uniform_real_distribution<Real> dis;
Vector<Real> vector(dim);
for (auto s : arange(dim))
vector(s) = dis(gen);
return vector;
}
Vector<Real> getRandomNormal() {
auto normal = getRandomVector();
normal.normalize();
#if defined(debug_)
normal.set(0.);
normal(0) = 1.;
#endif
return normal;
}
Matrix<Real> getRandomTangents() {
auto dim = normal.size();
Matrix<Real> tangent(dim, dim - 1);
if (dim == 2) {
Math::normal2(normal.storage(), tangent(0).storage());
}
if (dim == 3) {
auto v = getRandomVector();
tangent(0) = (v - v.dot(normal) * normal).normalize();
Math::normal3(normal.storage(), tangent(0).storage(),
tangent(1).storage());
}
#if defined(debug_)
if (dim == 2)
tangent(0) = Vector<Real>{0., 1};
if (dim == 3)
tangent = Matrix<Real>{{0., 0.}, {1., 0.}, {0., 1.}};
#endif
return tangent;
}
/* ------------------------------------------------------------------------ */
void output_csv() {
const ::testing::TestInfo * const test_info =
::testing::UnitTest::GetInstance()->current_test_info();
std::ofstream cout(std::string(test_info->name()) + ".csv");
auto print_vect_name = [&](auto name) {
for (auto s : arange(dim)) {
if (s != 0) {
cout << ", ";
}
cout << name << "_" << s;
}
};
auto print_vect = [&](const auto & vect) {
cout << vect.dot(normal);
if (dim > 1)
cout << ", " << vect.dot(tangents(0));
if (dim > 2)
cout << ", " << vect.dot(tangents(1));
};
cout << "delta, ";
print_vect_name("opening");
cout << ", ";
print_vect_name("traction");
cout << std::endl;
for (auto && data : zip(make_view(*this->openings, this->dim),
make_view(*this->tractions, this->dim))) {
const auto & opening = std::get<0>(data);
auto & traction = std::get<1>(data);
cout << this->material->delta(opening, normal) << ", ";
print_vect(opening);
cout << ", ";
print_vect(traction);
cout << std::endl;
}
}
/* ------------------------------------------------------------------------ */
Real dissipated() {
Vector<Real> prev_opening(dim, 0.);
Vector<Real> prev_traction(dim, 0.);
Real etot = 0.;
Real erev = 0.;
for (auto && data : zip(make_view(*this->openings, this->dim),
make_view(*this->tractions, this->dim))) {
const auto & opening = std::get<0>(data);
const auto & traction = std::get<1>(data);
etot += (opening - prev_opening).dot(traction + prev_traction) / 2.;
erev = traction.dot(opening) / 2.;
prev_opening = opening;
prev_traction = traction;
}
return etot - erev;
}
/* ------------------------------------------------------------------------ */
void checkModeI(Real max_opening, Real expected_dissipated) {
this->material->insertion_stress_ = this->material->sigma_c_ * normal;
addOpening(normal, 0., max_opening, 100);
this->material->computeTractions(*openings, normal, *tractions);
for (auto && data : zip(make_view(*this->openings, this->dim),
make_view(*this->tractions, this->dim))) {
const auto & opening = std::get<0>(data);
auto & traction = std::get<1>(data);
auto T = traction.dot(normal);
EXPECT_NEAR(0, (traction - T * normal).norm(), 1e-9);
auto T_expected =
this->material->tractionModeI(opening, normal).dot(normal);
EXPECT_NEAR(T_expected, T, 1e-9);
}
EXPECT_NEAR(expected_dissipated, dissipated(), 1e-5);
this->output_csv();
}
/* ------------------------------------------------------------------------ */
void checkModeII(Real max_opening) {
if (this->dim == 1) {
SUCCEED();
return;
}
std::uniform_real_distribution<Real> dis;
auto direction = Vector<Real>(tangents(0));
auto alpha = dis(gen) + 0.1;
auto beta = dis(gen) + 0.2;
#ifndef debug_
direction = alpha * Vector<Real>(tangents(0));
if (dim > 2)
direction += beta * Vector<Real>(tangents(1));
direction = direction.normalize();
#endif
beta = this->material->get("beta");
this->material->insertion_stress_ =
beta * this->material->sigma_c_ * direction;
addOpening(direction, 0., max_opening, 100);
this->material->computeTractions(*openings, normal, *tractions);
for (auto && data : zip(make_view(*this->openings, this->dim),
make_view(*this->tractions, this->dim))) {
const auto & opening = std::get<0>(data);
const auto & traction = std::get<1>(data);
// In ModeII normal traction should be 0
ASSERT_NEAR(0, traction.dot(normal), 1e-9);
// Normal opening is null
ASSERT_NEAR(0, opening.dot(normal), 1e-16);
auto T = traction.dot(direction);
auto T_expected =
this->material->tractionModeII(opening, normal).dot(direction);
EXPECT_NEAR(T_expected, T, 1e-9);
}
// EXPECT_NEAR(expected_dissipated, dissipated(), 1e-5);
this->output_csv();
}
protected:
Vector<Real> normal;
Matrix<Real> tangents;
std::unique_ptr<Mesh> mesh;
std::unique_ptr<SolidMechanicsModelCohesive> model;
std::unique_ptr<Material> material;
std::unique_ptr<Array<Real>> openings;
std::unique_ptr<Array<Real>> tractions;
std::mt19937 gen;
};
template <template <UInt> class Mat, UInt dim>
struct TestMaterialCohesive : public Mat<dim> {
TestMaterialCohesive(SolidMechanicsModel & model)
: Mat<dim>(model, "test"), insertion_stress_(dim, 0.) {}
virtual void SetUp() {}
virtual void resetInternal() {}
void SetUps() {
this->initMaterial();
this->SetUp();
this->updateInternalParameters();
this->resetInternals();
}
void resetInternals() { this->resetInternal(); }
virtual void computeTractions(Array<Real> & /*openings*/,
const Vector<Real> & /*normal*/,
Array<Real> & /*tractions*/) {}
Vector<Real> insertion_stress_;
Real sigma_c_{0};
bool is_extrinsic{true};
};
template <template <UInt> class Mat, typename dim_>
constexpr UInt TestMaterialCohesiveFixture<Mat, dim_>::dim;
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc
index 9af37d445..01e6f6ade 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc
@@ -1,455 +1,455 @@
/**
* @file test_cohesive_parallel_buildfragments.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 05 2014
* @date last modification: Tue Feb 20 2018
*
* @brief Test to build fragments in parallel
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <fstream>
#include <functional>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "fragment_manager.hh"
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
void verticalInsertionLimit(SolidMechanicsModelCohesive &);
void displaceElements(SolidMechanicsModelCohesive &, const Real, const Real);
bool isInertiaEqual(const Vector<Real> &, const Vector<Real> &);
void rotateArray(Array<Real> & array, Real angle);
UInt getNbBigFragments(FragmentManager &, UInt);
const UInt spatial_dimension = 3;
const UInt total_nb_fragment = 4;
const Real rotation_angle = M_PI / 4.;
const Real global_tolerance = 1.e-9;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
Math::setTolerance(global_tolerance);
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
// Read the mesh
mesh.read("mesh.msh");
/// partition the mesh
MeshUtils::purifyMesh(mesh);
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition, NULL, true);
delete partition;
/// model initialization
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
mesh.computeBoundingBox();
Real L = mesh.getUpperBounds()(0) - mesh.getLowerBounds()(0);
Real h = mesh.getUpperBounds()(1) - mesh.getLowerBounds()(1);
Real rho = model.getMaterial("bulk").getParam<Real>("rho");
Real theoretical_mass = L * h * h * rho;
Real frag_theo_mass = theoretical_mass / total_nb_fragment;
UInt nb_element =
mesh.getNbElement(spatial_dimension, _not_ghost, _ek_regular);
comm.allReduce(&nb_element, 1, _so_sum);
UInt nb_element_per_fragment = nb_element / total_nb_fragment;
FragmentManager fragment_manager(model);
fragment_manager.computeAllData();
getNbBigFragments(fragment_manager, nb_element_per_fragment + 1);
model.setBaseName("extrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("stress");
model.addDumpField("partitions");
model.addDumpField("fragments");
model.addDumpField("fragments mass");
model.addDumpField("moments of inertia");
model.addDumpField("elements per fragment");
model.dump();
model.setBaseNameToDumper("cohesive elements", "cohesive_elements_test");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
/// set check facets
verticalInsertionLimit(model);
model.assembleMassLumped();
model.synchronizeBoundaries();
/// impose initial displacement
Array<Real> & displacement = model.getDisplacement();
Array<Real> & velocity = model.getVelocity();
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes; ++n) {
displacement(n, 0) = position(n, 0) * 0.1;
velocity(n, 0) = position(n, 0);
}
rotateArray(mesh.getNodes(), rotation_angle);
// rotateArray(displacement, rotation_angle);
// rotateArray(velocity, rotation_angle);
model.updateResidual();
model.checkCohesiveStress();
model.dump();
model.dump("cohesive elements");
const Array<Real> & fragment_mass = fragment_manager.getMass();
const Array<Real> & fragment_center = fragment_manager.getCenterOfMass();
Real el_size = L / total_nb_fragment;
Real lim = -L / 2 + el_size * 0.99;
/// define theoretical inertia moments
Vector<Real> small_frag_inertia(spatial_dimension);
small_frag_inertia(0) = frag_theo_mass * (h * h + h * h) / 12.;
small_frag_inertia(1) = frag_theo_mass * (el_size * el_size + h * h) / 12.;
small_frag_inertia(2) = frag_theo_mass * (el_size * el_size + h * h) / 12.;
std::sort(small_frag_inertia.storage(),
small_frag_inertia.storage() + spatial_dimension,
std::greater<Real>());
const Array<Real> & inertia_moments = fragment_manager.getMomentsOfInertia();
Array<Real>::const_iterator<Vector<Real>> inertia_moments_begin =
inertia_moments.begin(spatial_dimension);
/// displace one fragment each time
for (UInt frag = 1; frag <= total_nb_fragment; ++frag) {
if (prank == 0)
std::cout << "Generating fragment: " << frag << std::endl;
fragment_manager.computeAllData();
/// check number of big fragments
UInt nb_big_fragment =
getNbBigFragments(fragment_manager, nb_element_per_fragment + 1);
model.dump();
model.dump("cohesive elements");
if (frag < total_nb_fragment) {
if (nb_big_fragment != 1) {
AKANTU_ERROR(
"The number of big fragments is wrong: " << nb_big_fragment);
return EXIT_FAILURE;
}
} else {
if (nb_big_fragment != 0) {
AKANTU_ERROR(
"The number of big fragments is wrong: " << nb_big_fragment);
return EXIT_FAILURE;
}
}
/// check number of fragments
UInt nb_fragment_num = fragment_manager.getNbFragment();
if (nb_fragment_num != frag) {
AKANTU_ERROR("The number of fragments is wrong! Numerical: "
<< nb_fragment_num << " Theoretical: " << frag);
return EXIT_FAILURE;
}
/// check mass computation
if (frag < total_nb_fragment) {
Real total_mass = 0.;
UInt small_fragments = 0;
for (UInt f = 0; f < nb_fragment_num; ++f) {
const Vector<Real> & current_inertia = inertia_moments_begin[f];
if (Math::are_float_equal(fragment_mass(f, 0), frag_theo_mass)) {
/// check center of mass
if (fragment_center(f, 0) > (L * frag / total_nb_fragment - L / 2)) {
AKANTU_ERROR("Fragment center is wrong!");
return EXIT_FAILURE;
}
/// check moment of inertia
if (!isInertiaEqual(current_inertia, small_frag_inertia)) {
AKANTU_ERROR("Inertia moments are wrong");
return EXIT_FAILURE;
}
++small_fragments;
total_mass += frag_theo_mass;
} else {
/// check the moment of inertia for the biggest fragment
Real big_frag_mass = frag_theo_mass * (total_nb_fragment - frag + 1);
Real big_frag_size = el_size * (total_nb_fragment - frag + 1);
Vector<Real> big_frag_inertia(spatial_dimension);
big_frag_inertia(0) = big_frag_mass * (h * h + h * h) / 12.;
big_frag_inertia(1) =
big_frag_mass * (big_frag_size * big_frag_size + h * h) / 12.;
big_frag_inertia(2) =
big_frag_mass * (big_frag_size * big_frag_size + h * h) / 12.;
std::sort(big_frag_inertia.storage(),
big_frag_inertia.storage() + spatial_dimension,
std::greater<Real>());
if (!isInertiaEqual(current_inertia, big_frag_inertia)) {
AKANTU_ERROR("Inertia moments are wrong");
return EXIT_FAILURE;
}
}
}
if (small_fragments != nb_fragment_num - 1) {
AKANTU_ERROR("The number of small fragments is wrong!");
return EXIT_FAILURE;
}
if (!Math::are_float_equal(total_mass,
small_fragments * frag_theo_mass)) {
AKANTU_ERROR("The mass of small fragments is wrong!");
return EXIT_FAILURE;
}
}
/// displace fragments
rotateArray(mesh.getNodes(), -rotation_angle);
// rotateArray(displacement, -rotation_angle);
displaceElements(model, lim, el_size * 2);
rotateArray(mesh.getNodes(), rotation_angle);
// rotateArray(displacement, rotation_angle);
model.updateResidual();
lim += el_size;
}
model.dump();
model.dump("cohesive elements");
/// check centers
const Array<Real> & fragment_velocity = fragment_manager.getVelocity();
Real initial_position = -L / 2. + el_size / 2.;
for (UInt frag = 0; frag < total_nb_fragment; ++frag) {
Real theoretical_center = initial_position + el_size * frag;
UInt f_index = 0;
while (
f_index < total_nb_fragment &&
!Math::are_float_equal(fragment_center(f_index, 0), theoretical_center))
++f_index;
if (f_index == total_nb_fragment) {
AKANTU_ERROR("The fragments' center is wrong!");
return EXIT_FAILURE;
}
f_index = 0;
while (f_index < total_nb_fragment &&
!Math::are_float_equal(fragment_velocity(f_index, 0),
theoretical_center))
++f_index;
if (f_index == total_nb_fragment) {
AKANTU_ERROR("The fragments' velocity is wrong!");
return EXIT_FAILURE;
}
}
finalize();
if (prank == 0)
std::cout << "OK: test_cohesive_buildfragments was passed!" << std::endl;
return EXIT_SUCCESS;
}
void verticalInsertionLimit(SolidMechanicsModelCohesive & model) {
UInt spatial_dimension = model.getSpatialDimension();
const Mesh & mesh_facets = model.getMeshFacets();
const Array<Real> & position = mesh_facets.getNodes();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for (; it != end; ++it) {
ElementType type = *it;
Array<bool> & check_facets =
model.getElementInserter().getCheckFacets(type, ghost_type);
const Array<UInt> & connectivity =
mesh_facets.getConnectivity(type, ghost_type);
UInt nb_nodes_per_facet = connectivity.getNbComponent();
for (UInt f = 0; f < check_facets.getSize(); ++f) {
if (!check_facets(f))
continue;
UInt nb_aligned_nodes = 1;
Real first_node_pos = position(connectivity(f, 0), 0);
for (; nb_aligned_nodes < nb_nodes_per_facet; ++nb_aligned_nodes) {
Real other_node_pos = position(connectivity(f, nb_aligned_nodes), 0);
if (!Math::are_float_equal(first_node_pos, other_node_pos))
break;
}
if (nb_aligned_nodes != nb_nodes_per_facet) {
check_facets(f) = false;
}
}
}
}
}
void displaceElements(SolidMechanicsModelCohesive & model, const Real lim,
const Real amount) {
UInt spatial_dimension = model.getSpatialDimension();
Array<Real> & displacement = model.getDisplacement();
Mesh & mesh = model.getMesh();
UInt nb_nodes = mesh.getNbNodes();
Array<bool> displaced(nb_nodes);
- displaced.clear();
+ displaced.zero();
Vector<Real> barycenter(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, ghost_type);
for (; it != end; ++it) {
ElementType type = *it;
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_element = connectivity.getSize();
UInt nb_nodes_per_element = connectivity.getNbComponent();
Array<UInt>::const_vector_iterator conn_el =
connectivity.begin(nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter(el, type, barycenter.storage(), ghost_type);
if (barycenter(0) < lim) {
const Vector<UInt> & conn = conn_el[el];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = conn(n);
if (!displaced(node)) {
displacement(node, 0) -= amount;
displaced(node) = true;
}
}
}
}
}
}
}
bool isInertiaEqual(const Vector<Real> & a, const Vector<Real> & b) {
UInt nb_terms = a.size();
UInt equal_terms = 0;
while (equal_terms < nb_terms &&
std::abs(a(equal_terms) - b(equal_terms)) / a(equal_terms) <
Math::getTolerance())
++equal_terms;
return equal_terms == nb_terms;
}
void rotateArray(Array<Real> & array, Real angle) {
UInt spatial_dimension = array.getNbComponent();
Real rotation_values[] = {std::cos(angle),
std::sin(angle),
0,
-std::sin(angle),
std::cos(angle),
0,
0,
0,
1};
Matrix<Real> rotation(rotation_values, spatial_dimension, spatial_dimension);
RVector displaced_node(spatial_dimension);
auto node_it = array.begin(spatial_dimension);
auto node_end = array.end(spatial_dimension);
for (; node_it != node_end; ++node_it) {
displaced_node.mul<false>(rotation, *node_it);
*node_it = displaced_node;
}
}
UInt getNbBigFragments(FragmentManager & fragment_manager,
UInt minimum_nb_elements) {
fragment_manager.computeNbElementsPerFragment();
const Array<UInt> & nb_elements_per_fragment =
fragment_manager.getNbElementsPerFragment();
UInt nb_fragment = fragment_manager.getNbFragment();
UInt nb_big_fragment = 0;
for (UInt frag = 0; frag < nb_fragment; ++frag) {
if (nb_elements_per_fragment(frag) >= minimum_nb_elements) {
++nb_big_fragment;
}
}
return nb_big_fragment;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc
index c53436965..4c2647916 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc
@@ -1,712 +1,712 @@
/**
* @file test_cohesive_parallel_intrinsic_tetrahedron.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 05 2014
* @date last modification: Wed Nov 08 2017
*
* @brief Test for 3D intrinsic cohesive elements simulation in parallel
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_paraview.hh"
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
void updateDisplacement(SolidMechanicsModelCohesive & model,
const ElementTypeMapArray<UInt> & elements,
Vector<Real> & increment);
bool checkTractions(SolidMechanicsModelCohesive & model, Vector<Real> & opening,
Vector<Real> & theoretical_traction,
Matrix<Real> & rotation);
void findNodesToCheck(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements,
Array<UInt> & nodes_to_check, Int psize);
bool checkEquilibrium(const Mesh & mesh, const Array<Real> & residual);
bool checkResidual(const Array<Real> & residual, const Vector<Real> & traction,
const Array<UInt> & nodes_to_check,
const Matrix<Real> & rotation);
void findElementsToDisplace(const Mesh & mesh,
ElementTypeMapArray<UInt> & elements);
int main(int argc, char * argv[]) {
initialize("material_tetrahedron.dat", argc, argv);
const UInt spatial_dimension = 3;
const UInt max_steps = 60;
const Real increment_constant = 0.01;
ElementType type = _tetrahedron_10;
Math::setTolerance(1.e-10);
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
UInt nb_nodes_to_check_serial = 0;
UInt total_nb_nodes = 0;
UInt nb_elements_check_serial = 0;
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
// Read the mesh
mesh.read("tetrahedron.msh");
/// count nodes with zero position
const Array<Real> & position = mesh.getNodes();
for (UInt n = 0; n < position.getSize(); ++n) {
if (std::abs(position(n, 0) - 0.) < 1e-6)
++nb_nodes_to_check_serial;
}
// /// insert cohesive elements
// CohesiveElementInserter inserter(mesh);
// inserter.setLimit(0, -0.01, 0.01);
// inserter.insertIntrinsicElements();
/// find nodes to check in serial
ElementTypeMapArray<UInt> elements_serial("elements_serial", "");
findElementsToDisplace(mesh, elements_serial);
nb_elements_check_serial = elements_serial(type).getSize();
total_nb_nodes = mesh.getNbNodes() + nb_nodes_to_check_serial;
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
debug::setDebugLevel(dblDump);
partition->partitionate(psize);
debug::setDebugLevel(dblInfo);
}
comm.broadcast(&nb_nodes_to_check_serial, 1, 0);
comm.broadcast(&nb_elements_check_serial, 1, 0);
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition);
model.initFull();
model.limitInsertion(_x, -0.01, 0.01);
model.insertIntrinsicElements();
{
comm.broadcast(&total_nb_nodes, 1, 0);
Array<Int> nb_local_nodes(psize);
- nb_local_nodes.clear();
+ nb_local_nodes.zero();
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n))
++nb_local_nodes(prank);
}
comm.allGather(nb_local_nodes.storage(), 1);
UInt total_nb_nodes_parallel =
std::accumulate(nb_local_nodes.begin(), nb_local_nodes.end(), 0);
Array<UInt> global_nodes_list(total_nb_nodes_parallel);
UInt first_global_node = std::accumulate(nb_local_nodes.begin(),
nb_local_nodes.begin() + prank, 0);
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n)) {
global_nodes_list(first_global_node) = mesh.getNodeGlobalId(n);
++first_global_node;
}
}
comm.allGatherV(global_nodes_list.storage(), nb_local_nodes.storage());
if (prank == 0)
std::cout << "Maximum node index: "
<< *(std::max_element(global_nodes_list.begin(),
global_nodes_list.end()))
<< std::endl;
Array<UInt> repeated_nodes;
repeated_nodes.resize(0);
for (UInt n = 0; n < total_nb_nodes_parallel; ++n) {
UInt appearances =
std::count(global_nodes_list.begin() + n, global_nodes_list.end(),
global_nodes_list(n));
if (appearances > 1) {
std::cout << "Node " << global_nodes_list(n) << " appears "
<< appearances << " times" << std::endl;
std::cout << " in position: " << n;
repeated_nodes.push_back(global_nodes_list(n));
UInt * node_position = global_nodes_list.storage() + n;
for (UInt i = 1; i < appearances; ++i) {
node_position =
std::find(node_position + 1,
global_nodes_list.storage() + total_nb_nodes_parallel,
global_nodes_list(n));
UInt current_index = node_position - global_nodes_list.storage();
std::cout << ", " << current_index;
}
std::cout << std::endl << std::endl;
}
}
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
UInt global_node = mesh.getNodeGlobalId(n);
if (std::find(repeated_nodes.begin(), repeated_nodes.end(),
global_node) != repeated_nodes.end()) {
std::cout << "Repeated global node " << global_node
<< " corresponds to local node " << n << std::endl;
}
}
if (total_nb_nodes != total_nb_nodes_parallel) {
if (prank == 0) {
std::cout << "Error: total number of nodes is wrong in parallel"
<< std::endl;
std::cout << "Serial: " << total_nb_nodes
<< " Parallel: " << total_nb_nodes_parallel << std::endl;
}
finalize();
return EXIT_FAILURE;
}
}
model.updateResidual();
model.setBaseName("intrinsic_parallel_tetrahedron");
model.addDumpFieldVector("displacement");
model.addDumpField("residual");
model.addDumpField("partitions");
model.dump();
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_parallel_tetrahedron");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.dump("cohesive elements");
/// find elements to displace
ElementTypeMapArray<UInt> elements("elements", "");
findElementsToDisplace(mesh, elements);
UInt nb_elements_check = elements(type).getSize();
comm.allReduce(&nb_elements_check, 1, _so_sum);
if (nb_elements_check != nb_elements_check_serial) {
if (prank == 0) {
std::cout << "Error: number of elements to check is wrong" << std::endl;
std::cout << "Serial: " << nb_elements_check_serial
<< " Parallel: " << nb_elements_check << std::endl;
}
finalize();
return EXIT_FAILURE;
}
/// find nodes to check
Array<UInt> nodes_to_check;
findNodesToCheck(mesh, elements, nodes_to_check, psize);
Vector<Int> nodes_to_check_size(psize);
nodes_to_check_size(prank) = nodes_to_check.getSize();
comm.allGather(nodes_to_check_size.storage(), 1);
UInt nodes_to_check_global_size = std::accumulate(
nodes_to_check_size.storage(), nodes_to_check_size.storage() + psize, 0);
if (nodes_to_check_global_size != nb_nodes_to_check_serial) {
if (prank == 0) {
std::cout << "Error: number of nodes to check is wrong in parallel"
<< std::endl;
std::cout << "Serial: " << nb_nodes_to_check_serial
<< " Parallel: " << nodes_to_check_global_size << std::endl;
}
finalize();
return EXIT_FAILURE;
}
/// rotate mesh
Real angle = 1.;
Matrix<Real> rotation(spatial_dimension, spatial_dimension);
- rotation.clear();
+ rotation.zero();
rotation(0, 0) = std::cos(angle);
rotation(0, 1) = std::sin(angle) * -1.;
rotation(1, 0) = std::sin(angle);
rotation(1, 1) = std::cos(angle);
rotation(2, 2) = 1.;
Vector<Real> increment_tmp(spatial_dimension);
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
increment_tmp(dim) = (dim + 1) * increment_constant;
}
Vector<Real> increment(spatial_dimension);
increment.mul<false>(rotation, increment_tmp);
Array<Real> & position = mesh.getNodes();
Array<Real> position_tmp(position);
Array<Real>::iterator<Vector<Real>> position_it =
position.begin(spatial_dimension);
Array<Real>::iterator<Vector<Real>> position_end =
position.end(spatial_dimension);
Array<Real>::iterator<Vector<Real>> position_tmp_it =
position_tmp.begin(spatial_dimension);
for (; position_it != position_end; ++position_it, ++position_tmp_it)
position_it->mul<false>(rotation, *position_tmp_it);
model.dump();
model.dump("cohesive elements");
updateDisplacement(model, elements, increment);
Real theoretical_Ed = 0;
Vector<Real> opening(spatial_dimension);
Vector<Real> traction(spatial_dimension);
Vector<Real> opening_old(spatial_dimension);
Vector<Real> traction_old(spatial_dimension);
- opening.clear();
- traction.clear();
- opening_old.clear();
- traction_old.clear();
+ opening.zero();
+ traction.zero();
+ opening_old.zero();
+ traction_old.zero();
Vector<Real> Dt(spatial_dimension);
Vector<Real> Do(spatial_dimension);
const Array<Real> & residual = model.getResidual();
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.updateResidual();
opening += increment_tmp;
if (checkTractions(model, opening, traction, rotation) ||
checkEquilibrium(mesh, residual) ||
checkResidual(residual, traction, nodes_to_check, rotation)) {
finalize();
return EXIT_FAILURE;
}
/// compute energy
Do = opening;
Do -= opening_old;
Dt = traction_old;
Dt += traction;
theoretical_Ed += .5 * Do.dot(Dt);
opening_old = opening;
traction_old = traction;
updateDisplacement(model, elements, increment);
if (s % 10 == 0) {
if (prank == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
model.dump();
model.dump("cohesive elements");
}
}
model.dump();
model.dump("cohesive elements");
Real Ed = model.getEnergy("dissipated");
theoretical_Ed *= 4.;
if (prank == 0)
std::cout << "Dissipated energy: " << Ed
<< ", theoretical value: " << theoretical_Ed << std::endl;
if (!Math::are_float_equal(Ed, theoretical_Ed) || std::isnan(Ed)) {
if (prank == 0)
std::cout << "Error: the dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
if (prank == 0)
std::cout << "OK: Test passed!" << std::endl;
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void updateDisplacement(SolidMechanicsModelCohesive & model,
const ElementTypeMapArray<UInt> & elements,
Vector<Real> & increment) {
UInt spatial_dimension = model.getSpatialDimension();
Mesh & mesh = model.getFEEngine().getMesh();
UInt nb_nodes = mesh.getNbNodes();
Array<Real> & displacement = model.getDisplacement();
Array<bool> update(nb_nodes);
- update.clear();
+ update.zero();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last; ++it) {
ElementType type = *it;
const Array<UInt> & elem = elements(type, ghost_type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_nodes_per_element = connectivity.getNbComponent();
for (UInt el = 0; el < elem.getSize(); ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(elem(el), n);
if (!update(node)) {
Vector<Real> node_disp(displacement.storage() +
node * spatial_dimension,
spatial_dimension);
node_disp += increment;
update(node) = true;
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
bool checkTractions(SolidMechanicsModelCohesive & model, Vector<Real> & opening,
Vector<Real> & theoretical_traction,
Matrix<Real> & rotation) {
UInt spatial_dimension = model.getSpatialDimension();
const Mesh & mesh = model.getMesh();
const MaterialCohesive & mat_cohesive =
dynamic_cast<const MaterialCohesive &>(model.getMaterial(1));
Real sigma_c =
mat_cohesive.getParam<RandomInternalField<Real, FacetInternalField>>(
"sigma_c");
const Real beta = mat_cohesive.getParam<Real>("beta");
const Real G_cI = mat_cohesive.getParam<Real>("G_c");
// Real G_cII = mat_cohesive.getParam<Real>("G_cII");
const Real delta_0 = mat_cohesive.getParam<Real>("delta_0");
const Real kappa = mat_cohesive.getParam<Real>("kappa");
Real delta_c = 2 * G_cI / sigma_c;
sigma_c *= delta_c / (delta_c - delta_0);
Vector<Real> normal_opening(spatial_dimension);
- normal_opening.clear();
+ normal_opening.zero();
normal_opening(0) = opening(0);
Real normal_opening_norm = normal_opening.norm();
Vector<Real> tangential_opening(spatial_dimension);
- tangential_opening.clear();
+ tangential_opening.zero();
for (UInt dim = 1; dim < spatial_dimension; ++dim)
tangential_opening(dim) = opening(dim);
Real tangential_opening_norm = tangential_opening.norm();
Real beta2_kappa2 = beta * beta / kappa / kappa;
Real beta2_kappa = beta * beta / kappa;
Real delta = std::sqrt(tangential_opening_norm * tangential_opening_norm *
beta2_kappa2 +
normal_opening_norm * normal_opening_norm);
delta = std::max(delta, delta_0);
Real theoretical_damage = std::min(delta / delta_c, 1.);
if (Math::are_float_equal(theoretical_damage, 1.))
