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rAKA/src/model/dof_manager_default.cc
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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 "node_synchronizer.hh"
#include "non_linear_solver_default.hh"
#include "periodic_node_synchronizer.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<UInt> & 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<UInt> & 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<UInt> & 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), residual(0, 1, std::string(id + ":residual")),
global_residual(nullptr),
global_solution(0, 1, std::string(id + ":global_solution")),
global_blocked_dofs(0, 1, std::string(id + ":global_blocked_dofs")),
previous_global_blocked_dofs(
0, 1, std::string(id + ":previous_global_blocked_dofs")),
dofs_flag(0, 1, std::string(id + ":dofs_type")),
data_cache(0, 1, std::string(id + ":data_cache_array")),
global_equation_number(0, 1, "global_equation_number"),
synchronizer(nullptr) {}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: DOFManager(mesh, id, memory_id),
residual(0, 1, std::string(id + ":residual")), global_residual(nullptr),
global_solution(0, 1, std::string(id + ":global_solution")),
global_blocked_dofs(0, 1, std::string(id + ":global_blocked_dofs")),
previous_global_blocked_dofs(
0, 1, std::string(id + ":previous_global_blocked_dofs")),
dofs_flag(0, 1, std::string(id + ":dofs_type")),
data_cache(0, 1, std::string(id + ":data_cache_array")),
global_equation_number(0, 1, "global_equation_number"),
first_global_dof_id(0), synchronizer(nullptr) {
if (this->mesh->isDistributed())
this->synchronizer = std::make_unique<DOFSynchronizer>(
*this, this->id + ":dof_synchronizer", this->memory_id);
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::~DOFManagerDefault() = default;
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFManagerDefault::makeConsistentForPeriodicity(const ID & dof_id,
Array<T> & 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>(array);
}
/* -------------------------------------------------------------------------- */
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();
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFDataDefault::DOFDataDefault(const ID & dof_id)
: DOFData(dof_id), associated_nodes(0, 1, dof_id + "associated_nodes") {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData & DOFManagerDefault::getNewDOFData(const ID & dof_id) {
this->dofs[dof_id] = std::make_unique<DOFDataDefault>(dof_id);
return *this->dofs[dof_id];
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFsInternal(const ID & dof_id, UInt nb_dofs,
UInt nb_pure_local_dofs) {
// auto prank = this->communicator.whoAmI();
// auto psize = this->communicator.getNbProc();
// access the relevant data to update
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
const auto & support_type = dof_data.support_type;
const auto & group = dof_data.group_support;
switch (support_type) {
case _dst_nodal:
if (group != "__mesh__") {
auto & support_nodes =
this->mesh->getElementGroup(group).getNodeGroup().getNodes();
this->updateDOFsData(
dof_data, nb_dofs, nb_pure_local_dofs, support_nodes.size(),
[&support_nodes](UInt node) -> UInt { return support_nodes[node]; });
} else {
this->updateDOFsData(dof_data, nb_dofs, nb_pure_local_dofs,
mesh->getNbNodes(),
[](UInt node) -> UInt { return node; });
}
break;
case _dst_generic:
this->updateDOFsData(dof_data, nb_dofs, nb_pure_local_dofs);
break;
}
// update the synchronizer if needed
if (this->synchronizer)
this->synchronizer->registerDOFs(dof_id);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFs(const ID & dof_id,
Array<Real> & dofs_array,
const DOFSupportType & support_type) {
// stores the current numbers of dofs
UInt nb_dofs_old = this->local_system_size;
UInt nb_pure_local_dofs_old = this->pure_local_system_size;
// update or create the dof_data
DOFManager::registerDOFs(dof_id, dofs_array, support_type);
UInt nb_dofs = this->local_system_size - nb_dofs_old;
UInt nb_pure_local_dofs =
this->pure_local_system_size - nb_pure_local_dofs_old;
this->registerDOFsInternal(dof_id, nb_dofs, nb_pure_local_dofs);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFs(const ID & dof_id,
Array<Real> & dofs_array,
const ID & group_support) {
