diff --git a/src/common/aka_grid_dynamic.hh b/src/common/aka_grid_dynamic.hh
index d717b12c8..9d7550fc4 100644
--- a/src/common/aka_grid_dynamic.hh
+++ b/src/common/aka_grid_dynamic.hh
@@ -1,512 +1,513 @@
/**
* @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
*
* @section LICENSE
*
* 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 <iostream>
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#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() {}
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)
this->it++;
}
neighbor_cells_iterator & operator++() {
UInt i = 0;
for (; i < position.size() && position(i) == 1; ++i)
;
if (i == position.size()) {
++it;
return *this;
}
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)
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())
return it->second;
return empty_cell;
}
decltype(auto) beginCell(const CellID & cell_id) {
auto it = cells.find(cell_id);
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())
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())
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())
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))
lower(i) = posl;
if (posu > upper(i))
upper(i) = posu;
}
return tmp;
} else {
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)
;
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)
stream << ", ";
stream << lower(i);
};
stream << "}" << std::endl;
stream << space << " + upper bounds : {";
for (UInt i = 0; i < upper.size(); ++i) {
if (i != 0)
stream << ", ";
stream << upper(i);
};
stream << "}" << std::endl;
stream << space << " + spacing : {";
for (UInt i = 0; i < spacing.size(); ++i) {
if (i != 0)
stream << ", ";
stream << spacing(i);
};
stream << "}" << std::endl;
stream << space << " + center : {";
for (UInt i = 0; i < center.size(); ++i) {
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 {
auto & nodes = const_cast<Array<Real> &>(mesh.getNodes());
- ElementType type;
+ ElementType type = _not_defined;
switch (dimension) {
case 1:
type = _segment_2;
break;
case 2:
type = _quadrangle_4;
break;
case 3:
type = _hexahedron_8;
break;
+
}
mesh.addConnectivityType(type);
auto & connectivity = const_cast<Array<UInt> &>(mesh.getConnectivity(type));
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)
pos(i) = center(i) + cell_id.getID(i) * spacing(i);
nodes.push_back(pos);
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__ */
diff --git a/src/fe_engine/element_class_structural.hh b/src/fe_engine/element_class_structural.hh
index d719c6e11..2dc673bdf 100644
--- a/src/fe_engine/element_class_structural.hh
+++ b/src/fe_engine/element_class_structural.hh
@@ -1,254 +1,254 @@
/**
* @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
*
* @section LICENSE
*
* 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__
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_classes/element_class_hermite_inline_impl.cc"
+#include "element_class_hermite_inline_impl.cc"
/* keep order */
-#include "element_classes/element_class_bernoulli_beam_inline_impl.cc"
-#include "element_classes/element_class_kirchhoff_shell_inline_impl.cc"
+#include "element_class_bernoulli_beam_inline_impl.cc"
+#include "element_class_kirchhoff_shell_inline_impl.cc"
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_ELEMENT_CLASS_STRUCTURAL_HH__ */
diff --git a/src/mesh_utils/global_ids_updater.cc b/src/mesh_utils/global_ids_updater.cc
index 0f906b957..8b64d3235 100644
--- a/src/mesh_utils/global_ids_updater.cc
+++ b/src/mesh_utils/global_ids_updater.cc
@@ -1,131 +1,136 @@
/**
* @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
*
* @section LICENSE
*
* 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) {
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 rank = comm.whoAmI();
Int nb_proc = comm.getNbProc();
if (nb_proc == 1)
return local_nb_new_nodes;
/// resize global ids array
Array<UInt> & nodes_global_ids = mesh.getGlobalNodesIds();
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
Matrix<UInt> local_master_nodes(2, nb_proc, 0);
for (UInt n = 0; n < old_nb_nodes; ++n)
if (mesh.isLocalOrMasterNode(n))
++local_master_nodes(0, rank);
/// compute amount of local or master doubled nodes
for (UInt n = old_nb_nodes; n < mesh.getNbNodes(); ++n)
if (mesh.isLocalOrMasterNode(n))
++local_master_nodes(1, rank);
comm.allGather(local_master_nodes);
local_master_nodes = local_master_nodes.transpose();
UInt old_global_nodes =
std::accumulate(local_master_nodes(0).storage(),
local_master_nodes(0).storage() + nb_proc, 0);
/// update global number of nodes
UInt total_nb_new_nodes =
std::accumulate(local_master_nodes(1).storage(),
local_master_nodes(1).storage() + nb_proc, 0);
if (total_nb_new_nodes == 0)
return 0;
/// set global ids of local and master nodes
UInt starting_index =
std::accumulate(local_master_nodes(1).storage(),
local_master_nodes(1).storage() + rank, old_global_nodes);
for (UInt n = old_nb_nodes; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n)) {
nodes_global_ids(n) = starting_index;
++starting_index;
} else {
nodes_global_ids(n) = -1;
}
}
MeshAccessor mesh_accessor(mesh);
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, _gst_giu_global_conn);
+#ifndef AKANTU_NDEBUG
for (auto node : nodes_types) {
auto node_type = mesh.getNodeType(node.first);
if (node_type != _nt_pure_ghost)
continue;
auto n = 0u;
+
for (auto & pair : node.second) {
if (std::get<1>(pair) == _nt_pure_ghost)
++n;
}
- if (n == node.second.size())
+
+ 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, _gst_giu_global_conn);
}
} // akantu
diff --git a/src/mesh_utils/global_ids_updater_inline_impl.cc b/src/mesh_utils/global_ids_updater_inline_impl.cc
index 390e9cfbb..14f427431 100644
--- a/src/mesh_utils/global_ids_updater_inline_impl.cc
+++ b/src/mesh_utils/global_ids_updater_inline_impl.cc
@@ -1,120 +1,128 @@
/**
* @file global_ids_updater_inline_impl.cc
*
* @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
*
* @section LICENSE
*
* 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"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_CC__
#define __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt GlobalIdsUpdater::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
UInt size = 0;
- if (tag == _gst_giu_global_conn)
+ if (tag == _gst_giu_global_conn){
size += Mesh::getNbNodesPerElementList(elements) *
- (sizeof(UInt) + sizeof(NodeType)) +
- sizeof(int);
-
+ sizeof(UInt);
+#ifndef AKANTU_NDEBUG
+ size += sizeof(NodeType) * Mesh::getNbNodesPerElementList(elements) + sizeof(int);
+#endif
+ }
return size;
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag != _gst_giu_global_conn)
return;
auto & global_nodes_ids = mesh.getGlobalNodesIds();
+#ifndef AKANTU_NDEBUG
buffer << int(mesh.getCommunicator().whoAmI());
-
+#endif
for (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.getNodeType(node);
+#endif
}
}
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag != _gst_giu_global_conn)
return;
auto & global_nodes_ids = mesh.getGlobalNodesIds();
+#ifndef AKANTU_NDEBUG
int proc;
buffer >> proc;
+#endif
for (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
NodeType node_type;
buffer >> node_type;
-
if (reduce)
nodes_types[node].push_back(std::make_pair(proc, node_type));
+#endif
if (index == UInt(-1))
continue;
if (mesh.isSlaveNode(node))
global_nodes_ids(node) = index;
}
}
}
} // akantu
#endif /* __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_CC__ */