- theoretical_traction.clear();
+ theoretical_traction.zero();
else {
theoretical_traction = tangential_opening;
theoretical_traction *= beta2_kappa;
theoretical_traction += normal_opening;
theoretical_traction *= sigma_c / delta * (1. - theoretical_damage);
}
Vector<Real> theoretical_traction_rotated(spatial_dimension);
theoretical_traction_rotated.mul<false>(rotation, theoretical_traction);
// adjust damage
theoretical_damage = std::max((delta - delta_0) / (delta_c - delta_0), 0.);
theoretical_damage = std::min(theoretical_damage, 1.);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_cohesive);
Mesh::type_iterator last =
mesh.lastType(spatial_dimension, ghost_type, _ek_cohesive);
for (; it != last; ++it) {
ElementType type = *it;
const Array<Real> & traction = mat_cohesive.getTraction(type, ghost_type);
const Array<Real> & damage = mat_cohesive.getDamage(type, ghost_type);
UInt nb_quad_per_el =
model.getFEEngine("CohesiveFEEngine").getNbIntegrationPoints(type);
UInt nb_element = model.getMesh().getNbElement(type, ghost_type);
UInt tot_nb_quad = nb_element * nb_quad_per_el;
for (UInt q = 0; q < tot_nb_quad; ++q) {
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
if (!Math::are_float_equal(
std::abs(theoretical_traction_rotated(dim)),
std::abs(traction(q, dim)))) {
std::cout << "Error: tractions are incorrect" << std::endl;
return 1;
}
}
if (ghost_type == _not_ghost)
if (!Math::are_float_equal(theoretical_damage, damage(q))) {
std::cout << "Error: damage is incorrect" << std::endl;
return 1;
}
}
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
void findNodesToCheck(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements,
Array<UInt> & nodes_to_check, Int psize) {
const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
nodes_to_check.resize(0);
Array<UInt> global_nodes_to_check;
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = position.getSize();
Array<bool> checked_nodes(nb_nodes);
- checked_nodes.clear();
+ checked_nodes.zero();
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator last = mesh.lastType(spatial_dimension);
for (; it != last; ++it) {
ElementType type = *it;
const Array<UInt> & elem = elements(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
UInt nb_nodes_per_elem = connectivity.getNbComponent();
for (UInt el = 0; el < elem.getSize(); ++el) {
UInt element = elem(el);
Vector<UInt> conn_el(connectivity.storage() + nb_nodes_per_elem * element,
nb_nodes_per_elem);
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = conn_el(n);
if (std::abs(position(node, 0) - 0.) < 1.e-6 && !checked_nodes(node)) {
checked_nodes(node) = true;
nodes_to_check.push_back(node);
global_nodes_to_check.push_back(mesh.getNodeGlobalId(node));
}
}
}
}
std::vector<CommunicationRequest *> requests;
for (Int p = prank + 1; p < psize; ++p) {
requests.push_back(comm.asyncSend(global_nodes_to_check.storage(),
global_nodes_to_check.getSize(), p,
prank));
}
Array<UInt> recv_nodes;
for (Int p = 0; p < prank; ++p) {
CommunicationStatus status;
comm.probe<UInt>(p, p, status);
UInt recv_nodes_size = recv_nodes.getSize();
recv_nodes.resize(recv_nodes_size + status.getSize());
comm.receive(recv_nodes.storage() + recv_nodes_size, status.getSize(), p,
p);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
for (UInt i = 0; i < recv_nodes.getSize(); ++i) {
Array<UInt>::iterator<UInt> node_position =
std::find(global_nodes_to_check.begin(), global_nodes_to_check.end(),
recv_nodes(i));
if (node_position != global_nodes_to_check.end()) {
UInt index = node_position - global_nodes_to_check.begin();
nodes_to_check.erase(index);
global_nodes_to_check.erase(index);
}
}
}
/* -------------------------------------------------------------------------- */
bool checkEquilibrium(const Mesh & mesh, const Array<Real> & residual) {
UInt spatial_dimension = residual.getNbComponent();
Vector<Real> residual_sum(spatial_dimension);
- residual_sum.clear();
+ residual_sum.zero();
Array<Real>::const_iterator<Vector<Real>> res_it =
residual.begin(spatial_dimension);
for (UInt n = 0; n < residual.getSize(); ++n, ++res_it) {
if (mesh.isLocalOrMasterNode(n))
residual_sum += *res_it;
}
const auto & comm = Communicator::getStaticCommunicator();
comm.allReduce(residual_sum.storage(), spatial_dimension, _so_sum);
for (UInt s = 0; s < spatial_dimension; ++s) {
if (!Math::are_float_equal(residual_sum(s), 0.)) {
if (comm.whoAmI() == 0)
std::cout << "Error: system is not in equilibrium!" << std::endl;
return 1;
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
bool checkResidual(const Array<Real> & residual, const Vector<Real> & traction,
const Array<UInt> & nodes_to_check,
const Matrix<Real> & rotation) {
UInt spatial_dimension = residual.getNbComponent();
Vector<Real> total_force(spatial_dimension);
- total_force.clear();
+ total_force.zero();
for (UInt n = 0; n < nodes_to_check.getSize(); ++n) {
UInt node = nodes_to_check(n);
Vector<Real> res(residual.storage() + node * spatial_dimension,
spatial_dimension);
total_force += res;
}
const auto & comm = Communicator::getStaticCommunicator();
comm.allReduce(total_force.storage(), spatial_dimension, _so_sum);
Vector<Real> theoretical_total_force(spatial_dimension);
theoretical_total_force.mul<false>(rotation, traction);
theoretical_total_force *= -1 * 2 * 2;
for (UInt s = 0; s < spatial_dimension; ++s) {
if (!Math::are_float_equal(total_force(s), theoretical_total_force(s))) {
if (comm.whoAmI() == 0)
std::cout << "Error: total force isn't correct!" << std::endl;
return 1;
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
void findElementsToDisplace(const Mesh & mesh,
ElementTypeMapArray<UInt> & elements) {
UInt spatial_dimension = mesh.getSpatialDimension();
mesh.initElementTypeMapArray(elements, 1, spatial_dimension);
Vector<Real> bary(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last; ++it) {
ElementType type = *it;
Array<UInt> & elem = elements(type, ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter(el, type, bary.storage(), ghost_type);
if (bary(0) > 0.0001)
elem.push_back(el);
}
}
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc b/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc
index 6a83f9244..689743600 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc
@@ -1,233 +1,233 @@
/**
* @file test_embedded_interface_model_prestress.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Tue Apr 28 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Embedded model test for prestressing (bases on stress norm)
*
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "aka_common.hh"
#include "embedded_interface_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
#define YG 0.483644859
#define I_eq 0.012488874
#define A_eq (1e-2 + 1. / 7. * 1.)
/* -------------------------------------------------------------------------- */
struct StressSolution : public BC::Neumann::FromHigherDim {
Real M;
Real I;
Real yg;
Real pre_stress;
StressSolution(UInt dim, Real M, Real I, Real yg = 0, Real pre_stress = 0)
: BC::Neumann::FromHigherDim(Matrix<Real>(dim, dim)), M(M), I(I), yg(yg),
pre_stress(pre_stress) {}
virtual ~StressSolution() {}
void operator()(const IntegrationPoint & /*quad_point*/, Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const {
UInt dim = coord.size();
if (dim < 2)
AKANTU_ERROR("Solution not valid for 1D");
Matrix<Real> stress(dim, dim);
- stress.clear();
+ stress.zero();
stress(0, 0) = this->stress(coord(1));
dual.mul<false>(stress, normals);
}
inline Real stress(Real height) const {
return -M / I * (height - yg) + pre_stress;
}
inline Real neutral_axis() const { return -I * pre_stress / M + yg; }
};
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("prestress.dat", argc, argv);
debug::setDebugLevel(dblError);
Math::setTolerance(1e-6);
const UInt dim = 2;
/* --------------------------------------------------------------------------
*/
Mesh mesh(dim);
mesh.read("embedded_mesh_prestress.msh");
// mesh.createGroupsFromMeshData<std::string>("physical_names");
Mesh reinforcement_mesh(dim, "reinforcement_mesh");
try {
reinforcement_mesh.read("embedded_mesh_prestress_reinforcement.msh");
} catch (debug::Exception & e) {
}
// reinforcement_mesh.createGroupsFromMeshData<std::string>("physical_names");
EmbeddedInterfaceModel model(mesh, reinforcement_mesh, dim);
model.initFull(EmbeddedInterfaceModelOptions(_static));
/* --------------------------------------------------------------------------
*/
/* Computation of analytical residual */
/* --------------------------------------------------------------------------
*/
/*
* q = 1000 N/m
* L = 20 m
* a = 1 m
*/
Real steel_area = model.getMaterial("reinforcement").get("area");
Real pre_stress = model.getMaterial("reinforcement").get("pre_stress");
Real stress_norm = 0.;
StressSolution *concrete_stress = nullptr, *steel_stress = nullptr;
Real pre_force = pre_stress * steel_area;
Real pre_moment = -pre_force * (YG - 0.25);
Real neutral_axis = YG - I_eq / A_eq * pre_force / pre_moment;
concrete_stress = new StressSolution(dim, pre_moment, 7. * I_eq, YG,
-pre_force / (7. * A_eq));
steel_stress = new StressSolution(dim, pre_moment, I_eq, YG,
pre_stress - pre_force / A_eq);
stress_norm =
std::abs(concrete_stress->stress(1)) * (1 - neutral_axis) * 0.5 +
std::abs(concrete_stress->stress(0)) * neutral_axis * 0.5 +
std::abs(steel_stress->stress(0.25)) * steel_area;
model.applyBC(*concrete_stress, "XBlocked");
auto end_node = *mesh.getElementGroup("EndNode").getNodeGroup().begin();
Vector<Real> end_node_force = model.getExternalForce().begin(dim)[end_node];
end_node_force(0) += steel_stress->stress(0.25) * steel_area;
Array<Real> analytical_residual(mesh.getNbNodes(), dim,
"analytical_residual");
analytical_residual.copy(model.getExternalForce());
- model.getExternalForce().clear();
+ model.getExternalForce().zero();
delete concrete_stress;
delete steel_stress;
/* --------------------------------------------------------------------------
*/
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "XBlocked");
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "YBlocked");
try {
model.solveStep();
} catch (debug::Exception & e) {
std::cerr << e.what() << std::endl;
return EXIT_FAILURE;
}
/* --------------------------------------------------------------------------
*/
/* Computation of FEM residual norm */
/* --------------------------------------------------------------------------
*/
ElementGroup & xblocked = mesh.getElementGroup("XBlocked");
NodeGroup & boundary_nodes = xblocked.getNodeGroup();
NodeGroup::const_node_iterator nodes_it = boundary_nodes.begin(),
nodes_end = boundary_nodes.end();
model.assembleInternalForces();
Array<Real> residual(mesh.getNbNodes(), dim, "my_residual");
residual.copy(model.getInternalForce());
residual -= model.getExternalForce();
auto com_res = residual.begin(dim);
auto position = mesh.getNodes().begin(dim);
Real res_sum = 0.;
UInt lower_node = -1;
UInt upper_node = -1;
Real lower_dist = 1;
Real upper_dist = 1;
for (; nodes_it != nodes_end; ++nodes_it) {
UInt node_number = *nodes_it;
const Vector<Real> res = com_res[node_number];
const Vector<Real> pos = position[node_number];
if (!Math::are_float_equal(pos(1), 0.25)) {
if ((std::abs(pos(1) - 0.25) < lower_dist) && (pos(1) < 0.25)) {
lower_dist = std::abs(pos(1) - 0.25);
lower_node = node_number;
}
if ((std::abs(pos(1) - 0.25) < upper_dist) && (pos(1) > 0.25)) {
upper_dist = std::abs(pos(1) - 0.25);
upper_node = node_number;
}
}
for (UInt i = 0; i < dim; i++) {
if (!Math::are_float_equal(pos(1), 0.25)) {
res_sum += std::abs(res(i));
}
}
}
const Vector<Real> upper_res = com_res[upper_node],
lower_res = com_res[lower_node];
const Vector<Real> end_node_res = com_res[end_node];
Vector<Real> delta = upper_res - lower_res;
delta *= lower_dist / (upper_dist + lower_dist);
Vector<Real> concrete_residual = lower_res + delta;
Vector<Real> steel_residual = end_node_res - concrete_residual;
for (UInt i = 0; i < dim; i++) {
res_sum += std::abs(concrete_residual(i));
res_sum += std::abs(steel_residual(i));
}
Real relative_error = std::abs(res_sum - stress_norm) / stress_norm;
if (relative_error > 1e-3) {
std::cerr << "Relative error = " << relative_error << std::endl;
return EXIT_FAILURE;
}
finalize();
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc
index a5cd01d66..912029411 100644
--- a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc
@@ -1,145 +1,145 @@
/**
* @file test_solid_mechanics_model_work_quasistatic.cc
*
* @author Tobias Brink <tobias.brink@epfl.ch>
*
* @date creation: Wed Nov 29 2017
* @date last modification: Fri Jan 26 2018
*
* @brief test work in quasistatic
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section description
*
* Assuming that the potential energy of a linear elastic material
* works correctly, the work in a static simulation must equal the
* potential energy of the material. Since the work in static is an
* infinitesimal work Fds, we need to integrate by increasing F from 0
* to F_final in steps. This test uses one Dirichlet boundary
* condition (with u = 0.0, 0.1, and -0.1) and one Neumann boundary
* condition for F on the opposite side. The final work must be the
* same for all u.
*
*/
/* -------------------------------------------------------------------------- */
#include "../test_solid_mechanics_model_fixture.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
TYPED_TEST(TestSMMFixture, WorkQuasistatic) {
const auto spatial_dimension = this->spatial_dimension;
getStaticParser().parse("test_solid_mechanics_model_"
"work_material.dat");
/// model initialization
this->model->initFull(_analysis_method = _static);
/// Create a node group for Neumann BCs.
auto & apply_force_grp = this->mesh->createNodeGroup("apply_force");
auto & fixed_grp = this->mesh->createNodeGroup("fixed");
const auto & pos = this->mesh->getNodes();
auto & flags = this->model->getBlockedDOFs();
auto & lower = this->mesh->getLowerBounds();
auto & upper = this->mesh->getUpperBounds();
UInt i = 0;
for (auto && data : zip(make_view(pos, spatial_dimension),
make_view(flags, spatial_dimension))) {
const auto & posv = std::get<0>(data);
auto & flag = std::get<1>(data);
if (posv(_x) > upper(_x) - 1e-6) {
apply_force_grp.add(i);
} else if (posv(_x) < lower(_x) + 1e-6) {
fixed_grp.add(i);
if ((spatial_dimension > 1) and (posv(_y) < lower(_y) + 1e-6)) {
flag(_y) = true;
if ((spatial_dimension > 2) and (posv(_z) < lower(_z) + 1e-6)) {
flag(_z) = true;
}
}
}
++i;
}
this->mesh->createElementGroupFromNodeGroup("el_apply_force", "apply_force",
spatial_dimension - 1);
this->mesh->createElementGroupFromNodeGroup("el_fixed", "fixed",
spatial_dimension - 1);
std::vector<Real> displacements{0.0, 0.1, -0.1};
for (auto && u : displacements) {
this->model->applyBC(BC::Dirichlet::FixedValue(u, _x), "el_fixed");
Vector<Real> surface_traction(spatial_dimension);
Real work = 0.0;
Real Epot;
static const UInt N = 100;
for (UInt i = 0; i <= N; ++i) {
- this->model->getExternalForce().clear(); // reset external forces to zero
+ this->model->getExternalForce().zero(); // reset external forces to zero
surface_traction(_x) = (1.0 * i) / N;
if (spatial_dimension == 1) {
// \TODO: this is a hack to work
// around non-implemented
// BC::Neumann::FromTraction for 1D
auto & force = this->model->getExternalForce();
for (auto && pair : zip(make_view(pos, spatial_dimension),
make_view(force, spatial_dimension))) {
auto & posv = std::get<0>(pair);
auto & forcev = std::get<1>(pair);
if (posv(_x) > upper(_x) - 1e-6) {
forcev(_x) = surface_traction(_x);
}
}
} else {
this->model->applyBC(BC::Neumann::FromTraction(surface_traction),
"el_apply_force");
}
/// Solve.
this->model->solveStep();
Epot = this->model->getEnergy("potential");
// In static, this is infinitesimal work!
auto Fds = this->model->getEnergy("external work");
work += Fds; // integrate
/// Check that no work was done for zero force.
if (i == 0) {
EXPECT_NEAR(work, 0.0, 1e-12);
}
}
// Due to the finite integration steps, we make a rather large error
// in our work integration, thus the allowed delta is 1e-2.
EXPECT_NEAR(work, Epot, 1e-2);
}
}
} // namespace
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.hh b/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.hh
index 70fe56eca..e995b6601 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.hh
+++ b/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.hh
@@ -1,125 +1,125 @@
/**
* @file local_material_damage.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Sep 11 2017
*
* @brief Material isotropic elastic
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_LOCAL_MATERIAL_DAMAGE_HH__
-#define __AKANTU_LOCAL_MATERIAL_DAMAGE_HH__
+#ifndef AKANTU_LOCAL_MATERIAL_DAMAGE_HH_
+#define AKANTU_LOCAL_MATERIAL_DAMAGE_HH_
namespace akantu {
class LocalMaterialDamage : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
LocalMaterialDamage(SolidMechanicsModel & model, const ID & id = "");
virtual ~LocalMaterialDamage(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real & damage);
/// compute tangent stiffness
virtual void computeTangentStiffness(__attribute__((unused))
- const ElementType & el_type,
+ ElementType el_type,
__attribute__((unused))
Array<Real> & tangent_matrix,
__attribute__((unused))
GhostType ghost_type = _not_ghost){};
/// compute the potential energy for all elements
void computePotentialEnergy(ElementType el_type);
/// compute the potential energy for on element
inline void computePotentialEnergyOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & epot);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// compute the celerity of wave in the material
inline Real getCelerity(const Element & element) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
private:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// resistance to damage
Real Yd;
/// damage threshold
Real Sd;
/// Bulk modulus
Real kpa;
/// damage internal variable
InternalField<Real> damage;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "local_material_damage_inline_impl.hh"
} // namespace akantu
-#endif /* __AKANTU_LOCAL_MATERIAL_DAMAGE_HH__ */
+#endif /* AKANTU_LOCAL_MATERIAL_DAMAGE_HH_ */
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_finite_deformation.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_finite_deformation.cc
index 5437424f0..71be02ea2 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_finite_deformation.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_finite_deformation.cc
@@ -1,110 +1,110 @@
/* -------------------------------------------------------------------------- */
#include <solid_mechanics_model.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <type_traits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
TEST(TestFiniteDeformation, NotUnit) {
getStaticParser().parse("material_finite_deformation.dat");
const double pi = std::atan(1) * 4;
constexpr int dim = 3;
Mesh mesh(dim);
mesh.read("1_tetrahedron.msh");
SolidMechanicsModel model(mesh);
model.initFull(_analysis_method = _static);
#if DEBUG_TEST
model.addDumpField("displacement");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("strain");
model.dump();
#endif
Matrix<Real> alpha{{0.00, 0.02, 0.03, 0.04},
{0.00, 0.06, 0.07, 0.08},
{0.00, 0.10, 0.11, 0.12}};
auto impose_disp = [&] {
- model.getDisplacement().clear();
+ model.getDisplacement().zero();
for (auto data : zip(make_view(mesh.getNodes(), dim),
make_view(model.getDisplacement(), dim),
make_view(model.getBlockedDOFs(), dim))) {
auto & pos = std::get<0>(data);
auto & dis = std::get<1>(data);
auto & blocked = std::get<2>(data);
blocked.set(true);
dis += Vector<Real>(alpha(0));
for (auto p : arange(dim)) {
dis += Vector<Real>(alpha(1+p)) * pos(p);
}
}
};
impose_disp();
model.solveStep();
#if DEBUG_TEST
model.dump();
#endif
auto stesses0 = model.getMaterial(0).getStress();
auto displacement0 = model.getDisplacement();
auto internal_force0 = model.getInternalForce();
auto theta = pi / 4;
Matrix<Real> R{{1., 0., 0.},
{0., std::cos(theta), -std::sin(theta)},
{0., std::sin(theta), std::cos(theta)}};
impose_disp();
for (auto data : zip(make_view(mesh.getNodes(), dim),
make_view(model.getDisplacement(), dim))) {
auto & X = std::get<0>(data);
auto & u = std::get<1>(data);
u = R * (X + u) - X;
}
model.solveStep();
#if DEBUG_TEST
model.dump();
#endif
for (auto data : zip(make_view(mesh.getNodes(), dim),
make_view(model.getDisplacement(), dim),
make_view(displacement0, dim),
make_view(model.getInternalForce(), dim),
make_view(internal_force0, dim))) {
auto pos = std::get<0>(data);
Vector<Real> refdis(dim, 0.);
refdis += Vector<Real>(alpha(0));
for (auto p : arange(dim)) {
refdis += Vector<Real>(alpha(1+p)) * pos(p);
}
auto dis = std::get<1>(data);
auto dis0 = std::get<2>(data);
auto err = refdis.distance(dis0);
EXPECT_NEAR(err, 0, 1e-14);
auto err1 = dis.distance(R * (pos + dis0) - pos);
EXPECT_NEAR(err1, 0, 1e-14);
auto f = std::get<3>(data);
auto f0 = std::get<4>(data);
auto err3 = f.distance(R * f0);
EXPECT_NEAR(err3, 0, 1e-5);
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.hh b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.hh
index d66a55e69..7308f5ef4 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.hh
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.hh
@@ -1,79 +1,79 @@
/**
* @file custom_non_local_test_material.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 23 2012
* @date last modification: Mon Sep 11 2017
*
* @brief Custom material to test the non local implementation
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
-#ifndef __CUSTOM_NON_LOCAL_TEST_MATERIAL_HH__
-#define __CUSTOM_NON_LOCAL_TEST_MATERIAL_HH__
+#ifndef CUSTOM_NON_LOCAL_TEST_MATERIAL_HH_
+#define CUSTOM_NON_LOCAL_TEST_MATERIAL_HH_
namespace akantu {
template <UInt dim>
class CustomNonLocalTestMaterial
: public MaterialNonLocal<dim, MaterialElastic<dim>> {
public:
using MyNonLocalParent = MaterialNonLocal<dim, MaterialElastic<dim>>;
CustomNonLocalTestMaterial(SolidMechanicsModel & model, const ID & id);
/* ------------------------------------------------------------------------ */
void initMaterial() override;
void computeNonLocalStress(ElementType el_type, GhostType ghost_type);
void computeStress(ElementType el_type, GhostType ghost_type) override;
protected:
void registerNonLocalVariables() override;
/* ------------------------------------------------------------------------ */
void computeNonLocalStresses(GhostType ghost_type) override {
AKANTU_DEBUG_IN();
for (auto & type : this->element_filter.elementTypes(dim, ghost_type)) {
computeNonLocalStress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
public:
void setDamage(Real dam) { this->local_damage.setDefaultValue(dam); }
protected:
InternalField<Real> local_damage;
InternalField<Real> damage;
};
} // namespace akantu
-#endif /* __CUSTOM_NON_LOCAL_TEST_MATERIAL_HH__ */
+#endif /* CUSTOM_NON_LOCAL_TEST_MATERIAL_HH_ */
diff --git a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh
index 1ac64bbd6..3f2cd46fb 100644
--- a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh
+++ b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh
@@ -1,129 +1,129 @@
/**
* @file test_solid_mechanics_model_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
* @date last modification: Tue Feb 20 2018
*
* @brief Main solif mechanics test file
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "solid_mechanics_model.hh"
#include "test_gtest_utils.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TEST_SOLID_MECHANICS_MODEL_FIXTURE_HH__
-#define __AKANTU_TEST_SOLID_MECHANICS_MODEL_FIXTURE_HH__
+#ifndef AKANTU_TEST_SOLID_MECHANICS_MODEL_FIXTURE_HH_
+#define AKANTU_TEST_SOLID_MECHANICS_MODEL_FIXTURE_HH_
using namespace akantu;
// This fixture uses very small meshes with a volume of 1.