// stores the current numbers of dofs
UInt nb_dofs_old = this->local_system_size;
UInt nb_pure_local_dofs_old = this->pure_local_system_size;
// update or create the dof_data
DOFManager::registerDOFs(dof_id, dofs_array, group_support);
UInt nb_dofs = this->local_system_size - nb_dofs_old;
UInt nb_pure_local_dofs =
this->pure_local_system_size - nb_pure_local_dofs_old;
this->registerDOFsInternal(dof_id, nb_dofs, nb_pure_local_dofs);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const MatrixType & matrix_type) {
ID matrix_id = this->id + ":mtx:" + id;
std::unique_ptr<SparseMatrix> sm =
std::make_unique<SparseMatrixAIJ>(*this, matrix_type, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const ID & matrix_to_copy_id) {
ID matrix_id = this->id + ":mtx:" + id;
SparseMatrixAIJ & sm_to_copy = this->getMatrix(matrix_to_copy_id);
std::unique_ptr<SparseMatrix> sm =
std::make_unique<SparseMatrixAIJ>(sm_to_copy, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ & DOFManagerDefault::getMatrix(const ID & id) {
SparseMatrix & matrix = DOFManager::getMatrix(id);
return dynamic_cast<SparseMatrixAIJ &>(matrix);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver &
DOFManagerDefault::getNewNonLinearSolver(const ID & id,
const NonLinearSolverType & type) {
ID non_linear_solver_id = this->id + ":nls:" + id;
std::unique_ptr<NonLinearSolver> nls;
switch (type) {
#if defined(AKANTU_IMPLICIT)
case _nls_newton_raphson:
case _nls_newton_raphson_modified: {
nls = std::make_unique<NonLinearSolverNewtonRaphson>(
*this, type, non_linear_solver_id, this->memory_id);
break;
}
case _nls_linear: {
nls = std::make_unique<NonLinearSolverLinear>(
*this, type, non_linear_solver_id, this->memory_id);
break;
}
#endif
case _nls_lumped: {
nls = std::make_unique<NonLinearSolverLumped>(
*this, type, non_linear_solver_id, this->memory_id);
break;
}
default:
AKANTU_EXCEPTION("The asked type of non linear solver is not supported by "
"this dof manager");
}
return this->registerNonLinearSolver(non_linear_solver_id, nls);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver &
DOFManagerDefault::getNewTimeStepSolver(const ID & id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) {
ID time_step_solver_id = this->id + ":tss:" + id;
std::unique_ptr<TimeStepSolver> tss = std::make_unique<TimeStepSolverDefault>(
*this, type, non_linear_solver, time_step_solver_id, this->memory_id);
return this->registerTimeStepSolver(time_step_solver_id, tss);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::clearResidual() {
this->residual.resize(this->local_system_size);
this->residual.clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::clearMatrix(const ID & mtx) {
this->getMatrix(mtx).clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::clearLumpedMatrix(const ID & mtx) {
this->getLumpedMatrix(mtx).clear();
}
/* -------------------------------------------------------------------------- */
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<UInt> & equation_number = this->getLocalEquationNumbers(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::getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->global_solution, solution_array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::getLumpedMatrixPerDOFs(const ID & dof_id,
const ID & lumped_mtx,
Array<Real> & lumped) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->getLumpedMatrix(lumped_mtx), lumped);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleToResidual(const ID & dof_id,
Array<Real> & array_to_assemble,
Real scale_factor) {
AKANTU_DEBUG_IN();
this->makeConsistentForPeriodicity(dof_id, array_to_assemble);
this->assembleToGlobalArray(dof_id, array_to_assemble, this->residual,
scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleToLumpedMatrix(const ID & dof_id,
Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor) {
AKANTU_DEBUG_IN();
this->makeConsistentForPeriodicity(dof_id, array_to_assemble);
Array<Real> & lumped = this->getLumpedMatrix(lumped_mtx);
this->assembleToGlobalArray(dof_id, array_to_assemble, lumped, scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor) {
SparseMatrixAIJ & A = this->getMatrix(A_id);
// Array<Real> data_cache(this->local_system_size, 1, 0.);
this->data_cache.resize(this->local_system_size);
this->data_cache.clear();
this->assembleToGlobalArray(dof_id, x, data_cache, 1.);
