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rAKA akantu
mesh.hh
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/**
* @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: Thu Jan 14 2016
*
* @brief the class representing the meshes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 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_MESH_HH__
#define __AKANTU_MESH_HH__
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_event_handler_manager.hh"
#include "aka_memory.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 <set>
/* -------------------------------------------------------------------------- */
namespace
akantu
{
class
Communicator
;
class
ElementSynchronizer
;
class
NodeSynchronizer
;
}
// namespace akantu
namespace
akantu
{
/* -------------------------------------------------------------------------- */
/* Mesh */
/* -------------------------------------------------------------------------- */
/**
* @class Mesh this contain the coordinates of the nodes in the Mesh.nodes
* 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
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 knowing its
/// ID
// Mesh(UInt spatial_dimension, const ID & nodes_id, const ID & id,
// 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
;
/// @typedef ConnectivityTypeList list of the types present in a Mesh
using
ConnectivityTypeList
=
std
::
set
<
ElementType
>
;
/// 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
);
private
:
/// initialize the connectivity to NULL and other stuff
void
init
();
/// function that computes the bounding box (fills xmin, xmax)
void
computeBoundingBox
();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public
:
/// patitionate the mesh among the processors involved in their computation
virtual
void
distribute
(
Communicator
&
communicator
);
virtual
void
distribute
();
/// 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
;
// /// 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 type <type>.
inline
void
addConnectivityType
(
const
ElementType
&
type
,
const
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
();
/* ------------------------------------------------------------------------ */
/* 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
(
NodesType
,
nodes_type
,
const
Array
<
NodeType
>
&
);
protected
:
AKANTU_GET_MACRO_NOT_CONST
(
NodesType
,
nodes_type
,
Array
<
NodeType
>
&
);
public
:
inline
NodeType
getNodeType
(
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
;
AKANTU_GET_MACRO
(
LowerBounds
,
lower_bounds
,
const
Vector
<
Real
>
&
);
AKANTU_GET_MACRO
(
UpperBounds
,
upper_bounds
,
const
Vector
<
Real
>
&
);
AKANTU_GET_MACRO
(
LocalLowerBounds
,
local_lower_bounds
,
const
Vector
<
Real
>
&
);
AKANTU_GET_MACRO
(
LocalUpperBounds
,
local_upper_bounds
,
const
Vector
<
Real
>
&
);
/// 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
;
/// 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
;
// /// get the connectivity list either for the elements or the ghost elements
// inline const ConnectivityTypeList &
// getConnectivityTypeList(const GhostType & ghost_type = _not_ghost) const;
/// compute the barycenter of a given element
private
:
inline
void
getBarycenter
(
UInt
element
,
const
ElementType
&
type
,
Real
*
barycenter
,
GhostType
ghost_type
=
_not_ghost
)
const
;
public
:
inline
void
getBarycenter
(
const
Element
&
element
,
Vector
<
Real
>
&
barycenter
)
const
;
void
getBarycenters
(
Array
<
Real
>
&
barycenter
,
const
ElementType
&
type
,
const
GhostType
&
ghost_type
)
const
;
#ifndef SWIG
/// get the element connected to a subelement
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
;
/// get the element connected to a subelement
auto
&
getElementToSubelement
(
const
ElementType
&
el_type
,
const
GhostType
&
ghost_type
=
_not_ghost
);
/// get the subelement connected to an element
const
auto
&
getSubelementToElement
(
const
ElementType
&
el_type
,
const
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
);
#endif
/// register a new ElementalTypeMap in the MeshData
template
<
typename
T
>
inline
ElementTypeMapArray
<
T
>
&
registerData
(
const
std
::
string
&
data_name
);
template
<
typename
T
>
inline
bool
hasData
(
const
ID
&
data_name
,
const
ElementType
&
el_type
,
const
GhostType
&
ghost_type
=
_not_ghost
)
const
;
/// 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
;
/// 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
);
/// tells if the data data_name is contained in the mesh or not
inline
bool
hasData
(
const
ID
&
data_name
)
const
;
/// 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
,
const
ElementKind
&
element_kind
);
template
<
typename
T
>
dumper
::
Field
*
createFieldFromAttachedData
(
const
std
::
string
&
field_id
,
const
std
::
string
&
group_name
,
const
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
,
bool
resize_with_parent
=
false
);
/// 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
;
}
/// defines is the mesh is distributed or not
inline
bool
isDistributed
()
const
{
return
this
->
is_distributed
;
}
#ifndef SWIG
/// return the dumper from a group and and a dumper name