template <typename type_> class TestSMMFixture : public ::testing::Test {
public:
static constexpr ElementType type = type_::value;
static constexpr size_t spatial_dimension =
ElementClass<type>::getSpatialDimension();
void SetUp() override {
this->mesh = std::make_unique<Mesh>(this->spatial_dimension);
auto prank = Communicator::getStaticCommunicator().whoAmI();
if (prank == 0) {
this->mesh->read(this->mesh_file);
if(spatial_dimension > 1 and mesh->getNbElement(spatial_dimension - 1) == 0) {
MeshUtils::buildFacets(*this->mesh);
}
}
mesh->distribute();
SCOPED_TRACE(std::to_string(this->type).c_str());
model = std::make_unique<SolidMechanicsModel>(*mesh, _all_dimensions,
std::to_string(this->type));
}
void initModel(const ID & input, const AnalysisMethod & analysis_method) {
getStaticParser().parse(input);
this->model->initFull(_analysis_method = analysis_method);
if (analysis_method != _static) {
auto time_step = this->model->getStableTimeStep() / 10.;
this->model->setTimeStep(time_step);
}
// std::cout << "timestep: " << time_step << std::endl;
if (this->dump_paraview) {
std::stringstream base_name;
base_name << "bar" << analysis_method << this->type;
this->model->setBaseName(base_name.str());
this->model->addDumpFieldVector("displacement");
this->model->addDumpFieldVector("blocked_dofs");
if (analysis_method != _static) {
this->model->addDumpField("velocity");
this->model->addDumpField("acceleration");
}
if (this->mesh->isDistributed()) {
this->model->addDumpField("partitions");
}
this->model->addDumpFieldVector("external_force");
this->model->addDumpFieldVector("internal_force");
this->model->addDumpField("stress");
this->model->addDumpField("strain");
}
}
void TearDown() override {
model.reset(nullptr);
mesh.reset(nullptr);
}
protected:
std::string mesh_file{std::to_string(this->type) + ".msh"};
std::unique_ptr<Mesh> mesh;
std::unique_ptr<SolidMechanicsModel> model;
bool dump_paraview{false};
};
template <typename type_> constexpr ElementType TestSMMFixture<type_>::type;
template <typename type_>
constexpr size_t TestSMMFixture<type_>::spatial_dimension;
template <typename T>
using is_not_pentahedron =
aka::negation<aka::disjunction<is_element<T, _pentahedron_6>,
is_element<T, _pentahedron_15>>>;
using TestElementTypesFiltered =
tuple_filter_t<is_not_pentahedron, TestElementTypes>;
// using gtest_element_types = gtest_list_t<TestElementTypesFiltered>;
using gtest_element_types = gtest_list_t<TestElementTypes>;
TYPED_TEST_SUITE(TestSMMFixture, gtest_element_types);
-#endif /* __AKANTU_TEST_SOLID_MECHANICS_MODEL_FIXTURE_HH__ */
+#endif /* AKANTU_TEST_SOLID_MECHANICS_MODEL_FIXTURE_HH_ */
diff --git a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_large_rotation.cc b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_large_rotation.cc
index b554639d0..5db4f541a 100644
--- a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_large_rotation.cc
+++ b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_large_rotation.cc
@@ -1,119 +1,119 @@
/**
* @file test_solid_mechanics_model_material_eigenstrain.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Apr 16 2011
* @date last modification: Thu Feb 01 2018
*
* @brief test the internal field prestrain
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_utils.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material_elastic.dat", argc, argv);
UInt dim = 3;
/// load mesh
Mesh mesh(dim);
mesh.read("cube_3d_tet_4.msh");
/// declaration of model
SolidMechanicsModel model(mesh);
/// model initialization
// model.initFull(_analysis_method=akantu._explicit_lumped_mass)
model.initFull(_analysis_method = _implicit_dynamic);
// model.initFull(_analysis_method = akantu._implicit_dynamic)
auto & solver = model.getNonLinearSolver();
solver.set("threshold", 1e-4);
solver.set("max_iterations", 100);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
model.setBaseName("waves");
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("acceleration");
model.addDumpFieldVector("velocity");
model.addDumpFieldVector("internal_force");
model.addDumpFieldVector("external_force");
model.addDumpField("strain");
model.addDumpField("stress");
model.addDumpField("blocked_dofs");
/* ------------------------------------------------------------------------ */
// get mass center
/* ------------------------------------------------------------------------ */
model.assembleMass();
auto & M = model.getDOFManager().getMatrix("M");
Array<Real> _mass(M.size(), 1);
- _mass.clear();
+ _mass.zero();
std::cout << "AAAA " << M.size() << std::endl;
std::cout << "AAAA " << _mass.size() << std::endl;
for (UInt i = 0; i < M.size(); ++i) {
for (UInt j = 0; j < M.size(); ++j) {
std::cout << i << ", " << j <<std::endl;
_mass[i] += M(i, j);
}
}
std::array<Real, 3> mass_center{0., 0., 0.};
std::cout << "AAAA " << _mass.size() << std::endl;
Real total_mass = 0.;
for (UInt i = 0; i < _mass.size(); ++i) {
for (UInt j = 0; j < 3; ++j) {
mass_center[j] += _mass(i * 3 + j);
total_mass += _mass(i * 3 + j);
}
}
mass_center[0] /= total_mass / 3.;
mass_center[1] /= total_mass / 3.;
mass_center[2] /= total_mass / 3.;
std::cout << "total mass" << total_mass << std::endl;
std::cout << mass_center[0] << " " << mass_center[1] << " " << mass_center[2]
<< std::endl;
/* ---------------------------------------------------------------------- */
/* Dynamic evolution */
/* ---------------------------------------------------------------------- */
model.dump();
model.solveStep();
model.dump();
std::cout << "Converged in " << Int(solver.get("nb_iterations")) << " ("
<< Real(solver.get("error")) << ")" << std::endl;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_3.cc b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_3.cc
index 72a034553..bdff772d6 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_3.cc
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_3.cc
@@ -1,101 +1,101 @@
/**
* @file test_structural_mechanics_model_bernoulli_beam_3.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Fri Feb 09 2018
*
* @brief Computation of the analytical exemple 1.1 in the TGC vol 6
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_structural_mechanics_model_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
class TestStructBernoulli3
: public TestStructuralFixture<element_type_t<_bernoulli_beam_3>> {
using parent = TestStructuralFixture<element_type_t<_bernoulli_beam_3>>;
public:
void readMesh(std::string filename) override {
parent::readMesh(filename);
auto & normals =
this->mesh->getElementalData<Real>("extra_normal")
.alloc(0, parent::spatial_dimension, parent::type, _not_ghost);
Vector<Real> normal = {0, 0, 1};
normals.push_back(normal);
normal = {0, 0, 1};
normals.push_back(normal);
}
void addMaterials() override {
StructuralMaterial mat;
mat.E = 1;
mat.Iz = 1;
mat.Iy = 1;
mat.A = 1;
mat.GJ = 1;
this->model->addMaterial(mat);
}
void setDirichlets() override {
// Boundary conditions (blocking all DOFs of nodes 2 & 3)
auto boundary = ++this->model->getBlockedDOFs().begin(parent::ndof);
// clang-format off
*boundary = {true, true, true, true, true, true}; ++boundary;
*boundary = {true, true, true, true, true, true}; ++boundary;
// clang-format on
}
void setNeumanns() override {
// Forces
Real P = 1; // N
auto & forces = this->model->getExternalForce();
- forces.clear();
+ forces.zero();
forces(0, 2) = -P; // vertical force on first node
}
void assignMaterials() override {
model->getElementMaterial(parent::type).set(0);
}
};
/* -------------------------------------------------------------------------- */
TEST_F(TestStructBernoulli3, TestDisplacements) {
model->solveStep();
auto vz = model->getDisplacement()(0, 2);
auto thy = model->getDisplacement()(0, 4);
auto thx = model->getDisplacement()(0, 3);
auto thz = model->getDisplacement()(0, 5);
Real tol = Math::getTolerance();
EXPECT_NEAR(vz, -5. / 48, tol);
EXPECT_NEAR(thy, -std::sqrt(2) / 8, tol);
EXPECT_NEAR(thz, 0, tol);
EXPECT_NEAR(thx, 0, tol);
}
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_dynamics.cc b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_dynamics.cc
index 34a153b8a..2a7a43402 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_dynamics.cc
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_dynamics.cc
@@ -1,207 +1,207 @@
/**
* @file test_structural_mechanics_model_bernoulli_beam_dynamics.cc
*
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
*
* @date creation: Mon Jul 07 2014
* @date last modification: Wed Feb 03 2016
*
* @brief Test for _bernouilli_beam in dynamic
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh_struct.hh"
#include "structural_mechanics_model.hh"
#include <iostream>
using namespace akantu;
/* -------------------------------------------------------------------------- */
#define TYPE _bernoulli_beam_2
static Real analytical_solution(Real time, Real L, Real rho, Real E,
__attribute__((unused)) Real A, Real I,
Real F) {
Real omega = M_PI * M_PI / L / L * sqrt(E * I / rho);
Real sum = 0.;
UInt i = 5;
for (UInt n = 1; n <= i; n += 2) {
sum += (1. - cos(n * n * omega * time)) / pow(n, 4);
}
return 2. * F * pow(L, 3) / pow(M_PI, 4) / E / I * sum;
}
// load
const Real F = 0.5e4;
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
Mesh beams(2);
debug::setDebugLevel(dblWarning);
const ElementType type = _bernoulli_beam_2;
/* --------------------------------------------------------------------------
*/
// Mesh
UInt nb_element = 8;
UInt nb_nodes = nb_element + 1;
Real total_length = 10.;
Real length = total_length / nb_element;
Real heigth = 1.;
Array<Real> & nodes = const_cast<Array<Real> &>(beams.getNodes());
nodes.resize(nb_nodes);
beams.addConnectivityType(type);
Array<UInt> & connectivity =
const_cast<Array<UInt> &>(beams.getConnectivity(type));
connectivity.resize(nb_element);
beams.initNormals();
Array<Real> & normals = const_cast<Array<Real> &>(beams.getNormals(type));
normals.resize(nb_element);
for (UInt i = 0; i < nb_nodes; ++i) {
nodes(i, 0) = i * length;
nodes(i, 1) = 0;
}
for (UInt i = 0; i < nb_element; ++i) {
connectivity(i, 0) = i;
connectivity(i, 1) = i + 1;
}
/* --------------------------------------------------------------------------
*/
// Materials
StructuralMechanicsModel model(beams);
StructuralMaterial mat1;
mat1.E = 120e6;
mat1.rho = 1000;
mat1.A = heigth;
mat1.I = heigth * heigth * heigth / 12;
model.addMaterial(mat1);
/* --------------------------------------------------------------------------
*/
// Forces
// model.initFull();
model.initFull(StructuralMechanicsModelOptions(_implicit_dynamic));
const Array<Real> & position = beams.getNodes();
Array<Real> & forces = model.getForce();
Array<Real> & displacement = model.getDisplacement();
Array<bool> & boundary = model.getBlockedDOFs();
UInt node_to_print = -1;
- forces.clear();
- displacement.clear();
- // boundary.clear();
+ forces.zero();
+ displacement.zero();
+ // boundary.zero();
// model.getElementMaterial(type)(i,0) = 0;
// model.getElementMaterial(type)(i,0) = 1;
for (UInt i = 0; i < nb_element; ++i) {
model.getElementMaterial(type)(i, 0) = 0;
}
for (UInt n = 0; n < nb_nodes; ++n) {
Real x = position(n, 0);
// Real y = position(n, 1);
if (Math::are_float_equal(x, total_length / 2.)) {
forces(n, 1) = F;
node_to_print = n;
}
}
std::ofstream pos;
pos.open("position.csv");
if (!pos.good()) {
std::cerr << "Cannot open file" << std::endl;
exit(EXIT_FAILURE);
}
pos << "id,time,position,solution" << std::endl;
// model.computeForcesFromFunction<type>(load, _bft_traction)
/* --------------------------------------------------------------------------
*/
// Boundary conditions
// true ~ displacement is blocked
boundary(0, 0) = true;
boundary(0, 1) = true;
boundary(nb_nodes - 1, 1) = true;
/* --------------------------------------------------------------------------
*/
// "Solve"
Real time = 0;
model.assembleStiffnessMatrix();
model.assembleMass();
model.dump();
model.getStiffnessMatrix().saveMatrix("K.mtx");
model.getMassMatrix().saveMatrix("M.mt");
Real time_step = 1e-4;
model.setTimeStep(time_step);
std::cout << "Time"
<< " | "
<< "Mid-Span Displacement" << std::endl;
/// time loop
for (UInt s = 1; time < 0.64; ++s) {
model.solveStep<_scm_newton_raphson_tangent,
SolveConvergenceCriteria::_increment>(1e-12, 1000);
pos << s << "," << time << "," << displacement(node_to_print, 1) << ","
<< analytical_solution(s * time_step, total_length, mat1.rho, mat1.E,
mat1.A, mat1.I, F)
<< std::endl;
// pos << s << "," << time << "," << displacement(node_to_print, 1) <<
// "," << analytical_solution(s*time_step) << std::endl;
time += time_step;
if (s % 100 == 0)
std::cout << time << " | " << displacement(node_to_print, 1)
<< std::endl;
model.dump();
}
pos.close();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
index 570579769..d254434cf 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
@@ -1,111 +1,111 @@
/**
* @file test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Wed Feb 21 2018
*
* @brief Computation of the analytical exemple 1.1 in the TGC vol 6
*
*
* Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix.hh"
#include "test_structural_mechanics_model_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
using namespace akantu;
/* -------------------------------------------------------------------------- */
class TestStructDKT18 : public TestStructuralFixture<
element_type_t<_discrete_kirchhoff_triangle_18>> {
using parent =
TestStructuralFixture<element_type_t<_discrete_kirchhoff_triangle_18>>;
public:
void addMaterials() override {
mat.E = 1;
mat.t = 1;
mat.nu = 0.3;
this->model->addMaterial(mat);
}
void assignMaterials() override {
auto & materials = this->model->getElementMaterial(parent::type);
std::fill(materials.begin(), materials.end(), 0);
}
void setDirichlets() override {
this->model->getBlockedDOFs().set(true);
auto center_node = this->model->getBlockedDOFs().end(parent::ndof) - 1;
*center_node = {false, false, false, false, false, true};
- this->model->getDisplacement().clear();
+ this->model->getDisplacement().zero();
auto disp = ++this->model->getDisplacement().begin(parent::ndof);
// Displacement field from Batoz Vol. 2 p. 392
// with theta to beta correction from discrete Kirchhoff condition
// see also the master thesis of Michael Lozano
// clang-format off
// This displacement field tests membrane and bending modes
*disp = {40, 20, -800 , -20, 40, 0}; ++disp;
*disp = {50, 40, -1400, -40, 50, 0}; ++disp;
*disp = {10, 20, -200 , -20, 10, 0}; ++disp;
// This displacement tests the bending mode
// *disp = {0, 0, -800 , -20, 40, 0}; ++disp;
// *disp = {0, 0, -1400, -40, 50, 0}; ++disp;
// *disp = {0, 0, -200 , -20, 10, 0}; ++disp;
// This displacement tests the membrane mode
// *disp = {40, 20, 0, 0, 0, 0}; ++disp;
// *disp = {50, 40, 0, 0, 0, 0}; ++disp;
// *disp = {10, 20, 0, 0, 0, 0}; ++disp;
// clang-format on
}
void setNeumanns() override {}
protected:
StructuralMaterial mat;
};
/* -------------------------------------------------------------------------- */
// Batoz Vol 2. patch test, ISBN 2-86601-259-3
TEST_F(TestStructDKT18, TestDisplacements) {
model->solveStep();
Vector<Real> solution = {22.5, 22.5, -337.5, -22.5, 22.5, 0};
auto nb_nodes = this->model->getDisplacement().size();
Vector<Real> center_node_disp =
model->getDisplacement().begin(solution.size())[nb_nodes - 1];
auto error = solution - center_node_disp;
EXPECT_NEAR(error.norm<L_2>(), 0., 1e-12);
}
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh
index dd8906230..b1bbc29bb 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh
@@ -1,104 +1,104 @@
/**
* @file test_structural_mechanics_model_fixture.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Tue Nov 14 2017
* @date last modification: Fri Feb 09 2018
*
* @brief Main test for structural model
*
*
* Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class_structural.hh"
#include "structural_mechanics_model.hh"
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_TEST_STRUCTURAL_MECHANICS_MODEL_FIXTURE_HH__
-#define __AKANTU_TEST_STRUCTURAL_MECHANICS_MODEL_FIXTURE_HH__
+#ifndef AKANTU_TEST_STRUCTURAL_MECHANICS_MODEL_FIXTURE_HH_
+#define AKANTU_TEST_STRUCTURAL_MECHANICS_MODEL_FIXTURE_HH_
using namespace akantu;
template <typename type_> class TestStructuralFixture : public ::testing::Test {
public:
static constexpr const ElementType type = type_::value;
static constexpr const size_t spatial_dimension =
ElementClass<type>::getSpatialDimension();
static const UInt ndof = ElementClass<type>::getNbDegreeOfFreedom();
void SetUp() override {
const auto spatial_dimension = this->spatial_dimension;
mesh = std::make_unique<Mesh>(spatial_dimension);
readMesh(makeMeshName());
std::stringstream element_type;
element_type << this->type;
model = std::make_unique<StructuralMechanicsModel>(*mesh, _all_dimensions,
element_type.str());
addMaterials();
model->initFull();
assignMaterials();
setDirichlets();
setNeumanns();
}
virtual void readMesh(std::string filename) {
mesh->read(filename, _miot_gmsh_struct);
}
virtual std::string makeMeshName() {
std::stringstream element_type;
element_type << type;
SCOPED_TRACE(element_type.str().c_str());
return element_type.str() + ".msh";
}
void TearDown() override {
model.reset(nullptr);
mesh.reset(nullptr);
}
virtual void addMaterials() = 0;
virtual void assignMaterials() = 0;
virtual void setDirichlets() = 0;
virtual void setNeumanns() = 0;
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<StructuralMechanicsModel> model;
};
template <typename type_>
constexpr ElementType TestStructuralFixture<type_>::type;
template <typename type_>
constexpr size_t TestStructuralFixture<type_>::spatial_dimension;
template <typename type_> const UInt TestStructuralFixture<type_>::ndof;
// using types = gtest_list_t<StructuralTestElementTypes>;
// TYPED_TEST_SUITE(TestStructuralFixture, types);
-#endif /* __AKANTU_TEST_STRUCTURAL_MECHANICS_MODEL_FIXTURE_HH__ */
+#endif /* AKANTU_TEST_STRUCTURAL_MECHANICS_MODEL_FIXTURE_HH_ */
diff --git a/test/test_python_interface/test_common.cc b/test/test_python_interface/test_common.cc
index 50a22949e..8f66670ed 100644
--- a/test/test_python_interface/test_common.cc
+++ b/test/test_python_interface/test_common.cc
@@ -1,121 +1,121 @@
/* -------------------------------------------------------------------------- */
#include "py_akantu.hh"
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
namespace _aka = akantu;
std::map<long, std::shared_ptr<_aka::Array<_aka::Real>>> arrays;
std::map<long, std::shared_ptr<_aka::Vector<_aka::Real>>> vectors;
std::map<long, std::shared_ptr<_aka::Matrix<_aka::Real>>> matrices;
PYBIND11_MODULE(py11_akantu_test_common, mod) {
mod.doc() = "Akantu Test function for common ";
mod.def("createArray",
[&](_aka::UInt size, _aka::UInt nb_components) {
auto ptr =
std::make_shared<_aka::Array<_aka::Real>>(size, nb_components);
- ptr->clear();
+ ptr->zero();
long addr = (long)ptr->storage();
py::print("initial pointer: " + std::to_string(addr));
arrays[addr] = ptr;
return std::tuple<long, _aka::Array<_aka::Real> &>(addr, *ptr);
},
py::return_value_policy::reference);
mod.def("getArray",
[&](long addr) -> _aka::Array<_aka::Real> & {
auto & array = *arrays[addr];
py::print("gotten pointer: " +
std::to_string((long)array.storage()));
return array;
},
py::return_value_policy::reference);
mod.def("copyArray",
[&](long addr) -> _aka::Array<_aka::Real> {
auto & array = *arrays[addr];
py::print("gotten pointer: " +
std::to_string((long)array.storage()));
return array;
},
py::return_value_policy::copy);
mod.def("getRawPointerArray", [](_aka::Array<_aka::Real> & _data) {
py::print("received proxy: " + std::to_string((long)&_data));
py::print("raw pointer: " + std::to_string((long)_data.storage()));
return (long)_data.storage();
});
mod.def("createVector",
[&](_aka::UInt size) {
auto ptr = std::make_shared<_aka::Vector<_aka::Real>>(size);
- ptr->clear();
+ ptr->zero();
long addr = (long)ptr->storage();
py::print("initial pointer: " + std::to_string(addr));
vectors[addr] = ptr;
return std::tuple<long, _aka::Vector<_aka::Real> &>(addr, *ptr);
},
py::return_value_policy::reference);
mod.def("getVector",
[&](long addr) -> _aka::Vector<_aka::Real> & {
auto & vector = *vectors[addr];
py::print("gotten pointer: " +
std::to_string((long)vector.storage()));
return vector;
},
py::return_value_policy::reference);
mod.def("copyVector",
[&](long addr) -> _aka::Vector<_aka::Real> {
auto & vector = *vectors[addr];
py::print("gotten pointer: " +
std::to_string((long)vector.storage()));
return vector;
},
py::return_value_policy::copy);
mod.def("getRawPointerVector", [](_aka::Vector<_aka::Real> & _data) {
py::print("received proxy: " + std::to_string((long)&_data));
py::print("raw pointer: " + std::to_string((long)_data.storage()));
return (long)_data.storage();
});
mod.def("createMatrix",
[&](_aka::UInt size1, _aka::UInt size2) {
auto ptr = std::make_shared<_aka::Matrix<_aka::Real>>(size1, size2);
- ptr->clear();
+ ptr->zero();
long addr = (long)ptr->storage();
py::print("initial pointer: " + std::to_string(addr));
matrices[addr] = ptr;
return std::tuple<long, _aka::Matrix<_aka::Real> &>(addr, *ptr);
},
py::return_value_policy::reference);
mod.def("getMatrix",
[&](long addr) -> _aka::Matrix<_aka::Real> & {
auto & matrix = *matrices[addr];
py::print("gotten pointer: " +
std::to_string((long)matrix.storage()));
return matrix;
},
py::return_value_policy::reference);
mod.def("copyMatrix",
[&](long addr) -> _aka::Matrix<_aka::Real> {
auto & matrix = *matrices[addr];
py::print("gotten pointer: " +
std::to_string((long)matrix.storage()));
return matrix;
},
py::return_value_policy::copy);
mod.def("getRawPointerMatrix", [](_aka::Matrix<_aka::Real> & _data) {
py::print("received proxy: " + std::to_string((long)&_data));
py::print("raw pointer: " + std::to_string((long)_data.storage()));
return (long)_data.storage();
});
} // Module akantu_test_common
diff --git a/third-party/iohelper/src/base64.hh b/third-party/iohelper/src/base64.hh
index 63576314c..555a37dbe 100644
--- a/third-party/iohelper/src/base64.hh
+++ b/third-party/iohelper/src/base64.hh
@@ -1,438 +1,437 @@
/**
* @file base64.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Wed Nov 13 2013
*
* @brief header for base64 handling
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHLPER_BASE64_H__
-#define __IOHLPER_BASE64_H__
+#ifndef IOHELPER_BASE64_H_
+#define IOHELPER_BASE64_H_
/* -------------------------------------------------------------------------- */
#include <vector>
#include "file_manager.hh"
#ifdef USING_ZLIB
#include <zlib.h>
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
#if defined(__INTEL_COMPILER)
#pragma warning ( push )
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
#endif //defined(__INTEL_COMPILER)
/** Class that allow to push binary data
in base64 format to any file.
This class is mainly used by the paraview helper
to create binary XML VTK files.