Array<Real> tmp_residual(this->residual.size(), 1, 0.);
A.matVecMul(data_cache, tmp_residual, scale_factor, 1.);
this->residual += 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);
// Array<Real> data_cache(this->local_system_size, 1, 0.);
this->data_cache.resize(this->local_system_size);
this->data_cache.clear();
this->assembleToGlobalArray(dof_id, x, data_cache, scale_factor);
auto A_it = A.begin();
auto A_end = A.end();
auto x_it = data_cache.begin();
auto r_it = this->residual.begin();
for (; A_it != A_end; ++A_it, ++x_it, ++r_it) {
*r_it += *A_it * *x_it;
}
}
/* -------------------------------------------------------------------------- */
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->getLocalEquationNumbers(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;
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom;
Vector<UInt> element_eq_nb(nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::const_matrix_iterator 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(), [&](UInt & local) -> UInt {
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 Array<UInt> & equation_number_m =
this->getLocalEquationNumbers(dof_id_m);
const Array<UInt> & equation_number_n =
this->getLocalEquationNumbers(dof_id_n);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
for (const auto & term : terms) {
UInt gi = this->localToGlobalEquationNumber(equation_number_m(term.i()));
UInt 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 DOFData & 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;
UInt nb_degree_of_freedom_per_node = dof_data.dof->getNbComponent();
const auto & equation_number = this->getLocalEquationNumbers(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;
UInt 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<UInt> 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(), [&](UInt & local) -> UInt {
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();
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManagerDefault::getGlobalResidual() {
if (this->synchronizer) {
if (not this->global_residual) {
this->global_residual =
std::make_unique<Array<Real>>(0, 1, "global_residual");
}
if (this->synchronizer->getCommunicator().whoAmI() == 0) {
this->global_residual->resize(this->system_size);
this->synchronizer->gather(this->residual, *this->global_residual);
} else {
this->synchronizer->gather(this->residual);
}
return *this->global_residual;
} else {
return this->residual;
}
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManagerDefault::getResidual() const {
return this->residual;
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::setGlobalSolution(const Array<Real> & solution) {
if (this->synchronizer) {
if (this->synchronizer->getCommunicator().whoAmI() == 0) {
this->synchronizer->scatter(this->global_solution, solution);
} else {
this->synchronizer->scatter(this->global_solution);
}
} else {
AKANTU_DEBUG_ASSERT(solution.size() == this->global_solution.size(),
"Sequential call to this function needs the solution "
"to be the same size as the global_solution");
this->global_solution.copy(solution);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) {
DOFManager::onNodesAdded(nodes_list, event);
if (this->synchronizer)
this->synchronizer->onNodesAdded(nodes_list);
}
/* -------------------------------------------------------------------------- */
std::pair<UInt, UInt>
DOFManagerDefault::updateNodalDOFs(const ID & dof_id,
const Array<UInt> & nodes_list) {
UInt nb_new_local_dofs, nb_new_pure_local;
std::tie(nb_new_local_dofs, nb_new_pure_local) =
DOFManager::updateNodalDOFs(dof_id, nodes_list);
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
updateDOFsData(dof_data, nb_new_local_dofs, nb_new_pure_local,
nodes_list.size(),
[&nodes_list](UInt pos) -> UInt { return nodes_list[pos]; });
return std::make_pair(nb_new_local_dofs, nb_new_pure_local);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class GlobalDOFInfoDataAccessor : public DataAccessor<UInt> {
public:
using size_type =
typename std::unordered_map<UInt, std::vector<UInt>>::size_type;
GlobalDOFInfoDataAccessor(DOFManagerDefault::DOFDataDefault & dof_data,
DOFManagerDefault & dof_manager)
: dof_data(dof_data), dof_manager(dof_manager) {
for (auto && pair :
zip(dof_data.local_equation_number, dof_data.associated_nodes)) {
