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dof_manager_default.cc
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/**
* @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
*
* @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 "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 "terms_to_assemble.hh"
#include "time_step_solver_default.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <memory>
#include <numeric>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::addSymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & elementary_mat,
const Vector<Int> & equation_numbers, UInt max_size) {
for (UInt i = 0; i < elementary_mat.rows(); ++i) {
UInt c_irn = equation_numbers(i);
if (c_irn < max_size) {
for (UInt j = i; j < elementary_mat.cols(); ++j) {
UInt c_jcn = equation_numbers(j);
if (c_jcn < max_size) {
matrix(c_irn, c_jcn) += elementary_mat(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::addUnsymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & elementary_mat,
const Vector<Int> & equation_numbers, UInt max_size) {
for (UInt i = 0; i < elementary_mat.rows(); ++i) {
UInt c_irn = equation_numbers(i);
if (c_irn < max_size) {
for (UInt j = 0; j < elementary_mat.cols(); ++j) {
UInt c_jcn = equation_numbers(j);
if (c_jcn < max_size) {
if (c_jcn >= c_irn) {
matrix(c_irn, c_jcn) += elementary_mat(i, j);
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::addElementalMatrixToUnsymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & elementary_mat,
const Vector<Int> & equation_numbers, UInt max_size) {
for (UInt i = 0; i < elementary_mat.rows(); ++i) {
UInt c_irn = equation_numbers(i);
if (c_irn < max_size) {
for (UInt j = 0; j < elementary_mat.cols(); ++j) {
UInt c_jcn = equation_numbers(j);
if (c_jcn < max_size) {
matrix(c_irn, c_jcn) += elementary_mat(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(const ID & id, const MemoryID & memory_id)
: DOFManager(id, memory_id),
global_blocked_dofs(0, 1, std::string(id + ":global_blocked_dofs")),
previous_global_blocked_dofs(
0, 1, std::string(id + ":previous_global_blocked_dofs")),
data_cache(0, 1, std::string(id + ":data_cache_array")),
synchronizer(nullptr) {
residual = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":residual"));
solution = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":solution"));
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: DOFManager(mesh, id, memory_id),
global_blocked_dofs(0, 1, std::string(id + ":global_blocked_dofs")),
previous_global_blocked_dofs(
0, 1, std::string(id + ":previous_global_blocked_dofs")),
data_cache(0, 1, std::string(id + ":data_cache_array")),
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"));
} else {
residual = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":residual"));
solution = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":solution"));
}
}
/* -------------------------------------------------------------------------- */
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)
return;
if (not mesh->isPeriodic())
return;
this->mesh->getPeriodicNodeSynchronizer()
.reduceSynchronizeWithPBCSlaves<AddOperation>(
dynamic_cast<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);
global_array(equ_num) +=
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,
dynamic_cast<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)
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 dynamic_cast<SparseMatrixAIJ &>(matrix);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver &
DOFManagerDefault::getNewNonLinearSolver(const ID & id,
const NonLinearSolverType & type) {
switch (type) {
#if defined(AKANTU_IMPLICIT)
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) {
return this->registerTimeStepSolver<TimeStepSolverDefault>(*this, id, type,
non_linear_solver);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::updateGlobalBlockedDofs() {
auto it = this->dofs.begin();
auto end = this->dofs.end();
this->previous_global_blocked_dofs.copy(this->global_blocked_dofs);
this->global_blocked_dofs.resize(this->local_system_size);
this->global_blocked_dofs.clear();
for (; it != end; ++it) {
if (!this->hasBlockedDOFs(it->first))
continue;
DOFData & dof_data = *it->second;
this->assembleToGlobalArray(it->first, *dof_data.blocked_dofs,
this->global_blocked_dofs, true);
}
}
/* -------------------------------------------------------------------------- */
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,
dynamic_cast<const SolverVectorDefault &>(global_array).getVector(),
local_array);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleMatMulVectToGlobalArray(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor) {
SparseMatrixAIJ & A = this->getMatrix(A_id);
// Array<Real> data_cache(this->local_system_size, 1, 0.);
auto && tmp_data_cache =
make_solver_vector_default_wrap(*this, this->data_cache);
tmp_data_cache.resize();
tmp_data_cache.clear();
this->assembleToGlobalArray(dof_id, x, data_cache, 1.);
auto && tmp_array = make_solver_vector_default_wrap(*this, array);
tmp_array.resize();
tmp_array.clear();
A.matVecMul(tmp_data_cache, tmp_array, scale_factor, 1.);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleMatMulVectToArray(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor) {
Array<Real> tmp_array(0, 1, id + ":tmp_array");
assembleMatMulVectToGlobalArray(dof_id, A_id, x, tmp_array, scale_factor);
getArrayPerDOFs(dof_id, tmp_array, array);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor) {
Array<Real> tmp_residual(0, 1, id + ":tmp_residual");
assembleMatMulVectToGlobalArray(dof_id, A_id, x, tmp_residual, scale_factor);
this->getResidualArray() += tmp_residual;
}
/* -------------------------------------------------------------------------- */
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);
this->data_cache.resize(this->local_system_size);
this->data_cache.clear();
this->assembleToGlobalArray(dof_id, x, data_cache, scale_factor);
for (auto && data : zip(make_view(A), make_view(data_cache),
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,
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");
this->addToProfile(matrix_id, dof_id, type, ghost_type);
const auto & equation_number = this->getLocalEquationsNumbers(dof_id);
auto & A = this->getMatrix(matrix_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)
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)
++filter_it;
else
++conn_it;
if (A.getMatrixType() == _symmetric)
if (elemental_matrix_type == _symmetric)
this->addSymmetricElementalMatrixToSymmetric(A, *el_mat_it,
element_eq_nb, A.size());
else
this->addUnsymmetricElementalMatrixToSymmetric(A, *el_mat_it,
element_eq_nb, A.size());
else
this->addElementalMatrixToUnsymmetric(A, *el_mat_it, element_eq_nb,
A.size());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assemblePreassembledMatrix(
const ID & dof_id_m, const ID & dof_id_n, const ID & matrix_id,
const TermsToAssemble & terms) {
const auto & equation_number_m = this->getLocalEquationsNumbers(dof_id_m);
const auto & equation_number_n = this->getLocalEquationsNumbers(dof_id_n);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
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);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::addToProfile(const ID & matrix_id, const ID & dof_id,
const ElementType & type,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
const auto & dof_data = this->getDOFData(dof_id);
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())
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);
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)
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)
++ge_it;
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();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::applyBoundary(const ID & matrix_id) {
SparseMatrixAIJ & J = this->getMatrix(matrix_id);
if (this->jacobian_release == J.getValueRelease()) {
auto are_equal =
std::equal(global_blocked_dofs.begin(), global_blocked_dofs.end(),
previous_global_blocked_dofs.begin());
if (not are_equal)
J.applyBoundary();
previous_global_blocked_dofs.copy(global_blocked_dofs);
} else {
J.applyBoundary();
}
this->jacobian_release = J.getValueRelease();
}
/* -------------------------------------------------------------------------- */
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)
this->synchronizer->onNodesAdded(nodes_list);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::resizeGlobalArrays() {
DOFManager::resizeGlobalArrays();
// resize all relevant arrays
this->residual->resize();
this->solution->resize();
this->global_blocked_dofs.resize(this->local_system_size, true);
this->previous_global_blocked_dofs.resize(this->local_system_size, true);
matrix_profiled_dofs.clear();
}
/* -------------------------------------------------------------------------- */
// 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);
});
} // namespace akantu
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