The conversion is a 4/3 size conversion. */
class Base64Writer{
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Base64Writer(File & f);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
//! for any packet in base64 a little header is used that is an int = nbBytes written
void WriteHeader();
//! this is used to allocate the memory for the final count of bytes
void CreateHeader();
//! when all stream is ready buffer is sent to file
inline void DumpToFile();
//! empty temporary buffer
void ClearBuffer();
- template<typename T>
- inline void push(T c);
+ template <typename T> inline void push(T t);
//! notify that we don't want to add any data. Closing the current buffer
void finish();
//! decode 3 bytes from 4 Base64 bytes (4/3 ratio)
int Decode(char c0,char c1,char c2,char c3,
char * r0,char * r1,char * r2);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
//! push to file a Byte
inline void PushByteInBase64(unsigned char c);
//! when 4 bytes are ready they are dumped to buffer by this function
inline void dumpToBuffer();
//! initialisation process
inline void InitBase64Stuff();
//! primitive function to push bytes to file
//void ochar(int c);
//! decoding table
char dtable[256];
//! encoding table
char etable[256];
//! stage in conversion process(1,2 or 3)
int n;
//! used to code/decode
unsigned char igroup[3],ogroup[4];
//!unused
int linelength;
//!unused
// int maxlinelength;
//! LM file descriptor
File & file;
//! buffer to cache data
std::vector<unsigned char> buffer;
//! number of bytes written to buffer
long nbBytes;
//! for rewind need o floating index
int start;
};
/* -------------------------------------------------------------------------- */
template<typename T> inline void Base64Writer::push(T t) {
auto * c = (unsigned char *)&t;
for (unsigned int i = 0 ; i < sizeof(T) ; ++i){
this->PushByteInBase64(c[i]);
}
}
-template<> inline void Base64Writer::push<char *>(char * str) {
- auto * c = (unsigned char *)str;
+template<> inline void Base64Writer::push<char *>(char * t) {
+ auto * c = (unsigned char *)t;
for (unsigned int i = 0 ; i < 512 ; ++i){
- if (str[i] == '\0') break;
+ if (t[i] == '\0') {
+ break;
+ }
PushByteInBase64(c[i]);
}
}
inline void Base64Writer::InitBase64Stuff(){
memset(dtable,0xFF,256);
memset(etable,0xFF,256);
for(int i=0;i<9;i++){
etable[i]= (char)('A'+i);
dtable[0+etable[i]] = (char)i;
etable[i+9]= (char)('J'+i);
dtable[(0+etable[i+9])] = (char)(i+9);
etable[26+i]= (char)('a'+i);
dtable[(0+etable[26+i])] = (char)(i + 26);
etable[(26+i+9)]= (char)('j'+i);
dtable[(0+etable[26+i+9])] = (char)(i + 26 + 9);
}
for(int i= 0;i<8;i++){
etable[i+18]= (char)('S'+i);
dtable[(0+etable[i+18])] = (char)(i + 18);
etable[26+i+18]= (char)('s'+i);
dtable[(0+etable[26+i+18])] = (char)(26 + i + 18);
}
for(char i= 0;i<10;i++){
etable[52+i]= (char)('0'+i);
dtable[(0+etable[i+52])] = (char)(i + 52);
}
etable[62]= '+';
dtable[0+etable[62]] = 62;
etable[63]= '/';
dtable[0+etable[63]] = 63;
}
/* -------------------------------------------------------------------------- */
// inline void Base64Writer::PushIntegerInBase64(int d){
// // DUMP("pushing " << d << " ( n = " << n << " )",DBG_ALL);
// unsigned char * c = (unsigned char*)&d;
// for (unsigned int i = 0 ; i < sizeof(int) ; ++i){
// PushByteInBase64(c[i]);
// }
// }
// /* -------------------------------------------------------------------------- */
// inline void Base64Writer::PushStrInBase64(char * str){
// unsigned char * c = (unsigned char*)str;
// for (unsigned int i = 0 ; i < 512 ; ++i){
// if (str[i] == '\0') break;
// PushByteInBase64(c[i]);
// }
// }
// /* -------------------------------------------------------------------------- */
// inline void Base64Writer::PushDoubleInBase64(double d){
// // DUMP("pushing double " << d << " as " << sizeof(double) << " bytes",DBG_ALL);
// unsigned char * c = (unsigned char*)&d;
// for (unsigned int i = 0 ; i < sizeof(double) ; ++i){
// PushByteInBase64(c[i]);
// }
// }
// /* -------------------------------------------------------------------------- */
inline void Base64Writer::PushByteInBase64(unsigned char c){
//initialise les blocs
// DUMP("pushing byte " << (int) c << " at position " << n,DBG_ALL);
if (n == 0){
igroup[0]= 0;
igroup[1]= 0;
igroup[2]= 0;
}
igroup[n]= c;
++n;
if(n == 3){
dumpToBuffer();
}
nbBytes += 1;
}
/* -------------------------------------------------------------------------- */
inline void Base64Writer::finish(){
- if (n == 0) return;
+ if (n == 0) {
+ return;
+ }
dumpToBuffer();
linelength = 0;
}
/* -------------------------------------------------------------------------- */
inline void Base64Writer::dumpToBuffer(){
if(n<3){
igroup[2]= 0;
if(n<2){
igroup[1]= 0;
}
}
//DUMP("premiere partie en base 64 : " << (igroup[0]>>2),DBG_ALL);
int index = igroup[0]>>2;
ogroup[0]= etable[index];
//DUMP("deuxieme partie en base 64 : " << (((igroup[0]&3)<<4)|(igroup[1]>>4)),DBG_ALL);
index = ((igroup[0]&3)<<4)|(igroup[1]>>4);
ogroup[1]= etable[index];
//DUMP("troisieme partie en base 64 : " << (((igroup[1]&0xF)<<2)|(igroup[2]>>6)),DBG_ALL);
index = ((igroup[1]&0xF)<<2)|(igroup[2]>>6);
ogroup[2]= etable[index];
//DUMP("last partie en base 64 : " << (igroup[2]&0x3F),DBG_ALL);
index = igroup[2]&0x3F;
ogroup[3]= etable[index];
if(n<3){
ogroup[3]= '=';
if(n<2){
ogroup[2]= '=';
}
}
for(int i= 0;i<4;i++){
//DUMP("dumped to buffer " << ogroup[i],DBG_ALL);
- if (start == -1)
+ if (start == -1) {
buffer.push_back(ogroup[i]);
- else{
+ } else {
buffer[start] = ogroup[i];
++start;
}
}
//remise a zero du compteur
n = 0;
}
/* inline void Base64Writer::ochar(int c) */
/* { */
/* if(file.dumpchar(c)==-1){ */
/* FATAL("error while writing to file (in compressed mode) ! no more space ?"); */
/* } */
/* linelength++; */
/* } */
/* -------------------------------------------------------------------------- */
inline int Base64Writer::Decode(char c0,char c1,char c2,char c3,
char * r0,char * r1,char * r2){
-
- unsigned char d0, d1, d2, d3;
-
- d0 = dtable[0+c0];
- d1 = dtable[0+c1];
- d2 = dtable[0+c2];
- d3 = dtable[0+c3];
-
-
+ auto d0 = dtable[0+c0];
+ auto d1 = dtable[0+c1];
+ auto d2 = dtable[0+c2];
+ auto d3 = dtable[0+c3];
//DUMP("d0 " << (int)d0 << " d1 " << (int)d1 << " d2 " << (int)d2 << " d3 " << (int)d3,DBG_ALL);
// Decode the 3 bytes
*r0 = (char)(((d0 << 2) & 0xFC) | ((d1 >> 4) & 0x03));
*r1 = (char)(((d1 << 4) & 0xF0) | ((d2 >> 2) & 0x0F));
*r2 = (char)(((d2 << 6) & 0xC0) | ((d3 >> 0) & 0x3F));
//DUMP("r0 " << (int)*r0 << " r1 " << (int)*r1 << " r2 " << (int)*r2,DBG_ALL);
// Return the number of bytes actually decoded
if (c2 == '=')
{
return 1;
}
if (c3 == '=')
{
return 2;
}
return 3;
}
/* -------------------------------------------------------------------------- */
inline void Base64Writer::WriteHeader(){
// if (bflag == BASE64){
// char byteC[8];
char byte[6];
finish();
/* long save_offset; */
/* save_offset = file.tell(); */
/* file.seek(header_offset,SEEK_SET); */
/* //reread the 4 bytes precedently written */
/* file.read(byteC,sizeof(char),4); */
/* DUMP("la chaine saisie " << byteC[0] << " " << byteC[1] << " " << byteC[2] << " " << byteC[3]); */
/* b64.Decode(byteC[0],byteC[0],byteC[0],byteC[0], */
/* byte,byte+1,byte+2); */
//DUMP("la chaine saisie " << buffer[0] << " " << buffer[1] << " " << buffer[2] << " " << buffer[3],DBG_ALL);
Decode(buffer[0], buffer[0], buffer[0], buffer[0],
byte, byte + 1, byte + 2);
/* file.read(byteC+4,sizeof(char),4); */
/* DUMP("la chaine saisie " << byteC[4] << " " << byteC[5] << " " << byteC[6] << " " << byteC[7]); */
/* int nb = b64.Decode(byteC[4],byteC[5],byteC[6],byteC[7], */
/* byte+3,byte+4,byte+5); */
//DUMP("la chaine saisie " << buffer[4] << " " << buffer[5] << " " << buffer[6] << " " << buffer[7],DBG_ALL);
int nb = Decode(buffer[4],buffer[5],buffer[6],buffer[7],
byte + 3,byte + 4,byte + 5);
/* //je me replace au debut du header */
/* file.seek(header_offset,SEEK_SET); */
/* //je viens de relire 6 octets */
/* //les quatres premiers seulement sont a changer */
//DUMP("placing number of writen bytes : " << nbBytes << " " << buffer.size(),DBG_ALL);
- int temp = nbBytes;
+ auto temp = static_cast<int>(nbBytes);
start = 0;
push(temp);
- if (nb > 1)
+ if (nb > 1) {
push(byte[4]);
- if (nb > 2)
+ }
+ if (nb > 2) {
push(byte[5]);
+ }
start = -1;
nbBytes = temp;
finish();
DumpToFile();
}
/* -------------------------------------------------------------------------- */
inline void Base64Writer::DumpToFile(){
file.write((char*)&buffer[0],buffer.size());
}
/* -------------------------------------------------------------------------- */
inline void Base64Writer::ClearBuffer(){
buffer.clear();
nbBytes = 0;
}
/* -------------------------------------------------------------------------- */
inline void Base64Writer::CreateHeader(){
ClearBuffer();
push<int>(0);
}
/* -------------------------------------------------------------------------- */
inline Base64Writer::Base64Writer(File & f):
file(f){
linelength = 0;
InitBase64Stuff();
n = 0;
start = -1;
igroup[0] = 0;
igroup[1] = 0;
igroup[2] = 0;
ogroup[0] = 0;
ogroup[1] = 0;
ogroup[2] = 0;
ogroup[3] = 0;
}
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( pop )
#endif //defined(__INTEL_COMPILER)
-__END_IOHELPER__
-
+}
-#endif /* __IOHLPER_BASE64_H__ */
+#endif /* IOHELPER_BASE64_H_ */
diff --git a/third-party/iohelper/src/container_array.hh b/third-party/iohelper/src/container_array.hh
index 2dcdd86f3..4e56223ff 100644
--- a/third-party/iohelper/src/container_array.hh
+++ b/third-party/iohelper/src/container_array.hh
@@ -1,137 +1,146 @@
/**
* @file container_array.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Oct 12 2012
* @date last modification: Tue Feb 05 2013
*
* @brief container array header
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
+/* -------------------------------------------------------------------------- */
+#include "iohelper_common.hh"
+/* -------------------------------------------------------------------------- */
-#ifndef __IOHELPER_CONTAINER_ARRAY_HH__
-#define __IOHELPER_CONTAINER_ARRAY_HH__
+#ifndef IOHELPER_CONTAINER_ARRAY_HH_
+#define IOHELPER_CONTAINER_ARRAY_HH_
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename T>
class ContainerArray {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
class iterator: public ::iohelper::iterator<T, iterator> {
public:
iterator(T * ptr, UInt dimension, UInt increment, const ElemType & el_type = MAX_ELEM_TYPE){
this->ptr = ptr;
this->increment = increment;
this->dimension = dimension;
this->el_type = el_type;
};
- bool operator!=(const iterator & it) const {
+ bool operator!=(const iterator & it) const override {
return it.ptr != this->ptr;
};
- iterator & operator++() { ptr += increment; return *this; };
+ iterator & operator++() override {
+ ptr += increment;
+ return *this;
+ };
- IOHelperVector<T> operator*(){
- return IOHelperVector<T>(ptr, increment);
+ IOHelperVector<T> operator*() override {
+ return IOHelperVector<T>(ptr, increment);
};
- virtual ElemType element_type() { return el_type; }
-
+ ElemType element_type() override { return el_type; }
+
private:
T * ptr;
UInt increment;
UInt dimension;
ElemType el_type;
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ContainerArray(T * data, UInt dimension, UInt size, UInt stride=1,ElemType el_type = MAX_ELEM_TYPE){
this->data = data;
this->dimension = dimension;
- if (this->data == NULL) this->_size = 0;
- else this->_size = size;
+ if (this->data == NULL) {
+ this->_size = 0;
+ } else {
+ this->_size = size;
+ }
this->stride = stride;
this->el_type = el_type;
};
virtual ~ContainerArray() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
iterator begin(){
return iterator(data,dimension,stride*dimension,el_type);
};
iterator end(){
return iterator(data+_size*dimension*stride,dimension,stride*dimension);
};
UInt getDim(){return dimension;};
UInt size(){return _size;};
bool isHomogeneous(){return true;};
DataType getDataType() { return ::iohelper::getDataType<T>(); }
const ElemType & getElemType() { return el_type;}
void setElemType(const ElemType & type) { el_type = type;}
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
T * data;
UInt dimension;
UInt stride;
UInt _size;
ElemType el_type;
};
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_ITERATOR_ARRAY_HH__ */
+#endif /* IOHELPER_ITERATOR_ARRAY_HH_ */
diff --git a/third-party/iohelper/src/dumper.cc b/third-party/iohelper/src/dumper.cc
index 791d5863d..f643a9dce 100644
--- a/third-party/iohelper/src/dumper.cc
+++ b/third-party/iohelper/src/dumper.cc
@@ -1,293 +1,283 @@
/**
* @file dumper.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Mon Jun 10 2013
*
* @brief implementation of main dumper
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * IOHelper is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * IOHelper is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the
+ * Free Software Foundation, either version 3 of the License, or (at your
+ * option) any later version.
*
- * IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ * IOHelper is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for
+ * more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cmath>
#include "dumper.hh"
#include "field_inline_impl.hh"
#include "variable_inline_impl.hh"
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
-#pragma warning ( disable : 981 )
-#endif //defined(__INTEL_COMPILER)
+#pragma warning(disable : 981)
+#endif // defined(__INTEL_COMPILER)
-__BEGIN_IOHELPER__
+namespace iohelper {
/* -------------------------------------------------------------------------- */
-Dumper::Dumper(std::string prefix) : dump_step(0), dump_step_width(4),
- time_step(0), current_time(0),
- write_time_desc_file(false),
- mode(0),
- world_size(-1), my_rank(-1),
- root_rank(0), my_rank_width(3),
- time_description_file_name("") {
+Dumper::Dumper(const std::string & prefix)
+ : dump_step(0), dump_step_width(4), time_step(0), current_time(0),
+ write_time_desc_file(false), mode(0), world_size(-1), my_rank(-1),
+ root_rank(0), my_rank_width(3), time_description_file_name("") {
// needs to be after the definition of the directory separator
this->setPrefix(prefix);
}
/* -------------------------------------------------------------------------- */
-Dumper::Dumper(std::string prefix, const std::string & base_name) : dump_step(0), dump_step_width(4),
- time_step(0), current_time(0),
- write_time_desc_file(false),
- mode(0),
- world_size(-1), my_rank(-1),
- root_rank(0), my_rank_width(3),
- time_description_file_name("") {
+Dumper::Dumper(const std::string & prefix, const std::string & base_name)
+ : dump_step(0), dump_step_width(4), time_step(0), current_time(0),
+ write_time_desc_file(false), mode(0), world_size(-1), my_rank(-1),
+ root_rank(0), my_rank_width(3), time_description_file_name("") {
// needs to be after the definition of the directory separator
this->setPrefix(prefix);
setBaseName(base_name);
}
/* -------------------------------------------------------------------------- */
-Dumper::~Dumper(){
+Dumper::~Dumper() {
{
- std::map<std::string,FieldInterface *>::iterator it = per_node_data.begin();
- std::map<std::string,FieldInterface *>::iterator end = per_node_data.end();
- while (it != end){
+ auto it = per_node_data.begin();
+ auto end = per_node_data.end();
+ while (it != end) {
delete (*it).second;
++it;
}
}
{
- std::map<std::string,FieldInterface *>::iterator it = per_element_data.begin();
- std::map<std::string,FieldInterface *>::iterator end = per_element_data.end();
- while (it != end){
+ auto it = per_element_data.begin();
+ auto end = per_element_data.end();
+ while (it != end) {
delete (*it).second;
++it;
}
}
{
- std::map<std::string,VariableInterface *>::iterator it = global_data.begin();
- std::map<std::string,VariableInterface *>::iterator end = global_data.end();
- while (it != end){
+ auto it = global_data.begin();
+ auto end = global_data.end();
+ while (it != end) {
delete (*it).second;
++it;
}
}
}
/* -------------------------------------------------------------------------- */
void Dumper::dump(const std::string & name, UInt count) {
- if(count != UInt(-1))
+ if (count != UInt(-1)) {
dump_step = count;
+ }
- if(name != "") base_name = name;
+ if (name != "") {
+ base_name = name;
+ }
- if(time_description_file_name == "") time_description_file_name = base_name;
+ if (time_description_file_name == "") {
+ time_description_file_name = base_name;
+ }
}
/* -------------------------------------------------------------------------- */
void Dumper::registerDumpOptions(const std::string & key,
- const std::string & folder,
- const std::string & extension,
- DumpFlag dump_flag) {
+ const std::string & folder,
+ const std::string & extension,
+ DumpFlag dump_flag) {
DumpOptions & dos = dump_options[key];
dos.setFolder(folder);
dos.extension = extension;
dos.dump_flags = dump_flag;
}
/* -------------------------------------------------------------------------- */
-void Dumper::init(){
- if (world_size == -1 || my_rank == -1){
- // DUMP("world_size and my_rank variables are not well set: going to sequential dump");
+void Dumper::init() {
+ if (world_size == -1 || my_rank == -1) {
+ // DUMP("world_size and my_rank variables are not well set: going to
+ // sequential dump");
world_size = 1;
my_rank = 0;
}
}
/* -------------------------------------------------------------------------- */
-void Dumper::setPoints(Real * points, int dimension, int nb, const std::string & name) {
+void Dumper::setPoints(Real * points, int dimension, int nb,
+ const std::string & name) {
addNodeDataField(std::string("positions"), points, dimension, nb);
setBaseName(name);
}
/* -------------------------------------------------------------------------- */
-void Dumper::setBaseName(const std::string & name) {
- this->base_name = name;
-}
+void Dumper::setBaseName(const std::string & name) { this->base_name = name; }
/* -------------------------------------------------------------------------- */
-void Dumper::setConnectivity(int * connectivity,
- ElemType elem_type,
- UInt nb_elem,
- int mode) {
- addElemDataField(std::string("connectivities"),
- connectivity,
- elem_type,
- nb_node_per_elem[elem_type],
- nb_elem);
+void Dumper::setConnectivity(int * connectivity, ElemType elem_type,
+ UInt nb_elem, int mode) {
+ addElemDataField(std::string("connectivities"), connectivity, elem_type,
+ nb_node_per_elem[elem_type], nb_elem);
// ElemType * types = new ElemType[nb_elem];
// for (UInt i = 0; i < nb_elem; ++i) {
// types[i] = elem_type;
// }
// addElemDataField(std::string("element_type"), types, 1, nb_elem);
connectivity_mode = mode;
}
/* -------------------------------------------------------------------------- */
void Dumper::DumpOptions::setFolder(const std::string & fld) {
- this->folder = Dumper::checkDirectoryName(fld);;
+ this->folder = Dumper::checkDirectoryName(fld);
+ ;
}
/* -------------------------------------------------------------------------- */
const std::string & Dumper::DumpOptions::getFolder() const {
return this->folder;
}
/* -------------------------------------------------------------------------- */
std::string Dumper::checkDirectoryName(std::string fname) {
if (fname.size() > 0 &&
- fname[fname.size()-1] != IOHELPER_DIRECTORY_SEPARATOR) {
+ fname[fname.size() - 1] != IOHELPER_DIRECTORY_SEPARATOR) {
fname += IOHELPER_DIRECTORY_SEPARATOR;
}
return fname;
}
/* -------------------------------------------------------------------------- */
Dumper::DumpOptions & Dumper::getDumpOptions(const std::string & key) {
- DumpOptionsMap::iterator it = this->dump_options.find(key);
- if(it == this->dump_options.end())
+ auto it = this->dump_options.find(key);
+ if (it == this->dump_options.end())
IOHELPER_THROW("No dump options registered under the name " << key,
- _et_options_error);
+ _et_options_error);
return it->second;
}
/* -------------------------------------------------------------------------- */
std::string Dumper::getRelativeFilePath(const std::string & name,
- const std::string & key,
- UInt proc) {
+ const std::string & key, UInt proc) {
return this->getRelativeFolderPath(key) + this->getFileName(name, key, proc);
}
/* -------------------------------------------------------------------------- */
std::string Dumper::getRelativeFilePath(const std::string & name,
- const std::string & key) {
+ const std::string & key) {
return this->getRelativeFolderPath(key) + this->getFileName(name, key);
}
-
/* -------------------------------------------------------------------------- */
std::string Dumper::getAbsoluteFilePath(const std::string & name,
- const std::string & key,
- UInt proc) {
+ const std::string & key, UInt proc) {
return prefix + this->getRelativeFilePath(name, key, proc);
}
/* -------------------------------------------------------------------------- */
std::string Dumper::getAbsoluteFilePath(const std::string & name,
- const std::string & key) {
+ const std::string & key) {
return prefix + this->getRelativeFilePath(name, key);
}
/* -------------------------------------------------------------------------- */
std::string Dumper::getFileName(const std::string & name,
const std::string & key) {
return this->getFileName(name, key, this->my_rank);
}
/* -------------------------------------------------------------------------- */
std::string Dumper::getFileName(const std::string & name,
- const std::string & key,
- UInt proc) {
+ const std::string & key, UInt proc) {
std::stringstream sstr;
sstr << name;
const DumpOptions & dos = this->getDumpOptions(key);
if (dos.dump_flags & _df_counter) {
sstr << "_";
sstr.width(this->dump_step_width);
sstr.fill('0');
sstr << dump_step;
}
if (world_size > 1 && (dos.dump_flags & _df_proc_id)) {
sstr << ".proc";
sstr.width(this->my_rank_width);
sstr.fill('0');
sstr << proc;
}
sstr << dos.extension;
return sstr.str();
}
/* -------------------------------------------------------------------------- */
std::string Dumper::getRelativeFolderPath(const std::string & key) {
return getDumpOptions(key).getFolder();
}
/* -------------------------------------------------------------------------- */
std::string Dumper::getAbsoluteFolderPath(const std::string & key) {
return prefix + this->getRelativeFolderPath(key);
}
/* -------------------------------------------------------------------------- */
-std::string Dumper::getBaseName() {
- return this->base_name;
-}
+std::string Dumper::getBaseName() { return this->base_name; }
/* -------------------------------------------------------------------------- */
void Dumper::setParallelContext(int me, int wld_size, int root) {
this->my_rank = me;
this->world_size = wld_size;
this->my_rank_width = std::ceil(std::log10(this->world_size));
this->root_rank = root;
}
/* -------------------------------------------------------------------------- */
void Dumper::printNodeDataFields() {
- std::map<std::string,FieldInterface *>::iterator it = per_node_data.begin();
- std::map<std::string,FieldInterface *>::iterator end = per_node_data.end();
+ auto it = per_node_data.begin();
+ auto end = per_node_data.end();
int count = 0;
- while (it != end){
- std::cout << "Field " << ++count << " : " << it->second->getName() << std::endl;
+ while (it != end) {
+ std::cout << "Field " << ++count << " : " << it->second->getName()
+ << std::endl;
++it;
}
}
/* -------------------------------------------------------------------------- */
void Dumper::activateTimeDescFiles(Real delta_t, Real initial_time) {
this->time_step = delta_t;
this->current_time = initial_time;
this->write_time_desc_file = true;
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
diff --git a/third-party/iohelper/src/dumper.hh b/third-party/iohelper/src/dumper.hh
index 87d5a39fb..ac34100ce 100644
--- a/third-party/iohelper/src/dumper.hh
+++ b/third-party/iohelper/src/dumper.hh
@@ -1,326 +1,312 @@
/**
* @file dumper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Wed Nov 13 2013
*
* @brief dumper interface
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * IOHelper is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * IOHelper is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the
+ * Free Software Foundation, either version 3 of the License, or (at your
+ * option) any later version.
*
- * IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ * IOHelper is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for
+ * more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHELPER_DUMPER_H__
-#define __IOHELPER_DUMPER_H__
+#ifndef IOHELPER_DUMPER_H_
+#define IOHELPER_DUMPER_H_
/* -------------------------------------------------------------------------- */
-#include <map>
-#include <string>
-#include "iohelper_common.hh"
-#include "field_interface.hh"
+#include "container_array.hh"
#include "field.hh"
-#include "variable_interface.hh"
+#include "field_interface.hh"
+#include "iohelper_common.hh"
#include "variable.hh"
-#include "container_array.hh"
+#include "variable_interface.hh"
+#include <map>
+#include <string>
/* -------------------------------------------------------------------------- */
#include "visitor.hh"
/* -------------------------------------------------------------------------- */
#if !defined(_WIN32)
-# define IOHELPER_DIRECTORY_SEPARATOR '/'
-# define iohelper_mkdir(path, mode) mkdir(path, mode)
+#define IOHELPER_DIRECTORY_SEPARATOR '/'
+#define iohelper_mkdir(path, mode) mkdir(path, mode)
#else
-# define IOHELPER_DIRECTORY_SEPARATOR '\\'
-# define iohelper_mkdir(path, mode) mkdir(path)
-# include <io.h>
+#define IOHELPER_DIRECTORY_SEPARATOR '\\'
+#define iohelper_mkdir(path, mode) mkdir(path)
+#include <io.h>
#endif
-__BEGIN_IOHELPER__
+namespace iohelper {
/** Class Dumper
* Interface of a dumper
*/
-
class Dumper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
- public:
- Dumper(const std::string prefix, const std::string & base_name);
- Dumper(const std::string prefix);
+public:
+ Dumper(const std::string & prefix, const std::string & base_name);
+ Dumper(const std::string & prefix);
virtual ~Dumper();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
//! dump to file
virtual void dump(const std::string & name = std::string(),
UInt count = UInt(-1));
//! initialisation of the dumper
void init();
//! TODO set comment
void printNodeDataFields();
//! dump of field information
- virtual void dumpDescription(__attribute__((unused)) const char descr_sep = ' ') {};
+ virtual void dumpDescription(__attribute__((unused))
+ const char descr_sep = ' '){};
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
//! give vector with coordinates
- void setPoints(Real * points, int dimension, int nb, const std::string & name);
+ void setPoints(Real * points, int dimension, int nb,
+ const std::string & name);
//! set number of filtered elements
void setNumberFilteredElements(int nb_filtered);
//! give vector to connectivity
- virtual void setConnectivity(int * connectivity,
- ElemType element_type,
- UInt nb_elem,
- int mode);
+ virtual void setConnectivity(int * connectivity, ElemType elem_type,
+ UInt nb_elem, int mode);
//! give vector to per node data
template <typename T>
- void addNodeDataField(const std::string & name,
- T * data,
- UInt dimension,
- UInt size,
- UInt stride=1);
+ void addNodeDataField(const std::string & name, T * data, UInt dimension,
+ UInt size, UInt stride = 1);
//! give a generic container as per node data
template <typename Cont>
void addNodeDataField(const std::string & name, Cont & data);
//! give vector to per element data
template <typename T>
- void addElemDataField(const std::string & name,
- T * data,
- ElemType elem_type,
- UInt dimension,
- UInt size,
- UInt stride=1);
+ void addElemDataField(const std::string & name, T * data, ElemType elem_type,
+ UInt dimension, UInt size, UInt stride = 1);
//! give a generic container as per elem data
template <typename Cont>
void addElemDataField(const std::string & name, Cont & data);
//! give a generic container as per node data
template <typename VarType>
void addVariable(const std::string & name, VarType & data);
//! set mode
- virtual void setMode(int mode){ this->mode = mode; }
+ virtual void setMode(int mode) { this->mode = mode; }
//! set rank and world size params for parallel treatment
- void setParallelContext(int me, int wld_size, int root=0);
+ void setParallelContext(int me, int wld_size, int root = 0);
//! set current value for the dump step
void setDumpStep(int s) { dump_step = s; };
- Int getDumpStep() { return dump_step; };
- Int getDumpStepWidth() { return dump_step_width; };
+ Int getDumpStep() const { return dump_step; };
+ Int getDumpStepWidth() const { return dump_step_width; };
//! increment the dumpstep
void incDumpStep(UInt s = 1) { dump_step += s; };
void setPrefix(const std::string & prefix) {
- this->prefix = this->checkDirectoryName(prefix);
+ this->prefix = Dumper::checkDirectoryName(prefix);
};
virtual void activateTimeDescFiles(Real delta_t, Real initial_time = 0.);
void setTimeStep(Real delta_t) { this->time_step = delta_t; }
void setCurrentTime(Real time) { this->current_time = time; }
- void setTimeDescriptionFileName(const std::string & name) { this->time_description_file_name = name; }
+ void setTimeDescriptionFileName(const std::string & name) {
+ this->time_description_file_name = name;
+ }
protected:
static std::string checkDirectoryName(std::string fname);
std::string getFolder(const std::string & key);
//! get file name with relative path
std::string getRelativeFilePath(const std::string & name,
- const std::string & key,
- UInt proc);
+ const std::string & key, UInt proc);
std::string getRelativeFilePath(const std::string & name,
const std::string & key);
std::string getAbsoluteFilePath(const std::string & name,
- const std::string & key,
- UInt proc);
+ const std::string & key, UInt proc);
std::string getAbsoluteFilePath(const std::string & name,
const std::string & key);
- std::string getFileName(const std::string & name,
- const std::string & key,
+ std::string getFileName(const std::string & name, const std::string & key,
UInt proc);
- std::string getFileName(const std::string & name,
- const std::string & key);
+ std::string getFileName(const std::string & name, const std::string & key);
- std::string getRelativeFolderPath(const std::string & folder);
- std::string getAbsoluteFolderPath(const std::string & folder);
+ std::string getRelativeFolderPath(const std::string & key);
+ std::string getAbsoluteFolderPath(const std::string & key);
//! get base_name
std::string getBaseName();
void setBaseName(const std::string & name);
-
public:
- enum DumpFlag {
- _df_no_flag = 0x0,
- _df_counter = 0x1,
- _df_proc_id = 0x2
- };
+ enum DumpFlag { _df_no_flag = 0x0, _df_counter = 0x1, _df_proc_id = 0x2 };
protected:
struct DumpOptions {
private:
std::string folder;
+
public:
std::string extension;
DumpFlag dump_flags;
+
public:
void setFolder(const std::string & fld);
const std::string & getFolder() const;
};
using DumpOptionsMap = std::map<std::string, DumpOptions>;
protected:
- void registerDumpOptions(const std::string & key,
- const std::string & folder,
+ void registerDumpOptions(const std::string & key, const std::string & folder,
const std::string & extension,
DumpFlag dump_flag = _df_no_flag);
DumpOptions & getDumpOptions(const std::string & key);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
std::string base_name;
std::string prefix;
DumpOptionsMap dump_options;
UInt dump_step;
UInt dump_step_width;
protected:
//! current delta t
Real time_step;
//! current time (dah!)
