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dof_manager.cc
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/**
* @file dof_manager.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Aug 12 09:52:30 2015
*
* @brief Implementation of the common parts of the DOFManagers
*
* @section LICENSE
*
* 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.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
#include "sparse_matrix.hh"
#include "static_communicator.hh"
#include "non_linear_solver.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(nullptr), local_system_size(0),
pure_local_system_size(0), system_size(0),
communicator(StaticCommunicator::getStaticCommunicator()) {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(Mesh & mesh, const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(&mesh), local_system_size(0),
pure_local_system_size(0), system_size(0),
communicator(mesh.getCommunicator()) {
this->mesh->registerEventHandler(*this, 20);
UInt nb_nodes = this->mesh->getNbNodes();
this->nodes_to_elements.resize(nb_nodes);
for (UInt n = 0; n < nb_nodes; ++n) {
this->nodes_to_elements[n] = new std::set<Element>();
}
}
/* -------------------------------------------------------------------------- */
DOFManager::~DOFManager() {
NodesToElements::scalar_iterator nte_it = this->nodes_to_elements.begin();
NodesToElements::scalar_iterator nte_end = this->nodes_to_elements.end();
for (; nte_it != nte_end; ++nte_it)
delete *nte_it;
DOFStorage::iterator ds_it = dofs.begin();
DOFStorage::iterator ds_end = dofs.end();
for (; ds_it != ds_end; ++ds_it)
delete ds_it->second;
SparseMatricesMap::iterator sm_it = matrices.begin();
SparseMatricesMap::iterator sm_end = matrices.end();
for (; sm_it != sm_end; ++sm_it)
delete sm_it->second;
NonLinearSolversMap::iterator nls_it = non_linear_solvers.begin();
NonLinearSolversMap::iterator nls_end = non_linear_solvers.end();
for (; nls_it != nls_end; ++nls_it)
delete nls_it->second;
TimeStepSolversMap::iterator tss_it = time_step_solvers.begin();
TimeStepSolversMap::iterator tss_end = time_step_solvers.end();
for (; tss_it != tss_end; ++tss_it)
delete tss_it->second;
}
/* -------------------------------------------------------------------------- */
void DOFManager::getEquationsNumbers(const ID &, Array<UInt> &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
std::vector<ID> DOFManager::getDOFIDs() const {
std::vector<ID> keys;
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,
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 = NULL;
if (filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
filter_it = filter_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
AKANTU_DEBUG_ASSERT(elementary_vect.getSize() == 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<UInt>::const_vector_iterator conn_begin =
// connectivity.begin(nb_nodes_per_element);
// Array<UInt>::const_vector_iterator conn_it = conn_begin;
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 != NULL) {
// 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 != NULL)
++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,
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();
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 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();
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();
}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::DOFData(const ID & dof_id)
: support_type(_dst_generic), group_support("mesh"), dof(NULL),
blocked_dofs(NULL), increment(NULL), previous(NULL),
solution(0, 1, dof_id + ":solution"),
local_equation_number(0, 1, dof_id + ":local_equation_number") {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::~DOFData() {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData & DOFManager::getNewDOFData(const ID & dof_id) {
DOFStorage::iterator it = this->dofs.find(dof_id);
if (it != this->dofs.end()) {
AKANTU_EXCEPTION("This dof array has already been registered");
}
DOFData * dofs_storage = new DOFData(dof_id);
this->dofs[dof_id] = dofs_storage;
return *dofs_storage;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsInternal(const ID & dof_id,
Array<Real> & dofs_array) {
DOFData & dofs_storage = this->getDOFData(dof_id);
dofs_storage.dof = &dofs_array;
UInt nb_local_dofs = 0;
UInt nb_pure_local = 0;
const DOFSupportType &support_type = dofs_storage.support_type;
switch (support_type) {
case _dst_nodal: {
UInt nb_nodes = 0;
const ID & group = dofs_storage.group_support;
NodeGroup * node_group = NULL;
if (group == "mesh") {
nb_nodes = this->mesh->getNbNodes();
} else {
node_group = &this->mesh->getElementGroup(group).getNodeGroup();
nb_nodes = node_group->getSize();
}
nb_local_dofs = nb_nodes;
AKANTU_DEBUG_ASSERT(
dofs_array.getSize() == nb_local_dofs,
"The array of dof is too shot to be associated to nodes.");
for (UInt n = 0; n < nb_nodes; ++n) {
UInt node = n;
if (node_group)
node = node_group->getNodes()(n);
nb_pure_local += this->mesh->isLocalOrMasterNode(node) ? 1 : 0;
}
nb_pure_local *= dofs_array.getNbComponent();
nb_local_dofs *= dofs_array.getNbComponent();
break;
}
case _dst_generic: {
nb_local_dofs = nb_pure_local =
dofs_array.getSize() * dofs_array.getNbComponent();
break;
}
default: { AKANTU_EXCEPTION("This type of dofs is not handled yet."); }
}
this->pure_local_system_size += nb_pure_local;
this->local_system_size += nb_local_dofs;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
comm.allReduce(nb_pure_local, _so_sum);
this->system_size += nb_pure_local;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type) {
DOFData & dofs_storage = this->getNewDOFData(dof_id);
dofs_storage.support_type = support_type;
this->registerDOFsInternal(dof_id, dofs_array);
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & support_group) {
DOFData & dofs_storage = this->getNewDOFData(dof_id);
dofs_storage.support_type = _dst_nodal;
dofs_storage.group_support = support_group;
this->registerDOFsInternal(dof_id, dofs_array);
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsPrevious(const ID & dof_id, Array<Real> & array) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.previous != NULL) {
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 != NULL) {
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, NULL);
} else {
if (derivatives[order - 1] != NULL) {