DumperIOHelper
&
getGroupDumper
(
const
std
::
string
&
dumper_name
,
const
std
::
string
&
group_name
);
#endif
/* ------------------------------------------------------------------------ */
/* Wrappers on ElementClass functions */
/* ------------------------------------------------------------------------ */
public
:
/// get the number of nodes per element for a given element type
static
inline
UInt
getNbNodesPerElement
(
const
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
);
/// get the kind of the element type
static
inline
ElementKind
getKind
(
const
ElementType
&
type
);
/// get spatial dimension of a type of element
static
inline
UInt
getSpatialDimension
(
const
ElementType
&
type
);
/// get number of facets of a given element type
static
inline
UInt
getNbFacetsPerElement
(
const
ElementType
&
type
);
/// get number of facets of a given element type
static
inline
UInt
getNbFacetsPerElement
(
const
ElementType
&
type
,
UInt
t
);
#ifndef SWIG
/// get local connectivity of a facet for a given facet type
static
inline
auto
getFacetLocalConnectivity
(
const
ElementType
&
type
,
UInt
t
=
0
);
/// get connectivity of facets for a given element
inline
auto
getFacetConnectivity
(
const
Element
&
element
,
UInt
t
=
0
)
const
;
#endif
/// 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
);
#ifndef SWIG
/// get the type of the surface element associated to a given element
static
inline
constexpr
auto
getFacetType
(
const
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
);
#endif
/// get the number of nodes in the given element list
static
inline
UInt
getNbNodesPerElementList
(
const
Array
<
Element
>
&
elements
);
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
using
type_iterator
=
ElementTypeMapArray
<
UInt
,
ElementType
>::
type_iterator
;
using
ElementTypesIteratorHelper
=
ElementTypeMapArray
<
UInt
,
ElementType
>::
ElementTypesIteratorHelper
;
template
<
typename
...
pack
>
ElementTypesIteratorHelper
elementTypes
(
pack
&&
...
_pack
)
const
;
inline
type_iterator
firstType
(
UInt
dim
=
_all_dimensions
,
GhostType
ghost_type
=
_not_ghost
,
ElementKind
kind
=
_ek_regular
)
const
{
return
connectivities
.
firstType
(
dim
,
ghost_type
,
kind
);
}
inline
type_iterator
lastType
(
UInt
dim
=
_all_dimensions
,
GhostType
ghost_type
=
_not_ghost
,
ElementKind
kind
=
_ek_regular
)
const
{
return
connectivities
.
lastType
(
dim
,
ghost_type
,
kind
);
}
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_NOT_CONST(Communicator, *communicator, StaticCommunicator
// &);
#ifndef SWIG
AKANTU_GET_MACRO
(
Communicator
,
*
communicator
,
const
auto
&
);
AKANTU_GET_MACRO_NOT_CONST
(
Communicator
,
*
communicator
,
auto
&
);
#endif
/* ------------------------------------------------------------------------ */
/* Private methods for friends */
/* ------------------------------------------------------------------------ */
private
:
friend
class
MeshAccessor
;
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
<
NodeType
>
&
getNodesTypePointer
();
/// 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
);
/// get the ghost element counter
inline
Array
<
UInt
>
&
getGhostsCounters
(
const
ElementType
&
type
,
const
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
);
/// 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
);
AKANTU_GET_MACRO_NOT_CONST
(
MeshData
,
mesh_data
,
MeshData
&
);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private
:
/// array of the nodes coordinates
std
::
shared_ptr
<
Array
<
Real
>>
nodes
;
/// global node ids
std
::
unique_ptr
<
Array
<
UInt
>>
nodes_global_ids
;
/// node type, -3 pure ghost, -2 master for the node, -1 normal node, i in
/// [0-N] slave node and master is proc i
Array
<
NodeType
>
nodes_type
;
/// 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
;
/// list of all existing types in the mesh
// ConnectivityTypeList type_set;
/// the spatial dimension of this mesh
UInt
spatial_dimension
{
0
};
/// types offsets
// Array<UInt> types_offsets;
// /// list of all existing types in the mesh
// ConnectivityTypeList ghost_type_set;
// /// ghost types offsets
// Array<UInt> ghost_types_offsets;
/// min of coordinates
Vector
<
Real
>
lower_bounds
;
/// max of coordinates
Vector
<
Real
>
upper_bounds
;
/// size covered by the mesh on each direction
Vector
<
Real
>
size
;
/// local min of coordinates
Vector
<
Real
>
local_lower_bounds
;
/// local max of coordinates
Vector
<
Real
>
local_upper_bounds
;
/// 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
};
/// Communicator on which mesh is distributed
Communicator
*
communicator
;
/// Element synchronizer
std
::
unique_ptr
<
ElementSynchronizer
>
element_synchronizer
;
/// Node synchronizer
std
::
unique_ptr
<
NodeSynchronizer
>
node_synchronizer
;
using
NodesToElements
=
std
::
vector
<
std
::
unique_ptr
<
std
::
set
<
Element
>>>
;
/// This info is stored to simplify the dynamic changes
NodesToElements
nodes_to_elements
;
};
/// 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.cc"
#endif
/* __AKANTU_MESH_HH__ */
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