Real current_time;
//! if implemented the dumper will write a time description file
bool write_time_desc_file;
//! flag to produce zipped files
UInt mode;
using field_map = std::map<std::string, FieldInterface *>;
using variable_map = std::map<std::string, VariableInterface *>;
//! vector of additional per node data
field_map per_node_data;
//! vector of additional per element data
field_map per_element_data;
//! map of global variables
variable_map global_data;
//! for parallel runs is the total number of processors
Int world_size;
//! for parallel runs is rank of the process
Int my_rank;
//! fortran or C style connectivity indexing
Int connectivity_mode;
- //! for parallel runs is rank of the process that should write the data to file
+ //! for parallel runs is rank of the process that should write the data to
+ //! file
Int root_rank;
//! number of zeros to put to my_rank when creating files
Int my_rank_width;
- //! file name for the time description files (if not set use the first base name)
+ //! file name for the time description files (if not set use the first base
+ //! name)
std::string time_description_file_name;
};
-
-inline Dumper::DumpFlag operator|(const Dumper::DumpFlag & a, const Dumper::DumpFlag & b) {
+inline Dumper::DumpFlag operator|(const Dumper::DumpFlag & a,
+ const Dumper::DumpFlag & b) {
auto tmp = Dumper::DumpFlag(UInt(a) | UInt(b));
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T>
-void Dumper::addNodeDataField(const std::string & name, T * data,UInt dimension,
- UInt size, UInt stride) {
+void Dumper::addNodeDataField(const std::string & name, T * data,
+ UInt dimension, UInt size, UInt stride) {
auto * cont = new ContainerArray<T>(data, dimension, size, stride);
- addNodeDataField(name,*cont);
+ addNodeDataField(name, *cont);
}
/* -------------------------------------------------------------------------- */
template <typename Cont>
-void Dumper::addNodeDataField(const std::string & name, Cont & data){
+void Dumper::addNodeDataField(const std::string & name, Cont & data) {
auto * test = new Field<Cont>(data, name);
per_node_data[name] = test;
}
/* -------------------------------------------------------------------------- */
template <typename VarType>
void Dumper::addVariable(const std::string & name, VarType & data) {
auto * vari = new Variable<VarType>(data, name);
global_data[name] = vari;
}
/* -------------------------------------------------------------------------- */
template <typename T>
-void Dumper::addElemDataField(const std::string & name,
- T * data,
- ElemType elem_type,
- UInt dimension,
- UInt size, UInt stride){
+void Dumper::addElemDataField(const std::string & name, T * data,
+ ElemType elem_type, UInt dimension, UInt size,
+ UInt stride) {
auto * cont = new ContainerArray<T>(data, dimension, size, stride);
cont->setElemType(elem_type);
- addElemDataField(name,*cont);
+ addElemDataField(name, *cont);
}
/* -------------------------------------------------------------------------- */
template <typename Cont>
-void Dumper::addElemDataField(const std::string & name, Cont & data){
+void Dumper::addElemDataField(const std::string & name, Cont & data) {
auto * test = new Field<Cont>(data, name);
per_element_data[name] = test;
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_DUMPER_H__ */
+#endif /* IOHELPER_DUMPER_H_ */
diff --git a/third-party/iohelper/src/dumper_C_wrapper.cc b/third-party/iohelper/src/dumper_C_wrapper.cc
index d45f145be..619405373 100644
--- a/third-party/iohelper/src/dumper_C_wrapper.cc
+++ b/third-party/iohelper/src/dumper_C_wrapper.cc
@@ -1,131 +1,130 @@
/**
* @file dumper_C_wrapper.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Thu Nov 01 2012
*
* @brief dumper C api implementation
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "dumper.hh"
#include "dumper_paraview.hh"
#include "dumper_restart.hh"
/* -------------------------------------------------------------------------- */
extern "C" {
#include "dumper_C_wrapper.h"
}
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
extern "C" DumpHelper * getNewDumperHandle(int dumper_style){
DumpHelper * box;
switch (dumper_style){
case PARAVIEW:
{
DumperParaview * obj = new DumperParaview();
box = (DumpHelper*)malloc(sizeof(DumpHelper));
box->object_ptr = obj;
}
break;
case RESTART:
{
DumperRestart * obj = new DumperRestart();
box = (DumpHelper*)malloc(sizeof(DumpHelper));
box->object_ptr = obj;
}
break;
default:
FATAL("unknown dumper style");
}
return box;
}
/* -------------------------------------------------------------------------- */
extern "C" void Dump(DumpHelper * pH){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->dump();
}
extern "C" void DumperInit(DumpHelper * pH){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->init();
}
extern "C" void DumperSetPoints(DumpHelper * pH,double * points,int dimension,int nb,const char * name){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->setPoints(points,dimension,nb,name);
}
extern "C" void DumperSetConnectivity(DumpHelper * pH,int * connectivity,int element_type,int nb_elem,int mode){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->setConnectivity(connectivity,static_cast<iohelper::ElemType>(element_type),nb_elem,mode);
}
extern "C" void DumperAddNodeDataField(DumpHelper * pH,double * data,int dimension,const char * name){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->addNodeDataField(data,dimension,name);
}
extern "C" void DumperAddElemDataField(DumpHelper * pH,double * data,int dimension,const char * name){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->addElemDataField(data,dimension,name);
}
extern "C" void DumperSetMode(DumpHelper * pH,int mode){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->setMode(mode);
}
extern "C" void DumperSetEmbeddedValue(DumpHelper * pH,const char * name,int value){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->setEmbeddedValue(name,value);
}
extern "C" void DumperSetPrefix(DumpHelper * pH,const char * dir){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->setPrefix(dir);
}
extern "C" void DumperSetParallelContext(DumpHelper * pH,const int me,const int wld_size){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->setParallelContext(me,wld_size);
}
extern "C" void DumperFreeHandle(DumpHelper * pH){
Dumper * ptr = (Dumper *)pH->object_ptr;
delete(ptr);
free(pH);
}
//! set number of filtered elements
extern "C" void DumperSetNumberFilteredElements(DumpHelper * pH,int nb_filtered){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->setNumberFilteredElements(nb_filtered);
}
//! set internal dumper count
extern "C" void DumperSetDumpStep(DumpHelper * pH,int step){
Dumper * ptr = (Dumper *)pH->object_ptr;
ptr->setDumpStep(step);
}
-__END_IOHELPER__
-
+}
diff --git a/third-party/iohelper/src/dumper_lammps.cc b/third-party/iohelper/src/dumper_lammps.cc
index f9f455161..6e8744019 100644
--- a/third-party/iohelper/src/dumper_lammps.cc
+++ b/third-party/iohelper/src/dumper_lammps.cc
@@ -1,128 +1,136 @@
/**
* @file dumper_lammps.cc
*
* @author Till Junge <till.junge@epfl.ch>
*
* @date creation: Thu Nov 25 2010
* @date last modification: Mon Jun 10 2013
*
* @brief implementation of lammps dumper
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include "iohelper_common.hh"
#include "dumper_lammps.hh"
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
#endif //defined(__INTEL_COMPILER)
-__BEGIN_IOHELPER__
+namespace iohelper {
template<LammpsAtomStyle style>
DumperLammps<style>::DumperLammps(Real * bounds, const std::string & prefix)
:Dumper(prefix), bounds(bounds) {
this->registerDumpOptions("lammps","","", _df_proc_id);
}
/* -------------------------------------------------------------------------- */
template<LammpsAtomStyle style>
void DumperLammps<style>::dump(const std::string & current_name, const UInt count) {
Dumper::dump(current_name, count);
std::string filename = this->getAbsoluteFilePath(this->getBaseName(), "lammps");
std::ios_base::openmode mode = std::fstream::in | std::fstream::out | std::fstream::trunc;
this->lammps_dump_file.open(filename.c_str(), mode);
this->dumpHead(this->bounds);
this->dumpAdd();
this->dumpFinalize();
this->incDumpStep();
}
/* -------------------------------------------------------------------------- */
template<LammpsAtomStyle style>
void DumperLammps<style>::dumpHead(Real * bounds) {
this->curr_nb_atom = 0;
if (!this->lammps_dump_file.good()) {
std::cerr << "hach" << std::endl;
- if (this->lammps_dump_file.rdstate() & std::fstream::eofbit) std::cerr << " 1 " << std::endl;
- if (this->lammps_dump_file.rdstate() & std::fstream::failbit) std::cerr << " 2 " << std::endl;
- if (this->lammps_dump_file.rdstate() & std::fstream::badbit) std::cerr << " 3 " << std::endl;
- if (this->lammps_dump_file.rdstate() & std::fstream::goodbit) std::cerr << " 4 " << std::endl;
+ if (this->lammps_dump_file.rdstate() & std::fstream::eofbit) {
+ std::cerr << " 1 " << std::endl;
+ }
+ if (this->lammps_dump_file.rdstate() & std::fstream::failbit) {
+ std::cerr << " 2 " << std::endl;
+ }
+ if (this->lammps_dump_file.rdstate() & std::fstream::badbit) {
+ std::cerr << " 3 " << std::endl;
+ }
+ if (this->lammps_dump_file.rdstate() & std::fstream::goodbit) {
+ std::cerr << " 4 " << std::endl;
+ }
exit(-1);
}
this->lammps_dump_file << "LAMMPS data file" << std::endl << std::endl << std::endl;
this->nb_atom_position = lammps_dump_file.tellp();
//dump whitespaces to later fill in nb_atoms
this->lammps_dump_file << " " << std::endl;
this->lammps_dump_file << "0 bonds" << std::endl
<< "1 atom types" << std::endl
<< "0 bond types" << std::endl;
if (bounds != NULL) {
this->lammps_dump_file << std::endl;
this->lammps_dump_file << bounds[0] << " " << bounds[1] <<" xlo xhi" << std::endl;
this->lammps_dump_file << bounds[2] << " " << bounds[3] <<" ylo yhi" << std::endl;
this->lammps_dump_file << bounds[4] << " " << bounds[5] <<" zlo zhi" << std::endl;
this->lammps_dump_file << std::endl;
}
this->lammps_dump_file << "Atoms" << std::endl << std::endl;
this->lammps_dump_file.setf(std::ios::scientific, std::ios::floatfield);
this->lammps_dump_file.precision(16);
}
/* -------------------------------------------------------------------------- */
template<LammpsAtomStyle style>
void DumperLammps<style>::dumpAdd(int _grain_id) {
this->grain_id = _grain_id;
per_node_data[std::string("positions")]->accept(*this);
// ContainerArray<Real> cont(_points,_dimension,_nb);
// Field<ContainerArray<Real> > field(cont,"temporary");
// // set temporary values
// field.accept(*this);//this brings me to visit
}
/* -------------------------------------------------------------------------- */
template<LammpsAtomStyle style>
void DumperLammps<style>::dumpFinalize(){
this->lammps_dump_file.seekp(this->nb_atom_position);
this->lammps_dump_file << curr_nb_atom << " atoms";
this->lammps_dump_file.close();
}
/* -------------------------------------------------------------------------- */
template class DumperLammps<atomic>;
template class DumperLammps<bond>;
-__END_IOHELPER__
+}
diff --git a/third-party/iohelper/src/dumper_lammps.hh b/third-party/iohelper/src/dumper_lammps.hh
index 2fe1fdc9b..22d7243ee 100644
--- a/third-party/iohelper/src/dumper_lammps.hh
+++ b/third-party/iohelper/src/dumper_lammps.hh
@@ -1,143 +1,143 @@
/**
* @file dumper_lammps.hh
*
* @author Till Junge <till.junge@epfl.ch>
*
* @date creation: Thu Nov 25 2010
* @date last modification: Tue Jun 04 2013
*
* @brief header for lammps dumper
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHELPER_DUMPER_LAMMPS_H__
-#define __IOHELPER_DUMPER_LAMMPS_H__
+#ifndef IOHELPER_DUMPER_LAMMPS_H_
+#define IOHELPER_DUMPER_LAMMPS_H_
/* -------------------------------------------------------------------------- */
#include "dumper.hh"
#include <fstream>
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
enum LammpsAtomStyle {atomic, bond}; //please extend ad libidum
template<LammpsAtomStyle style>
class DumperLammps: public Dumper, public Visitor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperLammps(Real * bounds = nullptr, const std::string & prefix = "./");
~DumperLammps() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
//! dump to file
- void dump(const std::string & basename = std::string(),
+ void dump(const std::string & current_name = std::string(),
UInt count = UInt(-1)) override;
void dumpHead(Real * bounds = nullptr);
template<typename T>
- void visitField(T & cont);
+ void visitField(T & visited);
void dumpFinalize();
//! set mode for file creation : TEXT, BASE64, COMPRESSED
void setMode(int mode) override { Dumper::setMode(mode); }
void dumpAdd(int grain_id = 1);
void setEmbeddedValue(__attribute__((unused)) const std::string & name,
__attribute__((unused)) int value){}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
//position of where the number of atoms is printed;
std::streampos nb_atom_position;
//current number of atoms printed to the file
unsigned long int curr_nb_atom;
std::fstream lammps_dump_file;
Real * bounds;
//! flag to produce zipped files
bool flag_compressed;
//! current values
int grain_id;
};
/* -------------------------------------------------------------------------- */
template<>
template <typename T>
void DumperLammps<bond>::visitField(T & visited) {
typename T::iterator it = visited.begin();
typename T::iterator end = visited.end();
UInt dim = visited.getDim();
for (; it != end ; ++it) {
this->lammps_dump_file << this->curr_nb_atom + 1 << " "
<< this->grain_id + 2 << " 1 ";
for (UInt i = 0 ; i < dim ; ++i) {
this->lammps_dump_file << (*it)[i] << " ";
}
this->lammps_dump_file << std::endl;
++this->curr_nb_atom;
}
}
/* -------------------------------------------------------------------------- */
template<>
template <typename T>
void DumperLammps<atomic>::visitField(T & visited) {
typename T::iterator it = visited.begin();
typename T::iterator end = visited.end();
UInt dim = visited.getDim();
for (; it != end ; ++it) {
this->lammps_dump_file << this->curr_nb_atom + 1 << " 1 ";
for (UInt i = 0 ; i < dim ; ++i) {
this->lammps_dump_file << (*it)[i] << " ";
}
this->lammps_dump_file << std::endl;
++this->curr_nb_atom;
}
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
/* -------------------------------------------------------------------------- */
#include "field_inline_impl.hh"
/* -------------------------------------------------------------------------- */
-#endif /* __IOHELPER_DUMPER_LAMMPS_H__ */
+#endif /* IOHELPER_DUMPER_LAMMPS_H_ */
diff --git a/third-party/iohelper/src/dumper_paraview.cc b/third-party/iohelper/src/dumper_paraview.cc
index 00d34e4fa..91ce38ec9 100644
--- a/third-party/iohelper/src/dumper_paraview.cc
+++ b/third-party/iohelper/src/dumper_paraview.cc
@@ -1,213 +1,225 @@
/**
* @file dumper_paraview.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Mon Jun 10 2013
*
* @brief implementation of the paraview dumper
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sys/stat.h>
#include <sys/types.h>
#include <string>
#include <iomanip>
#include "dumper_paraview.hh"
#include "file_manager.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
/// remark #383: value copied to temporary, reference to temporary used
#pragma warning ( disable : 383 )
#endif //defined(__INTEL_COMPILER)
/* -------------------------------------------------------------------------- */
DumperParaview::DumperParaview(const std::string & prefix) :
Dumper(prefix), flag_compressed(false) {
mode_offset = 0;
this->mode = BASE64;
this->registerDumpOptions("pvtu", "", ".pvtu", _df_counter);
this->registerDumpOptions("vtu", "", ".vtu", _df_counter | _df_proc_id);
this->registerDumpOptions("pvd", "", ".pvd", _df_no_flag);
}
/* -------------------------------------------------------------------------- */
DumperParaview::~DumperParaview() {
}
/* -------------------------------------------------------------------------- */
void DumperParaview::setConnectivity(int * connectivity,
ElemType element_type,
UInt nb_elem,
int mode) {
Dumper::setConnectivity(connectivity,element_type,nb_elem,mode);
- if (connectivity_mode == FORTRAN_MODE) mode_offset = -1;
- else mode_offset = 0;
+ if (connectivity_mode == FORTRAN_MODE) {
+ mode_offset = -1;
+ } else {
+ mode_offset = 0;
+ }
}
/* -------------------------------------------------------------------------- */
void DumperParaview::setMode(int mode){
Dumper::setMode(mode);
}
/* -------------------------------------------------------------------------- */
void DumperParaview::dump(const std::string & current_name, UInt count) {
Dumper::dump(current_name, count);
File file;
//create directory to the files
iohelper_mkdir(std::string(this->getAbsoluteFolderPath("pvtu")).c_str(), 0755);
//create directory to store the per proc vtus
iohelper_mkdir(std::string(this->getAbsoluteFolderPath("vtu")).c_str(), 0755);
if (my_rank == root_rank){
std::string fname = this->getAbsoluteFilePath(this->getBaseName(),
"pvtu");
file.open(fname);
if (!file.is_open()) IOHELPER_THROW("could not open file " << fname,
_et_file_error);
ParaviewHelper paraHelper(file, this->mode);
std::vector<std::string> vtus;
for (Int i = 0; i < world_size; ++i) {
vtus.push_back(this->getRelativeFilePath(this->getBaseName(), "vtu", i));
}
paraHelper.writePVTU(per_node_data,per_element_data, vtus);
}
//open current file
std::string fullvtuname = this->getAbsoluteFilePath(this->getBaseName(), "vtu");
file.open(fullvtuname, std::fstream::out, flag_compressed);
if (!file.is_open()) IOHELPER_THROW("could not open file " << fullvtuname,
_et_file_error);
ParaviewHelper paraHelper(file, this->mode);
- field_map::iterator pos_it = per_node_data.find("positions");
+ auto pos_it = per_node_data.find("positions");
if (pos_it == per_node_data.end())
IOHELPER_THROW("positions field was not specified",
_et_missing_field);
FieldInterface & positions = *(pos_it->second);
UInt nb_nodes = positions.size();
//connectivity dump
bool point_set_flag = false;
-
- field_map::iterator conn_it = per_element_data.find("connectivities");
- if (conn_it == per_element_data.end())
+
+ auto conn_it = per_element_data.find("connectivities");
+ if (conn_it == per_element_data.end()) {
point_set_flag = true;
+ }
// IOHELPER_THROW("connectivities were not specified",
// _et_missing_field);
FieldInterface * connectivities_ptr = NULL;
if (!point_set_flag){
connectivities_ptr = (conn_it->second);
UInt nb_elems = connectivities_ptr->size();
paraHelper.writeHeader(nb_nodes, nb_elems);
+ } else {
+ paraHelper.writeHeader(nb_nodes, 1);
}
- else paraHelper.writeHeader(nb_nodes, 1);
FieldInterface & connectivities = *connectivities_ptr;
paraHelper.startDofList(3);
paraHelper.pushPosition(positions);
paraHelper.endDofList();
// start to push info on cells
paraHelper.startCells();
// push connectivities
paraHelper.startCellsConnectivityList();
- if (point_set_flag)
- for (UInt i = 0 ; i < positions.size() ; ++i)
+ if (point_set_flag) {
+ for (UInt i = 0; i < positions.size(); ++i) {
paraHelper.pushDatum(i);
- else
+ }
+ } else {
paraHelper.pushConnectivity(connectivities);
-
+ }
+
paraHelper.endCellsConnectivityList();
// build offsets
paraHelper.startCellsoffsetsList();
- if (point_set_flag) paraHelper.pushDatum(positions.size());
- else paraHelper.buildOffsets(connectivities);
+ if (point_set_flag) {
+ paraHelper.pushDatum(positions.size());
+ } else {
+ paraHelper.buildOffsets(connectivities);
+ }
paraHelper.endCellsoffsetsList();
// push cell types
paraHelper.startCellstypesList();
- if (point_set_flag) paraHelper.pushDatum(POINT_SET);
- else {
- field_map::iterator elty_it = per_element_data.find("element_type");
- if (elty_it != per_element_data.end())
+ if (point_set_flag) {
+ paraHelper.pushDatum(POINT_SET);
+ } else {
+ auto elty_it = per_element_data.find("element_type");
+ if (elty_it != per_element_data.end()) {
paraHelper.pushField(*(elty_it->second));
- else
+ } else {
paraHelper.pushElemType(connectivities);
+ }
}
paraHelper.endCellstypesList();
//close cell section
paraHelper.endCells();
//! add data fields
paraHelper.pushDataFields(per_node_data, per_element_data);
paraHelper.write_conclusion();
file.close();
if(my_rank == root_rank) {
if(write_time_desc_file) {
this->pvtu_file_names.push_back(std::make_pair(current_time,
this->getRelativeFilePath(this->getBaseName(),
"pvtu")));
ParaviewHelper::writeTimePVD(this->getAbsoluteFilePath(this->time_description_file_name, "pvd"),
this->pvtu_file_names);
current_time += time_step;
}
}
this->incDumpStep();
}
/* -------------------------------------------------------------------------- */
void DumperParaview::setVTUSubDirectory(const std::string & sub){
this->getDumpOptions("vtu").setFolder(sub);
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
diff --git a/third-party/iohelper/src/dumper_paraview.hh b/third-party/iohelper/src/dumper_paraview.hh
index 2933959f2..31a1cb69b 100644
--- a/third-party/iohelper/src/dumper_paraview.hh
+++ b/third-party/iohelper/src/dumper_paraview.hh
@@ -1,107 +1,107 @@
/**
* @file dumper_paraview.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Wed Jun 05 2013
*
* @brief header for paraview dumper
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __IOHELPER_DUMPER_PARAVIEW_H__
-#define __IOHELPER_DUMPER_PARAVIEW_H__
+#ifndef IOHELPER_DUMPER_PARAVIEW_H_
+#define IOHELPER_DUMPER_PARAVIEW_H_
/* -------------------------------------------------------------------------- */
#include <map>
#include <string>
#include "dumper.hh"
//#include "field.hh"
#include "paraview_helper.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/** Class DumperParaview
* Implementation of a dumper to paraview vtu files
*/
class DumperParaview : public Dumper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperParaview(const std::string & prefix = std::string("./"));
~DumperParaview() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
//! dump to file
void dump(const std::string & name = std::string(""),
UInt count = UInt(-1)) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
//! set mode for file creation : TEXT, BASE64, COMPRESSED
void setMode(Int mode) override;
//! set the sub directory where to store the vtu files
void setVTUSubDirectory(const std::string & sub);
//! push a single field nodal with templated type
template <typename T> void pushNodeField(ParaviewHelper & paraHelper, Field<T> & f);
//! push a single element field with templated type
template <typename T> void pushElemField(ParaviewHelper & paraHelper, Field<T> & f);
//! give vector to connectivity
void setConnectivity(int * connectivity, ElemType element_type, UInt nb_elem,
int mode) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
//! flag to produce zipped files
bool flag_compressed;
//! offset to compute connectivities
Int mode_offset;
//! subdirectory where to put the vtu files
//std::string vtu_subdirectory; //became sub_folder in dumper.hh
std::vector< std::pair<Real, std::string> > pvtu_file_names;
};
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_DUMPER_PARAVIEW_H__ */
+#endif /* IOHELPER_DUMPER_PARAVIEW_H_ */
diff --git a/third-party/iohelper/src/dumper_restart.cc b/third-party/iohelper/src/dumper_restart.cc
index 316838eca..9f0f558ca 100644
--- a/third-party/iohelper/src/dumper_restart.cc
+++ b/third-party/iohelper/src/dumper_restart.cc
@@ -1,77 +1,77 @@
/**
* @file dumper_restart.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Thu Dec 06 2012
*
* @brief implementation for restart dumper
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iomanip>
#include "dumper_restart.hh"
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
#endif //defined(__INTEL_COMPILER)
-__BEGIN_IOHELPER__
+namespace iohelper {
/* -------------------------------------------------------------------------- */
void DumperRestart::dump(__attribute__((unused)) const std::string & basename){
/* nodal data */
std::map<std::string,FieldInterface *>::iterator it = per_node_data.begin();
std::map<std::string,FieldInterface *>::iterator end = per_node_data.end();
for (; it != end ; ++it) {
(*it).second->accept(*this);
}
/* element data */
it = per_element_data.begin();
end = per_element_data.end();
for (; it != end ; ++it) {
(*it).second->accept(*this);
}
this->incDumpStep();
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
/* -------------------------------------------------------------------------- */
diff --git a/third-party/iohelper/src/dumper_restart.hh b/third-party/iohelper/src/dumper_restart.hh
index 8de80dc8b..cc6c2d3f9 100644
--- a/third-party/iohelper/src/dumper_restart.hh
+++ b/third-party/iohelper/src/dumper_restart.hh
@@ -1,125 +1,122 @@
/**
* @file dumper_restart.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Tue Jun 04 2013
*
* @brief header for dumper restart
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHLPER_DUMPER_RESTART_H__
-#define __IOHLPER_DUMPER_RESTART_H__
+#ifndef IOHELPER_DUMPER_RESTART_H_
+#define IOHELPER_DUMPER_RESTART_H_
/* -------------------------------------------------------------------------- */
#include <map>
#include <string>
#include "dumper.hh"
//#include "field.hh"
#include "file_manager.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/** Class DumperRestart
* Implementation of a dumper to restart
*/
class DumperRestart : public Dumper, public Visitor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperRestart(std::string prefix = "./"):Dumper(prefix){};
~DumperRestart(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
void dump(const std::string & name);
void setEmbeddedValue(__attribute__((unused)) const std::string & name,
__attribute__((unused)) int value) {};
//! visitor system
template <typename T> void visit(T & visited);
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
template <typename T>
void DumperRestart::visit(T & visited){
File file;
int nb = visited.size();
/* node coordinates */
// std::stringstream filename;
// filename << this->getFullName(visited.getName());
// filename << ".restart";
// file.open(filename.str(),std::fstream::out | std::fstream::binary);
// file << nb << "\t" << visited.getDim() << std::endl;
std::string fname = this->getAbsoluteFilePath(visited.getName(),
"",
".restart");
file.open(fname, std::fstream::out | std::fstream::binary);
file << nb << "\t" << visited.getDim() << std::endl;
typename T::iterator it = visited.begin();
typename T::iterator end = visited.end();
for (; it != end ; ++it) {
IOHelperVector<T> data = *it;
T * ptr = data.getPtr();
UInt nb = data.size();
file.write((char*)ptr,nb*visited.getDim()*sizeof(T));
}
file.close();
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
-
-
-#endif /* __IOHLPER_DUMPER_RESTART_H__ */
-
+}
+#endif /* IOHELPER_DUMPER_RESTART_H_ */
diff --git a/third-party/iohelper/src/dumper_text.cc b/third-party/iohelper/src/dumper_text.cc
index 3f0dbdb08..266735f6d 100644
--- a/third-party/iohelper/src/dumper_text.cc
+++ b/third-party/iohelper/src/dumper_text.cc
@@ -1,297 +1,300 @@
/**
* @file dumper_text.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue May 14 2013
* @date last modification: Tue Sep 02 2014
*
* @brief implementation for text dumper
*
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sys/stat.h>
#include <iomanip>
#include "dumper_text.hh"
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
#endif //defined(__INTEL_COMPILER)
-__BEGIN_IOHELPER__
+namespace iohelper {
/* -------------------------------------------------------------------------- */
DumperText::DumperText(TextDumpMode md, const std::string & prefix,
bool file_per_time_step) :
Dumper(prefix), sim_name("sim_description"),
time_name("time_description"), field_name("field_description"),
description_sep(' '), dump_mode(md), separator(' '), comment('#'),
precision(6), file_per_time_step(file_per_time_step), is_first_dump(true) {
// fields and variables dump options
- if (file_per_time_step)
+ if (file_per_time_step) {
this->registerDumpOptions("data_fields", "", ".out", _df_counter | _df_proc_id);
- else
+ } else {
this->registerDumpOptions("data_fields", "", ".out", _df_proc_id);
+ }
this->registerDumpOptions("data_variables", "", ".out");
// description dump options
this->registerDumpOptions(time_name, "", ".time");