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 != NULL) {
AKANTU_EXCEPTION("The blocked dofs array for "
<< dof_id << " has already been registered");
}
dof.blocked_dofs = &blocked_dofs;
}
/* -------------------------------------------------------------------------- */
void DOFManager::splitSolutionPerDOFs() {
DOFStorage::iterator it = this->dofs.begin();
DOFStorage::iterator end = this->dofs.end();
for (; it != end; ++it) {
DOFData & dof_data = *it->second;
dof_data.solution.resize(dof_data.dof->getSize() *
dof_data.dof->getNbComponent());
this->getSolutionPerDOFs(it->first, dof_data.solution);
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerSparseMatrix(const ID & matrix_id,
SparseMatrix & matrix) {
SparseMatricesMap::const_iterator it = this->matrices.find(matrix_id);
if (it != this->matrices.end()) {
AKANTU_EXCEPTION("The matrix " << matrix_id << " already exists in "
<< this->id);
}
this->matrices[matrix_id] = &matrix;
}
/* -------------------------------------------------------------------------- */
/// Get an instance of a new SparseMatrix
Array<Real> & DOFManager::getNewLumpedMatrix(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_EXCEPTION("The lumped matrix " << matrix_id << " already exists in "
<< this->id);
}
Array<Real> & mtx = this->alloc<Real>(matrix_id, this->local_system_size, 1);
this->lumped_matrices[matrix_id] = &mtx;
return mtx;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerNonLinearSolver(const ID & non_linear_solver_id,
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);
}
this->non_linear_solvers[non_linear_solver_id] = &non_linear_solver;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerTimeStepSolver(const ID & time_step_solver_id,
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);
}
this->time_step_solvers[time_step_solver_id] = &time_step_solver;
}
/* -------------------------------------------------------------------------- */
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;
SparseMatricesMap::const_iterator it = this->matrices.find(mtx_id);
return it != this->matrices.end();
}
/* -------------------------------------------------------------------------- */
Array<Real> & 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 Array<Real> & DOFManager::getLumpedMatrix(const ID & id) const {
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);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasLumpedMatrix(const ID & id) const {
ID mtx_id = this->id + ":lumped_mtx:" + id;
LumpedMatricesMap::const_iterator 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;
NonLinearSolversMap::const_iterator 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;
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
return it != this->time_step_solvers.end();
}
/* -------------------------------------------------------------------------- */
void DOFManager::fillNodesToElements() {
UInt spatial_dimension = this->mesh->getSpatialDimension();
Element e;
UInt nb_nodes = this->mesh->getNbNodes();
for (UInt n = 0; n < nb_nodes; ++n) {
this->nodes_to_elements[n]->clear();
}
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first =
this->mesh->firstType(spatial_dimension, *gt, _ek_not_defined);
Mesh::type_iterator last =
this->mesh->lastType(spatial_dimension, *gt, _ek_not_defined);
e.ghost_type = *gt;
for (; first != last; ++first) {
ElementType type = *first;
e.type = type;
e.kind = Mesh::getKind(type);
UInt nb_element = this->mesh->getNbElement(type, *gt);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
this->mesh->getConnectivity(type, *gt).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)
nodes_to_elements[conn(n)]->insert(e);
}
}
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::savePreviousDOFs(const ID & dofs_id) {
this->getPreviousDOFs(dofs_id).copy(this->getDOFs(dofs_id));
}
/* -------------------------------------------------------------------------- */
/* Mesh Events */
/* -------------------------------------------------------------------------- */
void DOFManager::onNodesAdded(const Array<UInt> & nodes_list,
__attribute__((unused))
const NewNodesEvent & event) {
Array<UInt>::const_scalar_iterator it = nodes_list.begin();
Array<UInt>::const_scalar_iterator end = nodes_list.end();
UInt nb_nodes = this->mesh->getNbNodes();
this->nodes_to_elements.resize(nb_nodes);
for (; it != end; ++it) {
this->nodes_to_elements[*it] = new std::set<Element>();
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::onNodesRemoved(const Array<UInt> & nodes_list,
const Array<UInt> & new_numbering,
__attribute__((unused))
const RemovedNodesEvent & event) {
Array<UInt>::const_scalar_iterator it = nodes_list.begin();
Array<UInt>::const_scalar_iterator end = nodes_list.end();
for (; it != end; ++it) {
delete this->nodes_to_elements[*it];
}
this->mesh->removeNodesFromArray(this->nodes_to_elements, new_numbering);
}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsAdded(const Array<Element> & elements_list,
__attribute__((unused))
const NewElementsEvent & event) {
Array<Element>::const_scalar_iterator it = elements_list.begin();
Array<Element>::const_scalar_iterator end = elements_list.end();
for (; it != end; ++it) {
const Element & elem = *it;
if (this->mesh->getSpatialDimension(elem.type) !=
this->mesh->getSpatialDimension())
continue;
const Array<UInt> & conn =
this->mesh->getConnectivity(elem.type, elem.ghost_type);
UInt nb_nodes_per_elem = this->mesh->getNbNodesPerElement(elem.type);
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
nodes_to_elements[conn(elem.element, n)]->insert(elem);
}
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsRemoved(
__attribute__((unused)) const Array<Element> & elements_list,
__attribute__((unused)) const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
this->fillNodesToElements();
}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsChanged(
__attribute__((unused)) const Array<Element> & old_elements_list,
__attribute__((unused)) const Array<Element> & new_elements_list,
__attribute__((unused)) const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const ChangedElementsEvent & event) {
this->fillNodesToElements();
}
/* -------------------------------------------------------------------------- */
} // akantu
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