this->registerDumpOptions(sim_name, "", ".info");
this->registerDumpOptions(field_name, "", ".fields");
this->setDumpMode(md);
}
/* -------------------------------------------------------------------------- */
DumperText::~DumperText() {
// only root rank has this files
// if (this->my_rank == this->root_rank) {
- FileMap::iterator it = this->file_map.begin();
- FileMap::iterator end = this->file_map.end();
-
+ auto it = this->file_map.begin();
+ auto end = this->file_map.end();
+
for (; it != end; ++it) {
it->second->close();
delete it->second;
}
file_map.clear();
//}
}
/* -------------------------------------------------------------------------- */
void DumperText::setDumpMode(const TextDumpMode & mode) {
this->dump_mode = mode;
switch(mode) {
case _tdm_space: {
this->separator = ' ';
this->setDataFileExtensions(".out");
break;
}
case _tdm_csv: {
this->separator = ',';
this->setDataFileExtensions(".csv");
break;
}
default: {
IOHELPER_THROW("Unkown dump mode " << mode, _et_options_error);
}
}
}
/* -------------------------------------------------------------------------- */
void DumperText::dump(const std::string & name, UInt count) {
Dumper::dump(name, count);
//create sub directory to store files
iohelper_mkdir(std::string(this->getAbsoluteFolderPath("data_fields")).c_str() , 0755);
iohelper_mkdir(std::string(this->getAbsoluteFolderPath("data_variables")).c_str(), 0755);
/* dump description file */
- if (this->is_first_dump)
+ if (this->is_first_dump) {
this->dumpDescription(this->description_sep);
+ }
/* nodal data */
- std::map<std::string,FieldInterface *>::iterator it = per_node_data.begin();
- std::map<std::string,FieldInterface *>::iterator end = per_node_data.end();
+ auto it = per_node_data.begin();
+ auto end = per_node_data.end();
for (; it != end ; ++it) {
(*it).second->accept(*this);
}
/* element data */
it = per_element_data.begin();
end = per_element_data.end();
for (; it != end ; ++it) {
(*it).second->accept(*this);
}
/* global data */
- std::map<std::string,VariableInterface *>::iterator git = global_data.begin();
- std::map<std::string,VariableInterface *>::iterator gend = global_data.end();
+ auto git = global_data.begin();
+ auto gend = global_data.end();
for (; git != gend; ++git) {
(*git).second->accept(*this);
}
if (this->write_time_desc_file) {
this->dumpTimeDescription(this->description_sep);
this->current_time += this->time_step;
}
this->is_first_dump = false;
this->incDumpStep();
}
/* -------------------------------------------------------------------------- */
void DumperText::setDataSubDirectory(const std::string & name) {
this->getDumpOptions("data_fields").setFolder(name);
this->getDumpOptions("data_variables").setFolder(name);
}
/* -------------------------------------------------------------------------- */
std::string DumperText::getDataSubDirectory() {
return this->getDumpOptions("data_fields").getFolder();
}
/* -------------------------------------------------------------------------- */
void DumperText::setDataFileExtensions(const std::string & ext) {
this->getDumpOptions("data_fields").extension = ext;
this->getDumpOptions("data_variables").extension = ext;
}
/* -------------------------------------------------------------------------- */
void DumperText::dumpDescription(const char descr_sep) {
this->dumpFieldDescription(descr_sep);
File file;
file.open(this->getAbsoluteFilePath(this->getBaseName(), this->sim_name),
std::fstream::out);
file << this->comment
<< " [0]-version [1]-counter-width [2]-world-size"
<< " [3]-proc-width [4]-file-per-time-step" << std::endl;
file << "0-1";
file << descr_sep << this->getDumpStepWidth();
file << descr_sep << this->world_size;
file << descr_sep << this->my_rank_width;
file << descr_sep << this->file_per_time_step;
file << std::endl << std::endl;
file << "base_name" << descr_sep << this->getBaseName() << std::endl;
// file << this->comment << " field description relative file path" << std::endl;
file << this->field_name << descr_sep
<< this->getRelativeFilePath(this->getBaseName(), this->field_name) << std::endl;
// file << this->comment << " time description relative file path" << std::endl;
if (this->write_time_desc_file) {
file << this->time_name << descr_sep
<< this->getRelativeFilePath(this->getBaseName(), this->time_name) << std::endl;
}
// file << this->comment << " time description relative file path" << std::endl;
// file << "datafolder" << descr_sep
// << this->getDataSubDirectory() << std::endl;
file.close();
}
/* -------------------------------------------------------------------------- */
void DumperText::dumpTimeDescription(const char descr_sep) {
// only root rank dumps variables
- if (this->my_rank != this->root_rank)
+ if (this->my_rank != this->root_rank) {
return;
+ }
- FileMap::iterator it = this->file_map.find(this->time_name);
- FileMap::iterator end = this->file_map.end();
+ auto it = this->file_map.find(this->time_name);
+ auto end = this->file_map.end();
File * file;
if (it == end) {
File * new_file = new File;
new_file->open(this->getAbsoluteFilePath(this->getBaseName(),
this->time_name),
std::fstream::out);
this->file_map[this->time_name] = new_file;
file = new_file;
(*file) << std::scientific << std::setprecision(this->precision);
}
else {
file = it->second;
}
(*file) << this->getDumpStep();
(*file) << descr_sep << this->current_time;
(*file) << std::endl;
}
/* -------------------------------------------------------------------------- */
void DumperText::dumpFieldDescription(const char descr_sep) {
File file;
file.open(this->getAbsoluteFilePath(this->getBaseName(),
this->field_name),
std::fstream::out);
file << this->comment
<< " [0]-field_name [1]-nodal_element_global_data [2]-data_type"
<< " [3]-dump_mode [4]-nb_components [5]-rel_file_path" << std::endl;
/* nodal data */
- field_map::iterator it = per_node_data.begin();
- field_map::iterator end = per_node_data.end();
+ auto it = per_node_data.begin();
+ auto end = per_node_data.end();
for (; it != end ; ++it) {
FieldInterface * fld = (*it).second;
file << fld->getName();
file << descr_sep << "N"; // nodal information
file << descr_sep << fld->getDataType();
file << descr_sep << this->dump_mode;
file << descr_sep << fld->getDim();
file << descr_sep << this->getRelativeFolderPath("data_fields");
file << std::endl;
}
/* element data */
it = per_element_data.begin();
end = per_element_data.end();
for (; it != end ; ++it) {
FieldInterface * fld = (*it).second;
file << fld->getName();
file << descr_sep << "E"; // element information
file << descr_sep << fld->getDataType();
file << descr_sep << this->dump_mode;
file << descr_sep << fld->getDim();
file << descr_sep << this->getRelativeFolderPath("data_fields");
file << std::endl;
}
/* global data */
- std::map<std::string,VariableInterface *>::iterator git = global_data.begin();
- std::map<std::string,VariableInterface *>::iterator gend = global_data.end();
+ auto git = global_data.begin();
+ auto gend = global_data.end();
for (; git != gend; ++git) {
VariableInterface * var = (*git).second;
file << var->getName();
file << descr_sep << "G"; // global information
file << descr_sep << var->getDataType();
file << descr_sep << this->dump_mode;
file << descr_sep << var->getDim();
file << descr_sep << this->getRelativeFolderPath("data_variables");
file << std::endl;
}
file.close();
}
-__END_IOHELPER__
+}
/* -------------------------------------------------------------------------- */
diff --git a/third-party/iohelper/src/dumper_text.hh b/third-party/iohelper/src/dumper_text.hh
index 0e84dcf76..486164e18 100644
--- a/third-party/iohelper/src/dumper_text.hh
+++ b/third-party/iohelper/src/dumper_text.hh
@@ -1,195 +1,198 @@
/**
* @file dumper_text.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue May 14 2013
* @date last modification: Tue Sep 02 2014
*
* @brief header for dumper text
*
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHLPER_DUMPER_TEXT_H__
-#define __IOHLPER_DUMPER_TEXT_H__
+#ifndef IOHELPER_DUMPER_TEXT_H_
+#define IOHELPER_DUMPER_TEXT_H_
/* -------------------------------------------------------------------------- */
#include <map>
#include <string>
#include "dumper.hh"
#include "file_manager.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/** Class DumperText
* Implementation of a dumper to text file
*/
class DumperText : public Dumper, public Visitor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperText(TextDumpMode md = _tdm_space,
const std::string & prefix = "./",
bool file_per_time_step = false);
~DumperText() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
void dump(const std::string & name, UInt count) override;
- void setEmbeddedValue(__attribute__((unused)) const std::string & name,
- __attribute__((unused)) int value) {};
+ void setEmbeddedValue(const std::string & /*name*/,
+ int /*value*/) {};
- void dumpDescription(const char descr_sep = ' ') override;
- virtual void dumpFieldDescription(const char descr_sep = ' ');
- virtual void dumpTimeDescription(const char descr_sep = ' ');
+ void dumpDescription(char descr_sep = ' ') override;
+ virtual void dumpFieldDescription(char descr_sep = ' ');
+ virtual void dumpTimeDescription(char descr_sep = ' ');
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
void setDataSubDirectory(const std::string & name);
std::string getDataSubDirectory();
void setDataFileExtensions(const std::string & ext);
void setDumpMode(const TextDumpMode & mode);
void setPrecision(UInt prec) { this->precision = prec; };
//! visitor system
template <typename T> void visitField(T & visited);
template <typename T> void visitVariable(T & visited);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using FileMap = std::map<std::string, File *>;
/**
* another base name so that you will never understand how iohelper
* does what it does (now useless so it is commented but not removed
* for historical reasons)
*/
// std::string yet_another_base_name;
/// name of simulation, time and field description options
std::string sim_name;
std::string time_name;
std::string field_name;
char description_sep;
/// this is a separator !!
TextDumpMode dump_mode;
char separator;
char comment;
UInt precision;
bool file_per_time_step;
bool is_first_dump;
FileMap file_map;
};
/* -------------------------------------------------------------------------- */
template <typename T>
void DumperText::visitField(T & visited) {
File file;
if (this->file_per_time_step || this->is_first_dump) {
file.open(this->getAbsoluteFilePath(this->getBaseName() + "_" + visited.getName(),
"data_fields"),
std::fstream::out);
}
else {
file.open(this->getAbsoluteFilePath(this->getBaseName() + "_" + visited.getName(),
"data_fields"),
std::fstream::out | std::fstream::app);
}
file << std::scientific << std::setprecision(this->precision);
typename T::iterator it = visited.begin();
typename T::iterator end = visited.end();
UInt dim = visited.getDim();
for (; it != end; ++it) {
for (UInt i=0; i<dim; ++i) {
- if (i != 0)
- file << this->separator;
+ if (i != 0) {
+ file << this->separator;
+ }
file << (*it)[i];
}
file << std::endl;
}
file << std::endl;
file.close();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void DumperText::visitVariable(T & visited) {
// only root rank dumps variables
- if (this->my_rank != this->root_rank)
+ if (this->my_rank != this->root_rank) {
return;
+ }
const std::string & name = visited.getName();
auto it = this->file_map.find(name);
auto end = this->file_map.end();
File * file;
if (it == end) {
auto * new_file = new File;
new_file->open(this->getAbsoluteFilePath(this->getBaseName() + "_" + name,
"data_variables"),
std::fstream::out);
this->file_map[name] = new_file;
file = new_file;
(*file) << std::scientific << std::setprecision(this->precision);
}
else {
file = it->second;
}
UInt dim = visited.getDim();
// File file = it->second;
for (UInt i=0; i<dim; ++i) {
- if (i != 0)
+ if (i != 0) {
(*file) << this->separator;
+ }
(*file) << (*visited)[i];
}
(*file) << std::endl;
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHLPER_DUMPER_TEXT_H__ */
+#endif /* IOHELPER_DUMPER_TEXT_H_ */
diff --git a/third-party/iohelper/src/field.cc b/third-party/iohelper/src/field.cc
index 9ac397304..5ffaf976d 100644
--- a/third-party/iohelper/src/field.cc
+++ b/third-party/iohelper/src/field.cc
@@ -1,70 +1,70 @@
/**
* @file field.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Wed Dec 14 2011
* @date last modification: Thu Nov 01 2012
*
* @brief implementation of the Field class
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "field.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/* -------------------------------------------------------------------------- */
template <>
FieldType Field<Real>::getFieldDataType(){
return REAL;
}
/* -------------------------------------------------------------------------- */
template <>
FieldType Field<UInt>::getFieldDataType(){
return UINT;
}
/* -------------------------------------------------------------------------- */
template <>
FieldType Field<bool>::getFieldDataType(){
return BOOL;
}
/* -------------------------------------------------------------------------- */
template <>
FieldType Field<int>::getFieldDataType(){
return INT;
}
/* -------------------------------------------------------------------------- */
template <>
FieldType Field<long int>::getFieldDataType(){
return INT;
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
diff --git a/third-party/iohelper/src/field.hh b/third-party/iohelper/src/field.hh
index 2a388a3ce..a554441b3 100644
--- a/third-party/iohelper/src/field.hh
+++ b/third-party/iohelper/src/field.hh
@@ -1,136 +1,136 @@
/**
* @file field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Tue Feb 05 2013
*
* @brief description of field
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __IOHELPER_FIELD_HH__
-#define __IOHELPER_FIELD_HH__
+#ifndef IOHELPER_FIELD_HH_
+#define IOHELPER_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "field_interface.hh"
// #include "paraview_helper.hh"
// #include "dumper_lammps.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
template <class Cont>
class Field : public FieldInterface {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using iterator = typename Cont::iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Field(Cont & c, const std::string & name) : my_field(c), name(name){};
~Field() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
//! return true if the data is a constant size per element
inline bool isHomogeneous() override;
//! return the size per element (valid only if isHomogeneous is true)
inline UInt getDim() override;
//! return the number of stored items (elements, nodes, etc...)
inline UInt size() override;
//! return the description name of the container
inline std::string getName() override;
//! accept to be visited by a visitor
void accept(Visitor & v) override;
//! begin method
iterator begin(){return my_field.begin();}
//! end method
iterator end(){return my_field.end();}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
inline DataType getDataType() override { return my_field.getDataType(); }
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
Cont & my_field;
std::string name;
};
/* -------------------------------------------------------------------------- */
template <class Cont>
bool Field<Cont>::isHomogeneous(){
return my_field.isHomogeneous();
}
/* -------------------------------------------------------------------------- */
template <class Cont>
UInt Field<Cont>::getDim(){
return my_field.getDim();
}
/* -------------------------------------------------------------------------- */
template <class Cont>
std::string Field<Cont>::getName(){
return name;
}
/* -------------------------------------------------------------------------- */
template <class Cont>
UInt Field<Cont>::size(){
return my_field.size();
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_FIELD_HH__ */
+#endif /* IOHELPER_FIELD_HH_ */
diff --git a/third-party/iohelper/src/field_inline_impl.hh b/third-party/iohelper/src/field_inline_impl.hh
index c5bac505b..971bfcb93 100644
--- a/third-party/iohelper/src/field_inline_impl.hh
+++ b/third-party/iohelper/src/field_inline_impl.hh
@@ -1,60 +1,60 @@
/**
* @file field_inline_impl.hh
*
* @author Till Junge <till.junge@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Wed Oct 31 2012
* @date last modification: Tue Jun 04 2013
*
* @brief inline implementation of dumper visitor
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "paraview_helper.hh"
#include "dumper_lammps.hh"
#include "dumper_text.hh"
-#ifndef __IOHELPER_FIELD_INLINE_IMPL_HH__
-#define __IOHELPER_FIELD_INLINE_IMPL_HH__
+#ifndef IOHELPER_FIELD_INLINE_IMPL_HH_
+#define IOHELPER_FIELD_INLINE_IMPL_HH_
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
template <class Cont>
inline void Field<Cont>::accept(Visitor & v){
if (auto * ptr_ph = dynamic_cast<ParaviewHelper *>(&v)) {
ptr_ph->visitField(*this);
} else if (auto * ptr_dlb = dynamic_cast<DumperLammps<bond> *>(&v)) {
ptr_dlb->visitField(*this);
} else if (auto * ptr_dla = dynamic_cast<DumperLammps<atomic> *>(&v)) {
ptr_dla->visitField(*this);
} else if (auto * ptr_txt = dynamic_cast<DumperText *>(&v)) {
ptr_txt->visitField(*this);
}
}
-__END_IOHELPER__
+}
/* -------------------------------------------------------------------------- */
-#endif /* __IOHELPER_FIELD_INLINE_IMPL_HH__ */
+#endif /* IOHELPER_FIELD_INLINE_IMPL_HH_ */
diff --git a/third-party/iohelper/src/field_interface.hh b/third-party/iohelper/src/field_interface.hh
index 021faafce..2b9b883b0 100644
--- a/third-party/iohelper/src/field_interface.hh
+++ b/third-party/iohelper/src/field_interface.hh
@@ -1,82 +1,82 @@
/**
* @file field_interface.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Wed Dec 14 2011
* @date last modification: Tue Feb 05 2013
*
* @brief header for the field interface
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __IOHELPER_CONTAINER_INTERFACE_HH__
-#define __IOHELPER_CONTAINER_INTERFACE_HH__
+#ifndef IOHELPER_CONTAINER_INTERFACE_HH_
+#define IOHELPER_CONTAINER_INTERFACE_HH_
/* -------------------------------------------------------------------------- */
#include "visitor.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
class FieldInterface {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FieldInterface() = default;
virtual ~FieldInterface() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void accept(Visitor & v) = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
//! return true if the data is a constant size per element
virtual bool isHomogeneous()=0;
//! return the size per element (valid only if isHomogeneous is true)
virtual UInt getDim()=0;
//! return the description name of the container
virtual std::string getName()=0;
//! return the number of stored items (elements, nodes, etc...)
virtual UInt size()=0;
virtual DataType getDataType()=0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_CONTAINER_INTERFACE_HH__ */
+#endif /* IOHELPER_CONTAINER_INTERFACE_HH_ */
diff --git a/third-party/iohelper/src/file_manager.hh b/third-party/iohelper/src/file_manager.hh
index 55049e883..6ea8fa981 100644
--- a/third-party/iohelper/src/file_manager.hh
+++ b/third-party/iohelper/src/file_manager.hh
@@ -1,350 +1,350 @@
/**
* @file file_manager.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Thu Dec 06 2012
*
* @brief file manager header
*
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHELPER_FILE_MANAGER_H__
-#define __IOHELPER_FILE_MANAGER_H__
+#ifndef IOHELPER_FILE_MANAGER_H_
+#define IOHELPER_FILE_MANAGER_H_
/* -------------------------------------------------------------------------- */
#include <zlib.h>
#include <stdio.h>
#include <stdarg.h>
#include <string>
#include <iostream>
#include <fstream>
#include <typeinfo>
#include "iohelper_common.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
template <class charT, class Traits=std::char_traits<charT> >
class GZfstream : public std::basic_fstream<charT,Traits> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GZfstream();
GZfstream(const std::string & fname,
std::fstream::openmode mode = std::fstream::out,
bool compr=false);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
///! opening methods
inline void open(const std::string & name,
std::fstream::openmode mode = std::fstream::out,
bool compr= false);
// inline void close();
// // //! writing methods
// template <typename T> GZfstream & operator << (const T & v);
// inline GZfstream & operator << (std::ostream& (*op)(std::ostream&)){};
// inline GZfstream & write(const void * buffer,std::streamsize n);
// inline GZfstream & flush();
// // //! reading methods
// template <typename T> GZfstream & operator >> (T & v);
// inline GZfstream & read(void * buffer,std::streamsize n);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
// #ifdef USING_ZLIB
// gzFile gzfile;
// #endif
// int compressed;
};
// /* -------------------------------------------------------------------------- */
template <class charT, class Traits>
inline GZfstream<charT,Traits>::GZfstream():
std::basic_fstream<charT,Traits>(){
// compressed = 0;
// #ifdef USING_ZLIB
// gzfile = NULL;
// #endif
}
// /* -------------------------------------------------------------------------- */
template <class charT, class Traits>
-inline GZfstream<charT,Traits>::GZfstream(const std::string & fname,
- std::fstream::openmode mode,bool) :
- std::basic_fstream<charT,Traits>(fname.c_str(),mode){
+inline GZfstream<charT, Traits>::GZfstream(const std::string & fname,
+ std::fstream::openmode mode,
+ bool /*unused*/)
+ : std::basic_fstream<charT, Traits>(fname.c_str(), mode) {
// compressed = compr;
// #ifdef USING_ZLIB
// gzfile = NULL;
// #endif
// open(fname,mode,compressed);
}
// /* -------------------------------------------------------------------------- */
// // inline void GZfstream::printf(const std::string & formated, ...){
// // if (!opened) {
// // FATAL("Warning : file not opened " << name);
// // }
// // // if (!opened) return;
// // if (_file == NULL) FATAL("fichier non ouvert mais ce n'est pas normal");
// // char buf[512];
// // va_list list;
// // va_start(list,formated);
// // int len = vsprintf(buf,formated.c_str(),list);
// // va_end(list);
// // #ifdef USING_ZLIB
// // if (compressed){
// // gzwrite(gzfile,buf,len);
// // return;
// // }
// // else
// // #endif
// // fwrite(buf,len,1,_file);
// // }
// /* -------------------------------------------------------------------------- */
// // inline void GZfstream::gets(std::string & buf){
// // char * ret;
// // const UInt len = 255;
// // char buffer[len] = "";
// // if (!opened) {
// // FATAL("Warning : file not opened " << name);
// // }
// // if (_file == NULL) FATAL("file not opened: exit");
// // DUMP("read to buf (" << buf << ") at most " << len << " characters");
// // #ifdef USING_ZLIB
// // if (compressed){
// // ret = gzgets(gzfile,buffer,len);
// // }
// // else
// // #endif
// // ret = fgets(buffer,len,_file);
// // if (ret == NULL) throw;
// // DUMP("read to buf (" << buf << ") at most " << len << " characters");
// // buf = buffer;
// // }
// /* -------------------------------------------------------------------------- */
// template <class charT, class Traits>
// inline void GZfstream<charT,Traits>::close(){
// #ifdef USING_ZLIB
// if (this->is_open() && compressed){
// gzclose(gzfile);
// gzfile = NULL;
// }
// #endif
// }
// /* -------------------------------------------------------------------------- */
-
template <class charT, class Traits>
-inline void GZfstream<charT,Traits>::open(const std::string & fname,
- std::fstream::openmode mode,
- bool){
+inline void GZfstream<charT, Traits>::open(const std::string & fname,
+ std::fstream::openmode mode,
+ bool /*unused*/) {
std::basic_fstream<charT,Traits>::open(fname.c_str(),mode);
// if (this->is_open()) this->close();
// compressed = compr;
// this->open(fname.c_str(),mode);
// if (!this->is_open()) FATAL("Could not open file "<< fname);
// #ifdef USING_ZLIB
// if (compressed){
// std::stringstream _mode;
// if (mode & std::fstream::in) _mode << "r";
// if (mode & std::fstream::out) _mode << "w";
// if (mode & std::fstream::app) _mode << "a";
// if (mode & std::fstream::binary) _mode << "b";
// std::cerr << typeid(*this->rdbuf()).name() << std::endl;
// int fd = this->rdbuf()->_M_file->fd();
// //gzfile = gzdopen(this->rdbuf()->fd(),_mode.str().c_str());
// throw;
// }
// #endif
// DUMP("file " << name << " opened , compressed = " << compressed);
}
// /* -------------------------------------------------------------------------- */
// // inline int GZfstream::dumpchar(int c){
// // if (!opened) {
// // FATAL("Warning : file not opened " << name);
// // }
// // // if (!opened) return EOF;
// // #ifdef USING_ZLIB
// // if (compressed){
// // int res = gzputc(gzfile,c);
// // //DUMP("file opened in compressed form " << name);
// // if (c != res)
// // FATAL("j'ai pas ecrit ce que je voulais (compressed) " << res);
// // return res;
// // }
// // else
// // #endif
// // if (c != putc(c,_file))
// // FATAL("j'ai pas ecrit ce que je voulais");
// // return c;
// // }
// /* -------------------------------------------------------------------------- */
// // inline int GZfstream::seek(int offset,int set){
// // if (!opened) {
// // FATAL("Warning : file not opened " << name);
// // }
// // #ifdef USING_ZLIB
// // if (compressed){
// // return gzseek(gzfile, offset,set);
// // }
// // else
// // #endif
// // return fseek(_file,offset,set);
// // }
// // /* -------------------------------------------------------------------------- */
// // inline int GZfstream::tell(){
// // if (!opened) {
// // FATAL("Warning : file not opened " << name);
// // }
// // #ifdef USING_ZLIB
// // if (compressed){
// // return gztell(gzfile);
// // }
// // else
// // #endif
// // return ftell(_file);
// // }
// // /* -------------------------------------------------------------------------- */
// //template <class charT, class Traits>
// //inline GZfstream<charT,Traits> & GZfstream<charT,Traits>::read(void * buffer,
// // std::streamsize size){
// // if (!opened) {
// // FATAL("Warning : file not opened " << name);
// // }
// // #ifdef USING_ZLIB
// // if (compressed){
// // return gzread(gzfile,buffer,size*number);
// // }
// // else
// // #endif
// // return fread(buffer,size,number,_file);
// //}
// /* -------------------------------------------------------------------------- */
// // template <class charT, class Traits>
// // inline GZfstream<charT,Traits> & GZfstream<charT,Traits>::write(const void * buffer,
// // std::streamsize size){
// // // if (!this->is_open()) throw std::ios_base::failure("file not opened");
// // Int nwrite;
// // #ifdef USING_ZLIB
// // if (compressed) nwrite = gzwrite(gzfile,buffer,size);
// // else
// // #endif
// // this->write(buffer,size);
// // // if (nwrite == 0) throw std::ios_base::failure("could not write any byte");
// // return *this;
// // }
// /* -------------------------------------------------------------------------- */
// // template <class charT, class Traits>
// // inline GZfstream<charT,Traits> & GZfstream<charT,Traits>::flush(){
// // // if (!this->is_open()) throw std::ios_base::failure("file not opened");
// // #ifdef USING_ZLIB
// // if (compressed){
// // gzflush(gzfile,Z_SYNC_FLUSH);
// // }
// // else
// // #endif
// // this->flush();
// // }
using File = GZfstream<char>;
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_FILE_MANAGER_H__ */
+#endif /* IOHELPER_FILE_MANAGER_H_ */
diff --git a/third-party/iohelper/src/iohelper_common.hh b/third-party/iohelper/src/iohelper_common.hh
index e56b89b3a..a1c698b3b 100644
--- a/third-party/iohelper/src/iohelper_common.hh
+++ b/third-party/iohelper/src/iohelper_common.hh
@@ -1,300 +1,284 @@
/**
* @file iohelper_common.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Thu Oct 10 2013
*
* @brief header for common types
*
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * IOHelper is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * IOHelper is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the
+ * Free Software Foundation, either version 3 of the License, or (at your
+ * option) any later version.
*
- * IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ * IOHelper is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for
+ * more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHELPER_COMMON_H__
-#define __IOHELPER_COMMON_H__
+#ifndef IOHELPER_COMMON_H_
+#define IOHELPER_COMMON_H_
/* -------------------------------------------------------------------------- */
#define USING_ZLIB
#include <iostream>
-#include <string>
#include <sstream>
-
-#define __BEGIN_IOHELPER__ namespace iohelper {
-#define __END_IOHELPER__ }
-
-#include <string.h>
#include <stdlib.h>
-
+#include <string.h>
+#include <string>
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
using UInt = unsigned int;
using Int = int;
using Real = double;
/* -------------------------------------------------------------------------- */
-enum DataType {
- _bool,
- _uint,
- _int,
- _float,
- _double,
- _int64,
- _uint64,
- _uint8
-};
+enum DataType { _bool, _uint, _int, _float, _double, _int64, _uint64, _uint8 };
-enum IndexingMode{
- C_MODE = 0,
- FORTRAN_MODE = 1
-};
+enum IndexingMode { C_MODE = 0, FORTRAN_MODE = 1 };
/* -------------------------------------------------------------------------- */
#if __cplusplus <= 199711L
enum ElemType {
#else
enum ElemType : unsigned int {
#endif
- TRIANGLE1 ,
- TRIANGLE2 ,
- TETRA1 ,
- TETRA2 ,
- POINT_SET ,
- LINE1 ,
- LINE2 ,
- QUAD1 ,
- QUAD2 ,
- HEX1 ,
- HEX2 ,
- BEAM2 ,
- BEAM3 ,
- PRISM1 ,
- PRISM2 ,
- COH1D2 ,
- COH2D4 ,
- COH2D6 ,
- COH3D6 ,
- COH3D12 ,
- COH3D8 ,
+ TRIANGLE1,
+ TRIANGLE2,
+ TETRA1,
+ TETRA2,
+ POINT_SET,
+ LINE1,
+ LINE2,
+ QUAD1,
+ QUAD2,
+ HEX1,
+ HEX2,
+ BEAM2,
+ BEAM3,
+ PRISM1,
+ PRISM2,
+ COH1D2,
+ COH2D4,
+ COH2D6,
+ COH3D6,
+ COH3D12,
+ COH3D8,
MAX_ELEM_TYPE
};
/* -------------------------------------------------------------------------- */
-enum FileStorageMode{
- TEXT = 0,
- BASE64 = 1,
- COMPRESSED = 2
-};
+enum FileStorageMode { TEXT = 0, BASE64 = 1, COMPRESSED = 2 };
-enum TextDumpMode {
- _tdm_space,
- _tdm_csv
-};
+enum TextDumpMode { _tdm_space, _tdm_csv };
/* -------------------------------------------------------------------------- */
static UInt nb_node_per_elem[MAX_ELEM_TYPE] __attribute__((unused)) = {
- 3, // TRIANGLE1
- 6, // TRIANGLE2
- 4, // TETRA1
- 10, // TETRA2
- 1, // POINT_SET
- 2, // LINE1
- 3, // LINE2
- 4, // QUAD1
- 8, // QUAD2
- 8, // HEX1
- 20, // HEX2
- 2, // BEAM2
- 2, // BEAM3
- 6, // PRISM1
- 15, // PRISM2
- 2, // COH1D2
- 4, // COH2D4
- 6, // COH2D6
- 6, // COH3D6
- 12, // COH3D12
- 8, // COH3D8
+ 3, // TRIANGLE1
+ 6, // TRIANGLE2
+ 4, // TETRA1
+ 10, // TETRA2
+ 1, // POINT_SET
+ 2, // LINE1
+ 3, // LINE2
+ 4, // QUAD1
+ 8, // QUAD2
+ 8, // HEX1
+ 20, // HEX2
+ 2, // BEAM2
+ 2, // BEAM3
+ 6, // PRISM1
+ 15, // PRISM2
+ 2, // COH1D2
+ 4, // COH2D4
+ 6, // COH2D6
+ 6, // COH3D6
+ 12, // COH3D12
+ 8, // COH3D8
};
/* -------------------------------------------------------------------------- */
static UInt nb_quad_points[MAX_ELEM_TYPE] __attribute__((unused)) = {
- 1, // TRIANGLE1
- 3, // TRIANGLE2
- 1, // TETRA1
- 4, // TETRA2
- 0, // POINT_SET
- 1, // LINE1
- 2, // LINE2
- 4, // QUAD1
- 9, // QUAD2
- 8, // HEX1
- 27, // HEX2
- 2, // BEAM2
- 3, // BEAM3
- 6, // PRISM1
- 8, // PRISM2
- 1, // COH1D2
- 1, // COH2D4
- 2, // COH2D6
- 1, // COH3D6
- 3, // COH3D12
- 1, // COH3D8
+ 1, // TRIANGLE1
+ 3, // TRIANGLE2
+ 1, // TETRA1
+ 4, // TETRA2
+ 0, // POINT_SET
+ 1, // LINE1
+ 2, // LINE2
+ 4, // QUAD1
+ 9, // QUAD2
+ 8, // HEX1
+ 27, // HEX2
+ 2, // BEAM2
+ 3, // BEAM3
+ 6, // PRISM1
+ 8, // PRISM2
+ 1, // COH1D2
+ 1, // COH2D4
+ 2, // COH2D6
+ 1, // COH3D6
+ 3, // COH3D12
+ 1, // COH3D8
};
/* -------------------------------------------------------------------------- */
-template <typename T>
-class IOHelperVector {
+template <typename T> class IOHelperVector {
public:
virtual ~IOHelperVector() = default;
- inline IOHelperVector(T * ptr, UInt size){
+ inline IOHelperVector(T * ptr, UInt size) {
this->ptr = ptr;
this->_size = size;
};
- inline UInt size() const {return _size;};
+ inline UInt size() const { return _size; };
- inline const T & operator[] (UInt i) const {
- return ptr[i];
- };
+ inline const T & operator[](UInt i) const { return ptr[i]; };
- inline const T * getPtr() const {
- return ptr;
- };
+ inline const T * getPtr() const { return ptr; };
private:
- T* ptr;
+ T * ptr;
UInt _size;
};
/* -------------------------------------------------------------------------- */
/* Iterator interface */
/* -------------------------------------------------------------------------- */
-template< typename T, class daughter, class ret_cont = IOHelperVector<T> > class iterator {
+template <typename T, class daughter, class ret_cont = IOHelperVector<T>>
+class iterator {
public:
using type = ret_cont;
virtual ~iterator() = default;
virtual bool operator!=(const daughter & it) const = 0;
virtual daughter & operator++() = 0;
virtual ret_cont operator*() = 0;
//! This function is only for the element iterators
virtual ElemType element_type() { return MAX_ELEM_TYPE; }
};
/* -------------------------------------------------------------------------- */
class IOHelperException : public std::exception {
public:
enum ErrorType {
_et_non_homogeneous_data,
_et_unknown_visitor_stage,
_et_file_error,
_et_missing_field,
_et_data_type,
_et_options_error
-};
+ };
public:
IOHelperException(const std::string & message,
const ErrorType type) noexcept {
this->message = message;
- this->type = type;
+ this->type = type;
};
~IOHelperException() noexcept override = default;
const char * what() const noexcept override { return message.c_str(); };
private:
-
std::string message;
ErrorType type;
};
/* -------------------------------------------------------------------------- */
-
-#define IOHELPER_THROW(x,type) { \
- std::stringstream ioh_throw_sstr; \
- ioh_throw_sstr << __FILE__ << ":" << __LINE__ << ":" \
- << __PRETTY_FUNCTION__ << ": " << x; \
- std::string ioh_message(ioh_throw_sstr.str()); \
- throw ::iohelper::IOHelperException(ioh_message, \
- ::iohelper::IOHelperException::type); \
+#define IOHELPER_THROW(x, type) \
+ { \
+ std::stringstream ioh_throw_sstr; \
+ ioh_throw_sstr << __FILE__ << ":" << __LINE__ << ":" \
+ << __PRETTY_FUNCTION__ << ": " << x; /* NOLINT */ \
+ std::string ioh_message(ioh_throw_sstr.str()); \
+ throw ::iohelper::IOHelperException(ioh_message, \
+ ::iohelper::IOHelperException::type); \
}
/* -------------------------------------------------------------------------- */
-
-
template <typename T> DataType getDataType();
-#define DEFINE_GET_DATA_TYPE(type, data_type ) \
+#define DEFINE_GET_DATA_TYPE(type, data_type) \
template <> inline DataType getDataType<type>() { return data_type; }
DEFINE_GET_DATA_TYPE(bool, _bool)
DEFINE_GET_DATA_TYPE(ElemType, _int)
DEFINE_GET_DATA_TYPE(int, _int)
DEFINE_GET_DATA_TYPE(unsigned int, _uint)
DEFINE_GET_DATA_TYPE(float, _float)
DEFINE_GET_DATA_TYPE(double, _double)
DEFINE_GET_DATA_TYPE(long int, _int64)
DEFINE_GET_DATA_TYPE(unsigned long int, _uint64)
DEFINE_GET_DATA_TYPE(std::uint8_t, _uint8)
#undef DEFINE_GET_DATA_TYPE
-inline std::ostream & operator <<(std::ostream & stream, DataType type)
-{
- switch(type)
- {
- case _bool : stream << "bool" ; break;
- case _uint : stream << "uint32" ; break;
- case _int : stream << "int32" ; break;
- case _float : stream << "float32" ; break;
- case _double : stream << "float64" ; break;
- case _uint64 : stream << "uint64" ; break;
- case _int64 : stream << "int64" ; break;
- case _uint8 : stream << "uint8" ; break;
- }
+inline std::ostream & operator<<(std::ostream & stream, DataType type) {
+ switch (type) {
+ case _bool:
+ stream << "bool";
+ break;
+ case _uint:
+ stream << "uint32";
+ break;
+ case _int:
+ stream << "int32";
+ break;
+ case _float:
+ stream << "float32";
+ break;
+ case _double:
+ stream << "float64";
+ break;
+ case _uint64:
+ stream << "uint64";
+ break;
+ case _int64:
+ stream << "int64";
+ break;
+ case _uint8:
+ stream << "uint8";
+ break;
+ }
return stream;
}
-inline std::ostream & operator <<(std::ostream & stream, TextDumpMode mode)
-{
- switch(mode)
- {
- case _tdm_space : stream << "space" ; break;
- case _tdm_csv : stream << "csv" ; break;
- }
+inline std::ostream & operator<<(std::ostream & stream, TextDumpMode mode) {
+ switch (mode) {
+ case _tdm_space:
+ stream << "space";
+ break;
+ case _tdm_csv:
+ stream << "csv";
+ break;
+ }
return stream;
}
+} // namespace iohelper
-__END_IOHELPER__
-
-#endif /* __IOHELPER_COMMON_H__ */
+#endif /* IOHELPER_COMMON_H_ */
diff --git a/third-party/iohelper/src/paraview_helper.cc b/third-party/iohelper/src/paraview_helper.cc
index d18ae7dd2..e208d463f 100644
--- a/third-party/iohelper/src/paraview_helper.cc
+++ b/third-party/iohelper/src/paraview_helper.cc
@@ -1,312 +1,324 @@
/**
* @file paraview_helper.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 12 2012
* @date last modification: Wed Jun 05 2013
*
* @brief implementation of paraview helper
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "paraview_helper.hh"
#include <fstream>
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
/// remark #383: value copied to temporary, reference to temporary used
#pragma warning ( disable : 383 )
#endif //defined(__INTEL_COMPILER)
-__BEGIN_IOHELPER__
+namespace iohelper {
/* -------------------------------------------------------------------------- */
ParaviewHelper::ParaviewHelper(File & f, UInt mode):
b64(f), file(f), position_flag(false) {
bflag = BASE64;
compteur = 0;
setMode(mode);
this->paraview_code_type[TRIANGLE1] = VTK_TRIANGLE;
this->paraview_code_type[TRIANGLE2] = VTK_QUADRATIC_TRIANGLE;
this->paraview_code_type[TETRA1 ] = VTK_TETRA;
this->paraview_code_type[TETRA2 ] = VTK_QUADRATIC_TETRA;
this->paraview_code_type[POINT_SET] = VTK_POLY_VERTEX;
this->paraview_code_type[LINE1 ] = VTK_LINE;
this->paraview_code_type[LINE2 ] = VTK_QUADRATIC_EDGE;
this->paraview_code_type[QUAD1 ] = VTK_QUAD;
this->paraview_code_type[QUAD2 ] = VTK_QUADRATIC_QUAD;
this->paraview_code_type[HEX1 ] = VTK_HEXAHEDRON;
this->paraview_code_type[HEX2 ] = VTK_QUADRATIC_HEXAHEDRON;
this->paraview_code_type[BEAM2 ] = VTK_LINE;
this->paraview_code_type[BEAM3 ] = VTK_LINE;
this->paraview_code_type[PRISM1 ] = VTK_WEDGE;
this->paraview_code_type[PRISM2 ] = VTK_QUADRATIC_WEDGE;
this->paraview_code_type[COH1D2 ] = VTK_LINE;
this->paraview_code_type[COH2D4 ] = VTK_POLYGON;
this->paraview_code_type[COH2D6 ] = VTK_POLYGON;
this->paraview_code_type[COH3D6 ] = VTK_WEDGE;
this->paraview_code_type[COH3D12 ] = VTK_QUADRATIC_LINEAR_WEDGE;
this->paraview_code_type[COH3D8 ] = VTK_HEXAHEDRON;
std::map<ElemType, VTKCellType>::iterator it;
for(it = paraview_code_type.begin();
it != paraview_code_type.end(); ++it) {
UInt nb_nodes = nb_node_per_elem[it->first];
UInt * tmp = new UInt[nb_nodes];
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch(it->first) {
case COH3D12:
tmp[ 0] = 0;
tmp[ 1] = 1;
tmp[ 2] = 2;
tmp[ 3] = 6;
tmp[ 4] = 7;
tmp[ 5] = 8;
tmp[ 6] = 3;
tmp[ 7] = 4;
tmp[ 8] = 5;
tmp[ 9] = 9;
tmp[10] = 10;
tmp[11] = 11;
break;
case COH2D6:
tmp[0] = 0;
tmp[1] = 2;
tmp[2] = 1;
tmp[3] = 4;
tmp[4] = 5;
tmp[5] = 3;
break;
case COH2D4:
tmp[0] = 0;
tmp[1] = 1;
tmp[2] = 3;
tmp[3] = 2;
break;
case HEX2:
tmp[12] = 16;
tmp[13] = 17;
tmp[14] = 18;
tmp[15] = 19;
tmp[16] = 12;
tmp[17] = 13;
tmp[18] = 14;
tmp[19] = 15;
break;
case PRISM2:
tmp[ 0] = 0;
tmp[ 1] = 1;
tmp[ 2] = 2;
tmp[ 3] = 3;
tmp[ 4] = 4;
tmp[ 5] = 5;
tmp[ 6] = 6;
tmp[ 7] = 7;
tmp[ 8] = 8;
tmp[ 9] = 12;
tmp[10] = 13;
tmp[11] = 14;
tmp[12] = 9;
tmp[13] = 10;
tmp[14] = 11;
break;
default:
//nothing to change
break;
}
this->write_reorder[it->first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
ParaviewHelper::~ParaviewHelper(){
std::map<ElemType, VTKCellType>::iterator it;
for(it = this->paraview_code_type.begin();
it != this->paraview_code_type.end(); ++it) {
delete [] this->write_reorder[it->first];
}
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::writeTimePVD(const std::string & filename,
const std::vector< std::pair<Real, std::string> > & pvtus) {
std::ofstream pvd_file;
pvd_file.open(filename.c_str());
if(!pvd_file.good()) {
IOHELPER_THROW("DumperParaview was not able to open the file \"" << filename, _et_file_error);
}
pvd_file << "<?xml version=\"1.0\"?>" << std::endl
<< "<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\">" << std::endl
<< " <Collection>" << std::endl;
- std::vector< std::pair<Real, std::string> >::const_iterator it = pvtus.begin();
- std::vector< std::pair<Real, std::string> >::const_iterator end = pvtus.end();
+ auto it = pvtus.begin();
+ auto end = pvtus.end();
for (;it != end; ++it) {
pvd_file << " <DataSet timestep=\"" << it->first << "\" group=\"\" part=\"0\" file=\""
<< it->second << "\"/>" << std::endl;
}
pvd_file << " </Collection>" << std::endl
<< "</VTKFile>" << std::endl;
pvd_file.close();
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::writeHeader(int nb_nodes,int nb_elems){
file << "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" " ;
file << "byte_order=\"LittleEndian\">" << std::endl;
file << " <UnstructuredGrid>" << std::endl
<< " <Piece NumberOfPoints= \""
<< nb_nodes << "\" NumberOfCells=\""
<< nb_elems << "\">" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::PDataArray(const std::string & name, int nb_components, const std::string & type){
file << " <PDataArray type=\"" << type << "\" NumberOfComponents=\""
<< nb_components << "\" Name=\"" << name << "\" format=\"";
- if (bflag == BASE64) file << "binary";
- else file << "ascii";
+ if (bflag == BASE64) {
+ file << "binary";
+ } else {
+ file << "ascii";
+ }
file << "\"></PDataArray>" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::write_conclusion(){
file << " </Piece>" << std::endl;
file << " </UnstructuredGrid>" << std::endl;
file << "</VTKFile>" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::startData(const std::string & name,
int nb_components,
const std::string & type){
file << " <DataArray type=\"" << type << "\" ";
- if (nb_components) file << "NumberOfComponents=\"" << nb_components << "\" ";
+ if (nb_components) {
+ file << "NumberOfComponents=\"" << nb_components << "\" ";
+ }
file << "Name=\"" << name << "\" format=\"";
- if (bflag == BASE64) file << "binary";
- else file << "ascii";
+ if (bflag == BASE64) {
+ file << "binary";
+ } else {
+ file << "ascii";
+ }
file << "\">" << std::endl;
- if (bflag == BASE64) b64.CreateHeader();
+ if (bflag == BASE64) {
+ b64.CreateHeader();
+ }
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::endData(){
- if (bflag == BASE64) b64.WriteHeader();
+ if (bflag == BASE64) {
+ b64.WriteHeader();
+ }
file << std::endl << " </DataArray>" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::startDofList(int dimension){
file << " <Points>" << std::endl;
startData("positions", dimension, "Float64");
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::endDofList(){
endData();
file << " </Points>" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::startCells(){
file << " <Cells>" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::endCells(){
file << " </Cells>" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::startCellsConnectivityList(){
startData("connectivity",0,"Int32");
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::endCellsConnectivityList(){
endData();
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::startCellsoffsetsList(){
startData("offsets",0,"Int32");
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::endCellsoffsetsList(){
endData();
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::startCellstypesList(){
startData("types",0,"UInt32");
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::endCellstypesList(){
endData();
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::startPointDataList(){
file << " <PointData>" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::endPointDataList(){
file << " </PointData>" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::startCellDataList(){
file << " <CellData>" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ParaviewHelper::endCellDataList(){
file << " </CellData>" << std::endl;
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
diff --git a/third-party/iohelper/src/paraview_helper.hh b/third-party/iohelper/src/paraview_helper.hh
index 681a2598b..c5aafa053 100644
--- a/third-party/iohelper/src/paraview_helper.hh
+++ b/third-party/iohelper/src/paraview_helper.hh
@@ -1,258 +1,258 @@
/**
* @file paraview_helper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Wed Jun 05 2013
*
* @brief paraview helper header
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __IOHELPER_PARAVIEW_HELPER_H__
-#define __IOHELPER_PARAVIEW_HELPER_H__
+#ifndef IOHELPER_PARAVIEW_HELPER_H_
+#define IOHELPER_PARAVIEW_HELPER_H_
/* -------------------------------------------------------------------------- */
#include "base64.hh"
#include <iomanip>
#include <map>
#include "visitor.hh"
#include "field_interface.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
// Taken from vtkCellType.h
enum VTKCellType {
// Linear cells
VTK_EMPTY_CELL = 0,
VTK_VERTEX = 1,
VTK_POLY_VERTEX = 2,
VTK_LINE = 3,
VTK_POLY_LINE = 4,
VTK_TRIANGLE = 5,
VTK_TRIANGLE_STRIP = 6,
VTK_POLYGON = 7,
VTK_PIXEL = 8,
VTK_QUAD = 9,
VTK_TETRA = 10,
VTK_VOXEL = 11,
VTK_HEXAHEDRON = 12,
VTK_WEDGE = 13,
VTK_PYRAMID = 14,
VTK_PENTAGONAL_PRISM = 15,
VTK_HEXAGONAL_PRISM = 16,
// Quadratic, isoparametric cells
VTK_QUADRATIC_EDGE = 21,
VTK_QUADRATIC_TRIANGLE = 22,
VTK_QUADRATIC_QUAD = 23,
VTK_QUADRATIC_POLYGON = 36,
VTK_QUADRATIC_TETRA = 24,
VTK_QUADRATIC_HEXAHEDRON = 25,
VTK_QUADRATIC_WEDGE = 26,
VTK_QUADRATIC_PYRAMID = 27,
VTK_BIQUADRATIC_QUAD = 28,
VTK_TRIQUADRATIC_HEXAHEDRON = 29,
VTK_QUADRATIC_LINEAR_QUAD = 30,
VTK_QUADRATIC_LINEAR_WEDGE = 31,
VTK_BIQUADRATIC_QUADRATIC_WEDGE = 32,
VTK_BIQUADRATIC_QUADRATIC_HEXAHEDRON = 33,
VTK_BIQUADRATIC_TRIANGLE = 34,
// Polyhedron cell (consisting of polygonal faces)
VTK_POLYHEDRON = 42,
// Higher order cells in parametric form
VTK_PARAMETRIC_CURVE = 51,
VTK_PARAMETRIC_SURFACE = 52,
VTK_PARAMETRIC_TRI_SURFACE = 53,
VTK_PARAMETRIC_QUAD_SURFACE = 54,
VTK_PARAMETRIC_TETRA_REGION = 55,
VTK_PARAMETRIC_HEX_REGION = 56,
// Higher order cells
VTK_HIGHER_ORDER_EDGE = 60,
VTK_HIGHER_ORDER_TRIANGLE = 61,
VTK_HIGHER_ORDER_QUAD = 62,
VTK_HIGHER_ORDER_POLYGON = 63,
VTK_HIGHER_ORDER_TETRAHEDRON = 64,
VTK_HIGHER_ORDER_WEDGE = 65,
VTK_HIGHER_ORDER_PYRAMID = 66,
VTK_HIGHER_ORDER_HEXAHEDRON = 67,
VTK_NUMBER_OF_CELL_TYPES
};
inline std::ostream & operator <<(std::ostream & stream, const VTKCellType & type) {
stream << UInt(type);
return stream;
}
class ParaviewHelper : public Visitor {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
enum Stage{
_s_writePosition,
_s_writeFieldProperty,
_s_writeField,
_s_writeConnectivity,
_s_writeElemType,
_s_buildOffsets
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ParaviewHelper(File & f, UInt mode);
~ParaviewHelper() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
//! write the PVTU file
template <typename T>
void writePVTU(T & per_node_data, T & per_elem_data,
const std::vector<std::string> & vtus);
//! write the PVD file for time description
static void writeTimePVD(const std::string & filename,
const std::vector< std::pair<Real, std::string> > & pvtus);
//! write the header of a vtu file
void writeHeader(int nb_nodes,int nb_elems);
//! write a field
template <typename T> void writeField(T & data);
//! write a connectivity field
template <typename T> void writeConnectivity(T & data);
//! write an element type field
template <typename T> void writeElemType(T & data);
//! write the field properties
template <typename T> void writeFieldProperty(T & data);
//! write the connectivities offset
template <typename T> void writeOffsets(T & data);
template <typename T>
void pushDataFields(T & per_node_data, T & per_elem_data);
//! push the position field to the paraview file
void pushPosition(FieldInterface & f);
//! push a field to the paraview file
void pushField(FieldInterface & f);
//! build the offset from connectivities
void buildOffsets(FieldInterface & f);
//! push a connectivity field
void pushConnectivity(FieldInterface & f);
//! push a element type field
void pushElemType(FieldInterface & f);
//! get the formated vtu name
// static std::string getVTUName(const std::string & basename, UInt proc);
//! push a small array of values
template <template<typename T> class Cont, typename T>
void pushData(const Cont<T> & n);
//! push a small array of values of homogeneous values with padding to size dim
template <template<typename T> class Cont, typename T>
inline void pushData(const Cont<T> & n, UInt dim);
//! pushing datum
template <typename T> void pushDatum(const T & n, UInt size = 3);
//! visitor system
template <typename T> void visitField(T & visited);
private:
void setMode(int mode);
- std::string dataTypeToStr(DataType data_type);
+ static std::string dataTypeToStr(DataType data_type);
/* ------------------------------------------------------------------------ */
/* Methods for writing control sequences in the paraview files */
/* ------------------------------------------------------------------------ */
public:
void startDofList(int dimension);
void endDofList();
void startCells();
void endCells();
void startCellsConnectivityList();
void endCellsConnectivityList();
void startCellsoffsetsList();
void endCellsoffsetsList();
void startCellstypesList();
void endCellstypesList();
void startPointDataList();
void endPointDataList();
void startCellDataList();
void endCellDataList();
void startData(const std::string & name, int nb_components, const std::string & type);
void PDataArray(const std::string & name, int nb_components, const std::string & type);
void endData();
void write_conclusion();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
Base64Writer b64;
int bflag;
File & file;
long header_offset;
unsigned int compteur;
Stage current_stage;
bool position_flag;
//! mapping between iohelper elements and paraview elements
std::map<ElemType, VTKCellType> paraview_code_type;
//! mapping of the connectivities between iohelper and paraview
std::map<ElemType, UInt *> write_reorder;
};
/* -------------------------------------------------------------------------- */
#include "paraview_helper.tcc"
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_PARAVIEW_HELPER_H__ */
+#endif /* IOHELPER_PARAVIEW_HELPER_H_ */
diff --git a/third-party/iohelper/src/paraview_helper.tcc b/third-party/iohelper/src/paraview_helper.tcc
index 27b7ecd82..b3901f4bc 100644
--- a/third-party/iohelper/src/paraview_helper.tcc
+++ b/third-party/iohelper/src/paraview_helper.tcc
@@ -1,310 +1,326 @@
#include <cassert>
#if defined(__INTEL_COMPILER)
#pragma warning ( push )
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
#endif //defined(__INTEL_COMPILER)
inline std::string ParaviewHelper::dataTypeToStr(DataType data_type) {
std::string str;
switch(data_type) {
case _bool : str = "UInt8" ; break;
case _uint : str = "UInt32" ; break;
case _int : str = "Int32" ; break;
case _float : str = "Float32"; break;
case _double : str = "Float64"; break;
case _uint64 : str = "UInt64" ; break;
case _int64 : str = "Int64" ; break;
case _uint8 : str = "UInt8" ; break;
}
return str;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::visitField(T & visited){
this->position_flag = false;
switch (current_stage){
case _s_writeFieldProperty: writeFieldProperty(visited); break;
case _s_writePosition: this->position_flag = true; /* FALLTHRU */
// [[fallthrough]] un-comment when compiler gets it
case _s_writeField: writeField(visited); break;
case _s_writeConnectivity: writeConnectivity(visited); break;
case _s_writeElemType: writeElemType(visited); break;
case _s_buildOffsets: writeOffsets(visited); break;
default:
std::stringstream sstr;
sstr << "the stage " << current_stage << " is not a known paraviewhelper stage";
IOHELPER_THROW(sstr.str(),
IOHelperException::_et_unknown_visitor_stage);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeFieldProperty(T & data){
- if (data.isHomogeneous() == false)
+ if (not static_cast<bool>(data.isHomogeneous()))
IOHELPER_THROW(std::string("try to write field property of a non homogeneous field"),
IOHelperException::_et_non_homogeneous_data);
UInt dim = data.getDim();
std::string name = data.getName();
PDataArray(name, dim, dataTypeToStr(data.getDataType()));
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeField(T & data){
typename T::iterator it = data.begin();
typename T::iterator end = data.end();
compteur = 0;
UInt dim;
if(data.isHomogeneous()) {
dim = data.getDim();
- if(position_flag)
+ if (position_flag) {
dim = 3;
- for (; it != end; ++it)
+ }
+ for (; it != end; ++it) {
pushData((*it), dim);
+ }
}
else {
- for (; it != end; ++it)
+ for (; it != end; ++it) {
pushData((*it));
+ }
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeConnectivity(T & data) {
typename T::iterator it = data.begin();
typename T::iterator end = data.end();
for (; it != end; ++it) {
auto type = (ElemType)it.element_type();
//typename T::iterator::type & n = *it;
UInt dim = (*it).size();
assert(nb_node_per_elem[type] == dim);
UInt * reorder = this->write_reorder[type];
for (UInt i = 0; i < dim; ++i) {
this->pushDatum((*it)[reorder[i]], dim);
}
}
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeElemType(T & data){
typename T::iterator it = data.begin();
typename T::iterator end = data.end();
for (; it != end; ++it) {
auto type = (ElemType)it.element_type();
this->pushDatum(this->paraview_code_type[type], 1);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeOffsets(T & data){
typename T::iterator it = data.begin();
typename T::iterator end = data.end();
UInt count = 0;
for (; it != end; ++it) {
count += (*it).size();
pushDatum(count);
}
}
/* -------------------------------------------------------------------------- */
template <template<typename T> class Cont, typename T>
inline void ParaviewHelper::pushData(const Cont<T> & n, UInt dim){
for (UInt i = 0; i < n.size(); ++i) {
pushDatum<T>(n[i], dim);
}
for (UInt i = n.size(); i < dim; ++i) { T t = T(); this->pushDatum<T>(t, dim); }
}
/* -------------------------------------------------------------------------- */
template <template<typename T> class Cont, typename T>
inline void ParaviewHelper::pushData(const Cont<T> & n) {
for (UInt i = 0; i < n.size(); ++i) {
pushDatum<T>(n[i], n.size());
}
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::setMode(int mode){
bflag = BASE64 & mode;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writePVTU(T & per_node_data, T & per_elem_data,
const std::vector<std::string> & vtus){
current_stage = _s_writeFieldProperty;
file << "<VTKFile type=\"PUnstructuredGrid\" version=\"0.1\" " << std::endl;
file << "byte_order=\"LittleEndian\">" << std::endl;
file << " <PUnstructuredGrid GhostLevel=\"0\">" << std::endl;
file << " <PPoints>" << std::endl;
file << " <PDataArray type=\"Float64\" NumberOfComponents=\"3\" format=\"";
- if (bflag == BASE64) file << "binary";
- else file << "ascii";
+ if (bflag == BASE64) {
+ file << "binary";
+ } else {
+ file << "ascii";
+ }
file << "\" />" << std::endl;
file << " </PPoints>" << std::endl;
file << " <PPointData>" << std::endl;
- typename T::iterator itNodeField = per_node_data.begin();
- typename T::iterator endNodeField = per_node_data.end();
- for ( ; itNodeField != endNodeField ; ++itNodeField)
- if ((*itNodeField).first != "positions")
+ auto itNodeField = per_node_data.begin();
+ auto endNodeField = per_node_data.end();
+ for (; itNodeField != endNodeField; ++itNodeField) {
+ if ((*itNodeField).first != "positions") {
(*itNodeField).second->accept(*this);
+ }
+ }
file << " </PPointData>" << std::endl;
file << " <PCellData>" << std::endl;
- typename T::iterator itElemField = per_elem_data.begin();
- typename T::iterator endElemField = per_elem_data.end();
+ auto itElemField = per_elem_data.begin();
+ auto endElemField = per_elem_data.end();
for (; itElemField != endElemField ; ++itElemField) {
std::string name = (*itElemField).first;
- if (name == "connectivities" ||
- name == "element_type") continue;
+ if (name == "connectivities" || name == "element_type") {
+ continue;
+ }
(*itElemField).second->accept(*this);
}
file << " </PCellData>" << std::endl;
- for (UInt l = 0 ; l < vtus.size() ; ++l)
+ for (UInt l = 0; l < vtus.size(); ++l) {
file << " <Piece Source=\"" << vtus[l] << "\" />" << std::endl;
+ }
file << " </PUnstructuredGrid>" << std::endl;
file << "</VTKFile>" << std::endl;
file.close();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParaviewHelper::pushDataFields(T & per_node_data, T & per_elem_data){
startPointDataList();
{
- typename T::iterator itNodeField = per_node_data.begin();
- typename T::iterator endNodeField = per_node_data.end();
- for ( ; itNodeField != endNodeField ; ++itNodeField) {
- std::string name = (*itNodeField).first;
- if (name == "positions") continue;
- FieldInterface & f = *(*itNodeField).second;
- startData(f.getName(), f.getDim(), dataTypeToStr(f.getDataType()));
- pushField(f);
- endData();
+ auto itNodeField = per_node_data.begin();
+ auto endNodeField = per_node_data.end();
+ for (; itNodeField != endNodeField; ++itNodeField) {
+ std::string name = (*itNodeField).first;
+ if (name == "positions") {
+ continue;
+ }
+ FieldInterface & f = *(*itNodeField).second;
+ startData(f.getName(), f.getDim(), dataTypeToStr(f.getDataType()));
+ pushField(f);
+ endData();
}
}
endPointDataList();
startCellDataList();
{
- typename T::iterator itElemField = per_elem_data.begin();
- typename T::iterator endElemField = per_elem_data.end();
- for ( ; itElemField != endElemField ; ++itElemField) {
- std::string name = (*itElemField).first;
- if (name == "connectivities" ||
- name == "element_type") continue;
-
- FieldInterface & f = *(*itElemField).second;
- startData(f.getName(),f.getDim(), dataTypeToStr(f.getDataType()));
- pushField(f);
- endData();
+ auto itElemField = per_elem_data.begin();
+ auto endElemField = per_elem_data.end();
+ for (; itElemField != endElemField; ++itElemField) {
+ std::string name = (*itElemField).first;
+ if (name == "connectivities" || name == "element_type") {
+ continue;
+ }
+
+ FieldInterface & f = *(*itElemField).second;
+ startData(f.getName(), f.getDim(), dataTypeToStr(f.getDataType()));
+ pushField(f);
+ endData();
}
}
endCellDataList();
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::pushDatum(const T & n,
__attribute__((unused)) UInt size){
- if (bflag == BASE64)
+ if (bflag == BASE64) {
b64.push<T>(n);
- else{
- if (compteur == 0)
+ } else {
+ if (compteur == 0) {
file << " ";
+ }
++compteur;
file << n << " ";
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void ParaviewHelper::pushDatum<double>(const double & n,
UInt size){
- if (bflag == BASE64)
+ if (bflag == BASE64) {
b64.push<double>(n);
- else {
- if (compteur % size == 0)
+ } else {
+ if (compteur % size == 0) {
file << " ";
+ }
file << std::setw(22);
file << std::setprecision(15);
file << std::scientific;
file << n;
file << " ";
++compteur;
- if (compteur % size == 0)
+ if (compteur % size == 0) {
file << std::endl;
+ }
}
}
/* -------------------------------------------------------------------------- */
template <>
-inline void ParaviewHelper::pushDatum<ElemType>(const ElemType & type,
+inline void ParaviewHelper::pushDatum<ElemType>(const ElemType & n,
__attribute__((unused)) UInt size){
- UInt n = this->paraview_code_type[type];
- pushDatum<UInt>(n);
+ UInt n_ = this->paraview_code_type[n];
+ pushDatum<UInt>(n_);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::pushPosition(FieldInterface & f){
current_stage = _s_writePosition;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::pushField(FieldInterface & f){
current_stage = _s_writeField;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::pushConnectivity(FieldInterface & f) {
current_stage = _s_writeConnectivity;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::pushElemType(FieldInterface & f) {
current_stage = _s_writeElemType;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::buildOffsets(FieldInterface & f){
current_stage = _s_buildOffsets;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
#pragma warning ( pop )
#endif //defined(__INTEL_COMPILER)
diff --git a/third-party/iohelper/src/reader.cc b/third-party/iohelper/src/reader.cc
index ca16498c1..c5098b1f2 100644
--- a/third-party/iohelper/src/reader.cc
+++ b/third-party/iohelper/src/reader.cc
@@ -1,163 +1,163 @@
/**
* @file reader.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Thu Nov 01 2012
*
* @brief reader implementation
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "reader.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/* -------------------------------------------------------------------------- */
Reader::Reader(){
position = NULL;
connec = NULL;
dump_step = 0;
elem_type = -1;
base_name[0] = '\0';
prefix[0] = '\0';
}
/* -------------------------------------------------------------------------- */
Reader::~Reader(){
if (position)
delete position;
if (connec)
delete connec;
{
std::map<std::string,Field<double> *>::iterator it = per_node_data.begin();
std::map<std::string,Field<double> *>::iterator end = per_node_data.end();
while (it != end){
delete (*it).second;
++it;
}
}
{
std::map<std::string,Field<double> *>::iterator it = per_element_data.begin();
std::map<std::string,Field<double> *>::iterator end = per_element_data.end();
while (it != end){
delete (*it).second;
++it;
}
}
}
/* -------------------------------------------------------------------------- */
void Reader::Init(){
}
/* -------------------------------------------------------------------------- */
void Reader::AddNodeDataField(const string & name){
if (per_node_data.count(name) != 0) delete(per_node_data[name]);
Field<double> * temp = new Field<double>();
temp->setName(name);
per_node_data[name] = temp;
}
/* -------------------------------------------------------------------------- */
void Reader::AddElemDataField(const char * name){
if (per_element_data.count(name) != 0) delete(per_element_data[name]);
if (connec == NULL) FATAL("connectivity should be provided before elemental fields ! Please use SetConnectivity function before AddElemDataField");
Field<double> * temp = new Field<double>();
temp->setName(name);
per_element_data[name] = temp;
}
/* -------------------------------------------------------------------------- */
void Reader::SetPoints(const std::string & n){
position = new Field<double>();
base_name = n;
}
/* -------------------------------------------------------------------------- */
void Reader::SetConnectivity(int elem_type){
connec = new Field<int>();
this->elem_type = elem_type;
}
/* -------------------------------------------------------------------------- */
void Reader::SetPrefix(const std::string & dir){
prefix = dir;
}
/* -------------------------------------------------------------------------- */
void Reader::SetParallelContext(int me, int wld_size){
my_rank = me;
world_size = wld_size;
}
/* -------------------------------------------------------------------------- */
double * Reader::GetPoints(){
return position->getData();
}
/* -------------------------------------------------------------------------- */
int * Reader::GetConnectivity(){
return connec->getData();
}
/* -------------------------------------------------------------------------- */
double * Reader::GetNodeDataField(const char * name){
if (per_node_data.count(name) == 0) FATAL("node data field named " << name << " was not reloaded");
return per_node_data[name]->getData();
}
/* -------------------------------------------------------------------------- */
double * Reader::GetElemDataField(const char * name){
if (per_element_data.count(name) == 0) FATAL("elem data field named " << name << " was not reloaded");
return per_element_data[name]->getData();
}
/* -------------------------------------------------------------------------- */
int Reader::GetNumberNodes(){
return position->getNbDof();
}
/* -------------------------------------------------------------------------- */
int Reader::GetNumberElements(){
return connec->getNbDof();
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
diff --git a/third-party/iohelper/src/reader.hh b/third-party/iohelper/src/reader.hh
index d58dc6d35..eccd21f3a 100644
--- a/third-party/iohelper/src/reader.hh
+++ b/third-party/iohelper/src/reader.hh
@@ -1,127 +1,120 @@
/**
* @file reader.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Thu Nov 01 2012
*
* @brief reader description
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * IOHelper is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * IOHelper is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the
+ * Free Software Foundation, either version 3 of the License, or (at your
+ * option) any later version.
*
- * IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ * IOHelper is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for
+ * more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
-#ifndef __IOHELPER_READER_H__
-#define __IOHELPER_READER_H__
+#ifndef IOHELPER_READER_H_
+#define IOHELPER_READER_H_
/* -------------------------------------------------------------------------- */
+#include "iohelper_common.hh"
#include <map>
#include <string>
-#include "iohelper_common.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/** Class Reader
* Interface of a reader
*/
-class Reader{
+class Reader {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
- public:
-
+public:
Reader();
virtual ~Reader();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
//! dump to file
- virtual void Read()=0;
+ virtual void Read() = 0;
//! do the allocation
void Init();
//! give vector with coordinates
void SetPoints(const std::string & name);
//! give vector with coordinates
void SetConnectivity(int elem_type);
//! give vector to per node data
void AddNodeDataField(const std::string & name);
//! give vector to per element data
- void AddElemDataField(const char *name);
+ void AddElemDataField(const char * name);
//! set prefix directory
void SetPrefix(const std::string & dir);
// ! set parallel context
void SetParallelContext(int me, int wld_size);
//! set mode
- virtual void SetMode(int mode){flag_compressed = mode & COMPRESSED;}
+ virtual void SetMode(int mode) { flag_compressed = mode & COMPRESSED; }
//! give vector with coordinates
double * GetPoints();
//! give vector to connectivity
int * GetConnectivity();
//! give vector to per node data
- double * GetNodeDataField(const char *name);
+ double * GetNodeDataField(const char * name);
//! give vector to per element data
- double * GetElemDataField(const char *name);
+ double * GetElemDataField(const char * name);
//! return number of read nodes
int GetNumberNodes();
//! return number of read elements
int GetNumberElements();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
- protected:
-
+protected:
std::string prefix;
std::string base_name;
int dump_step;
//! flag to produce zipped files
bool flag_compressed;
// //! vector of positions
// Field<double> * position;
// //! vector of connectivity
// Field<int> * connec;
// //! vector of additional per node data
// std::map<std::string,Field<double> *> per_node_data;
// //! vector of additional per element data
// std::map<std::string,Field<double> *> per_element_data;
int world_size;
int my_rank;
int elem_type;
int connectivity_mode;
-
};
+} // namespace iohelper
-
-
-__END_IOHELPER__
-
-
-#endif /* __IOHELPER_READER_H__ */
+#endif /* IOHELPER_READER_H_ */
diff --git a/third-party/iohelper/src/reader_restart.cc b/third-party/iohelper/src/reader_restart.cc
index 6b19c3245..a8dce637d 100644
--- a/third-party/iohelper/src/reader_restart.cc
+++ b/third-party/iohelper/src/reader_restart.cc
@@ -1,134 +1,131 @@
/**
* @file reader_restart.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Thu Nov 01 2012
*
* @brief implementation for the restart reader
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iomanip>
#include "reader_restart.hh"
#include "file_manager.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
void ReaderRestart::Read(){
stringstream temp;
File file;
string line;
stringstream buffer;
UInt tmp;
/* node coordinates */
temp << prefix << "/" << base_name << "-coordinates-" << std::setfill('0') << std::setw(4) << dump_step << ".restart";
// file.open(temp.str(),std::ios_base::in | std::ios_base::binary,flag_compressed);
file >> tmp;
position->setNbDof(tmp);
file >> tmp;
position->setDim(tmp);
position->AllocateData();
double * ptr_pos = position->getData();
file.read((char*)ptr_pos,position->getNbDof()*position->getDim()*sizeof(double));
file.close();
/* nodal data */
{
std::map<std::string,Field<double> *>::iterator it = per_node_data.begin();
std::map<std::string,Field<double> *>::iterator end = per_node_data.end();
while (it != end){
temp.str(std::string());
temp << prefix << "/" << base_name << "-" << (*it).second->getName() << "-" << std::setfill('0') << std::setw(4) << dump_step << ".restart";
// file.open(temp.str(),fstream::in | fstream::binary ,flag_compressed);
Field<double> * ptr_field = (*it).second;
file >> tmp;
ptr_field->setNbDof(tmp);
file >> tmp;
ptr_field->setDim(tmp);
if (ptr_field->getNbDof() != position->getNbDof())
DUMP("number of degree of freedom of " << ptr_field->name
<< " does not match that one of positions field");
ptr_field->AllocateData();
double * ptr = ptr_field->getData();
file.read((char*)ptr,ptr_field->getNbDof()*ptr_field->getDim()*sizeof(double));
file.close();
++it;
}
}
/* if only collection of points do not dump any element data */
if (elem_type == POINT_SET) return;
/* connectivity */
temp.str(std::string());
temp << prefix << "/" << base_name << "-connectivity-" << std::setfill('0') << std::setw(4) << dump_step << ".restart";
// file.open(temp.str(),fstream::in | fstream::binary,flag_compressed);
unsigned int offset;
offset = nb_node_per_elem[elem_type];
file >> tmp;
connec->setNbDof(tmp);
file >> tmp;
connec->setDim(tmp);
if (offset != connec->getDim())
FATAL("It appears that you are trying to reload a different kind of element !");
connec->AllocateData();
file.read((char*)connec->getData(),connec->getNbDof()*connec->getDim()*sizeof(int));
file.close();
/* element data */
{
std::map<std::string,Field<double> *>::iterator it = per_element_data.begin();
std::map<std::string,Field<double> *>::iterator end = per_element_data.end();
while (it != end){
temp.str(std::string());
temp << prefix << "/" << base_name << "-" << (*it).second->getName() << "-" << std::setfill('0') << std::setw(4) << dump_step << ".restart";
// file.open(temp.str(),fstream::in | fstream::binary,flag_compressed);
Field<double> * ptr_field = (*it).second;
file >> tmp;
ptr_field->setNbDof(tmp);
file >> tmp;
ptr_field->setDim(tmp);
if (ptr_field->getNbDof() != position->getNbDof())
DUMP("number of degree of freedom of " << ptr_field->name
<< " does not match that one of connectivity field");
ptr_field->AllocateData();
double * ptr = ptr_field->getData();
file.read((char*)ptr,ptr_field->getNbDof()*ptr_field->getDim()*sizeof(double));
file.close();
++it;
}
}
++dump_step;
}
-__END_IOHELPER__
-
-
-
+}
diff --git a/third-party/iohelper/src/reader_restart.hh b/third-party/iohelper/src/reader_restart.hh
index c324dfeca..e88a193e3 100644
--- a/third-party/iohelper/src/reader_restart.hh
+++ b/third-party/iohelper/src/reader_restart.hh
@@ -1,81 +1,79 @@
/**
* @file reader_restart.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Mar 11 2010
* @date last modification: Thu Nov 01 2012
*
* @brief header for restart reader
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHLPER_READER_RESTART_H__
-#define __IOHLPER_READER_RESTART_H__
+#ifndef IOHELPER_READER_RESTART_H_
+#define IOHELPER_READER_RESTART_H_
/* -------------------------------------------------------------------------- */
#include <map>
#include <string>
#include "reader.hh"
//#include "field.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/** Class ReadRestart
* Implementation of a read to restart
*/
class ReaderRestart : public Reader {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ReaderRestart():Reader(){};
~ReaderRestart(){
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
//! dump to file
void Read();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
-__END_IOHELPER__
-
-#endif /* __IOHLPER_READER_RESTART_H__ */
-
+}
+#endif /* IOHELPER_READER_RESTART_H_ */
diff --git a/third-party/iohelper/src/variable.cc b/third-party/iohelper/src/variable.cc
index d0484ed2f..c55529ca5 100644
--- a/third-party/iohelper/src/variable.cc
+++ b/third-party/iohelper/src/variable.cc
@@ -1,62 +1,62 @@
/**
* @file variable.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Jun 04 2013
* @date last modification: Tue Jun 04 2013
*
* @brief implementation of the Variable class
*
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "variable.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
/* -------------------------------------------------------------------------- */
template <>
VarType Variable<Real>::getVarDataType(){
return REAL;
}
/* -------------------------------------------------------------------------- */
template <>
VarType Variable<UInt>::getVarDataType(){
return UINT;
}
/* -------------------------------------------------------------------------- */
template <>
VarType Variable<bool>::getVarDataType(){
return BOOL;
}
/* -------------------------------------------------------------------------- */
template <>
VarType Variable<Int>::getVarDataType(){
return INT;
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
diff --git a/third-party/iohelper/src/variable.hh b/third-party/iohelper/src/variable.hh
index 9bcd53cb6..3b4adc268 100644
--- a/third-party/iohelper/src/variable.hh
+++ b/third-party/iohelper/src/variable.hh
@@ -1,85 +1,85 @@
/**
* @file variable.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Jun 04 2013
* @date last modification: Tue Jun 04 2013
*
* @brief for dump of global variables
*
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHELPER_VARIABLE_HH__
-#define __IOHELPER_VARIABLE_HH__
+#ifndef IOHELPER_VARIABLE_HH_
+#define IOHELPER_VARIABLE_HH_
/* -------------------------------------------------------------------------- */
#include "variable_interface.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
template <class Cont>
class Variable : public VariableInterface {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Variable(Cont & c, const std::string & name) : my_variable(c), name(name){};
~Variable() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
//! accept to be visited by a visitor
inline void accept(Visitor & v) const override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline DataType getDataType() const override {
return my_variable.getDataType();
}
//! return the dim
inline UInt getDim() const override { return my_variable.getDim(); }
//! return the description name of the container
inline std::string getName() const override { return name; }
inline const Cont & operator*() const { return my_variable; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
Cont & my_variable;
std::string name;
};
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_VARIABLE_HH__ */
+#endif /* IOHELPER_VARIABLE_HH_ */
diff --git a/third-party/iohelper/src/variable_inline_impl.hh b/third-party/iohelper/src/variable_inline_impl.hh
index c878868d1..0f560e94b 100644
--- a/third-party/iohelper/src/variable_inline_impl.hh
+++ b/third-party/iohelper/src/variable_inline_impl.hh
@@ -1,61 +1,61 @@
/**
* @file variable_inline_impl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Jun 04 2013
* @date last modification: Tue Jun 04 2013
*
* @brief inline implementation of dumper visitor
*
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "paraview_helper.hh"
#include "dumper_lammps.hh"
#include "dumper_text.hh"
-#ifndef __IOHELPER_VARIABLE_INLINE_IMPL_HH__
-#define __IOHELPER_VARIABLE_INLINE_IMPL_HH__
+#ifndef IOHELPER_VARIABLE_INLINE_IMPL_HH_
+#define IOHELPER_VARIABLE_INLINE_IMPL_HH_
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
template <class Cont>
inline void Variable<Cont>::accept(Visitor & v) const {
if (auto * ptr_txt = dynamic_cast<DumperText *>(&v)) {
ptr_txt->visitVariable(*this);
}
/*
else if (ParaviewHelper * ptr_ph = dynamic_cast<ParaviewHelper*>(&v)){
ptr_ph->visitVariable(*this);
} else if (iohelper::DumperLammps<iohelper::bond> * ptr_dlb = dynamic_cast<DumperLammps<bond>*>(&v)) {
ptr_dlb->visitVariable(*this);
} else if (DumperLammps<iohelper::atomic> * ptr_dla = dynamic_cast<DumperLammps<atomic>*>(&v)){
ptr_dla->visitVariable(*this);
}
*/
}
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_VARIABLE_INLINE_IMPL_HH__ */
+#endif /* IOHELPER_VARIABLE_INLINE_IMPL_HH_ */
diff --git a/third-party/iohelper/src/variable_interface.hh b/third-party/iohelper/src/variable_interface.hh
index e56c4267b..d0adc76e7 100644
--- a/third-party/iohelper/src/variable_interface.hh
+++ b/third-party/iohelper/src/variable_interface.hh
@@ -1,78 +1,78 @@
/**
* @file variable_interface.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Jun 04 2013
* @date last modification: Tue Jun 04 2013
*
* @brief variable interface
*
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHELPER_VARIABLE_INTERFACE_HH__
-#define __IOHELPER_VARIABLE_INTERFACE_HH__
+#ifndef IOHELPER_VARIABLE_INTERFACE_HH_
+#define IOHELPER_VARIABLE_INTERFACE_HH_
/* -------------------------------------------------------------------------- */
#include "visitor.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
class VariableInterface {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
VariableInterface() = default;
virtual ~VariableInterface() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void accept(Visitor & v) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
//! return the size per element (valid only if isHomogeneous is true)
virtual UInt getDim() const = 0;
//! return the description name of the container
virtual std::string getName() const = 0;
virtual DataType getDataType() const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_VARIABLE_INTERFACE_HH__ */
+#endif /* IOHELPER_VARIABLE_INTERFACE_HH_ */
diff --git a/third-party/iohelper/src/visitor.hh b/third-party/iohelper/src/visitor.hh
index 2673c193a..f6c1b9c3b 100644
--- a/third-party/iohelper/src/visitor.hh
+++ b/third-party/iohelper/src/visitor.hh
@@ -1,66 +1,66 @@
/**
* @file visitor.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Oct 12 2012
* @date last modification: Thu Nov 01 2012
*
* @brief visitor interface
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __IOHELPER_VISITOR_HH__
-#define __IOHELPER_VISITOR_HH__
+#ifndef IOHELPER_VISITOR_HH_
+#define IOHELPER_VISITOR_HH_
/* -------------------------------------------------------------------------- */
-__BEGIN_IOHELPER__
+namespace iohelper {
class Visitor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Visitor() = default;
virtual ~Visitor() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
-__END_IOHELPER__
+}
-#endif /* __IOHELPER_VISITOR_HH__ */
+#endif /* IOHELPER_VISITOR_HH_ */
diff --git a/third-party/iohelper/test/mesh_io_msh.hh b/third-party/iohelper/test/mesh_io_msh.hh
index cb5b2fd0e..d0cf2ec38 100644
--- a/third-party/iohelper/test/mesh_io_msh.hh
+++ b/third-party/iohelper/test/mesh_io_msh.hh
@@ -1,114 +1,114 @@
/**
* @file mesh_io_msh.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Oct 11 2012
* @date last modification: Thu Nov 01 2012
*
* @brief Read/Write for MSH files
*
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* IOHelper is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
-#ifndef __AKANTU_MESH_IO_MSH_HH__
-#define __AKANTU_MESH_IO_MSH_HH__
+#ifndef AKANTU_MESH_IO_MSH_HH_
+#define AKANTU_MESH_IO_MSH_HH_
/* -------------------------------------------------------------------------- */
#include <vector>
#include <map>
/* -------------------------------------------------------------------------- */
class MeshIOMSH {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
/// MSH element types
enum MSHElementType {
_msh_not_defined = 0,
_msh_segment_2 = 1, // 2-node line.
_msh_triangle_3 = 2, // 3-node triangle.
_msh_quadrangle_4 = 3, // 4-node quadrangle.
_msh_tetrahedron_4 = 4, // 4-node tetrahedron.
_msh_hexahedron_8 = 5, // 8-node hexahedron.
_msh_prism_1 = 6, // 6-node prism.
_msh_pyramid_1 = 7, // 5-node pyramid.
_msh_segment_3 = 8, // 3-node second order line
_msh_triangle_6 = 9, // 6-node second order triangle
_msh_quadrangle_9 = 10, // 9-node second order quadrangle
_msh_tetrahedron_10 = 11, // 10-node second order tetrahedron
_msh_hexahedron_27 = 12, // 27-node second order hexahedron
_msh_prism_18 = 13, // 18-node second order prism
_msh_pyramid_14 = 14, // 14-node second order pyramid
_msh_point = 15, // 1-node point.
_msh_quadrangle_8 = 16 // 8-node second order quadrangle
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSH();
virtual ~MeshIOMSH();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
virtual void read(const std::string & filename,
unsigned int spatial_dimension,
MSHElementType selected_type,
std::vector<double> & nodes,
std::vector<int> & connectivites);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
#define MAX_NUMBER_OF_NODE_PER_ELEMENT 10 // tetrahedron of second order
/// order in witch element as to be read
std::map<MSHElementType, unsigned int *> _read_order;
public:
/// number of nodes per msh element
std::map<MSHElementType, unsigned int> _msh_nodes_per_elem;
};
-#endif /* __AKANTU_MESH_IO_MSH_HH__ */
+#endif /* AKANTU_MESH_IO_MSH_HH_ */

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