UInt node, dof;
std::tie(dof, node) = pair;
dofs_per_node[node].push_back(dof);
}
}
UInt getNbData(const Array<UInt> & nodes,
const SynchronizationTag & tag) const override {
if (tag == _gst_ask_nodes or tag == _gst_giu_global_conn) {
return nodes.size() * dof_data.dof->getNbComponent() * sizeof(UInt);
}
return 0;
}
void packData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) const override {
if (tag == _gst_ask_nodes or tag == _gst_giu_global_conn) {
for (auto & node : nodes) {
auto & dofs = dofs_per_node.at(node);
for (auto & dof : dofs) {
buffer << dof_manager.global_equation_number(dof);
}
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) override {
if (tag == _gst_ask_nodes or tag == _gst_giu_global_conn) {
for (auto & node : nodes) {
auto & dofs = dofs_per_node[node];
for (auto dof : dofs) {
UInt global_dof;
buffer >> global_dof;
AKANTU_DEBUG_ASSERT(
(dof_manager.global_equation_number(dof) == UInt(-1) or
dof_manager.global_equation_number(dof) == global_dof),
"This dof already had a global_dof_id which is different from "
"the received one. "
<< dof_manager.global_equation_number(dof)
<< " != " << global_dof);
dof_manager.global_equation_number(dof) = global_dof;
dof_manager.global_to_local_mapping[global_dof] = dof;
}
}
}
}
protected:
std::unordered_map<UInt, std::vector<UInt>> dofs_per_node;
DOFManagerDefault::DOFDataDefault & dof_data;
DOFManagerDefault & dof_manager;
};
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::resizeGlobalArrays() {
// resize all relevant arrays
this->residual.resize(this->local_system_size, 0.);
this->dofs_flag.resize(this->local_system_size, NodeFlag::_normal);
this->global_solution.resize(this->local_system_size, 0.);
this->global_blocked_dofs.resize(this->local_system_size, true);
this->previous_global_blocked_dofs.resize(this->local_system_size, true);
this->global_equation_number.resize(this->local_system_size, -1);
for (auto & lumped_matrix : lumped_matrices)
lumped_matrix.second->resize(this->local_system_size);
matrix_profiled_dofs.clear();
for (auto & matrix : matrices) {
matrix.second->clearProfile();
}
}
/* -------------------------------------------------------------------------- */
auto DOFManagerDefault::computeFirstDOFIDs(UInt nb_new_local_dofs,
UInt nb_new_pure_local) {
auto prank = this->communicator.whoAmI();
auto psize = this->communicator.getNbProc();
// determine the first local/global dof id to use
Array<UInt> nb_dofs_per_proc(psize);
nb_dofs_per_proc(prank) = nb_new_pure_local;
this->communicator.allGather(nb_dofs_per_proc);
this->first_global_dof_id += std::accumulate(
nb_dofs_per_proc.begin(), nb_dofs_per_proc.begin() + prank, 0);
auto first_global_dof_id = this->first_global_dof_id;
auto first_local_dof_id = this->local_system_size - nb_new_local_dofs;
this->first_global_dof_id += std::accumulate(nb_dofs_per_proc.begin() + prank,
nb_dofs_per_proc.end(), 0);
return std::make_pair(first_local_dof_id, first_global_dof_id);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::updateDOFsData(
DOFDataDefault & dof_data, UInt nb_new_local_dofs, UInt nb_new_pure_local,
UInt nb_node, const std::function<UInt(UInt)> & getNode) {
auto nb_local_dofs_added = nb_node * dof_data.dof->getNbComponent();
resizeGlobalArrays();
auto first_dof_pos = dof_data.local_equation_number.size();
dof_data.local_equation_number.reserve(dof_data.local_equation_number.size() +
nb_local_dofs_added);
dof_data.associated_nodes.reserve(dof_data.associated_nodes.size() +
nb_local_dofs_added);
std::unordered_map<std::pair<UInt, UInt>, UInt> masters_dofs;
// update per dof info
UInt local_eq_num, first_global_dof_id;
std::tie(local_eq_num, first_global_dof_id) =
computeFirstDOFIDs(nb_new_local_dofs, nb_new_pure_local);
for (auto d : arange(nb_local_dofs_added)) {
auto node = getNode(d / dof_data.dof->getNbComponent());
auto dof_flag = this->mesh->getNodeFlag(node);
dof_data.associated_nodes.push_back(node);
auto is_local_dof = this->mesh->isLocalOrMasterNode(node);
auto is_periodic_slave = this->mesh->isPeriodicSlave(node);
auto is_periodic_master = this->mesh->isPeriodicMaster(node);
if (is_periodic_slave) {
dof_data.local_equation_number.push_back(UInt(-1));
continue;
}
// update equation numbers
this->dofs_flag(local_eq_num) = dof_flag;
dof_data.local_equation_number.push_back(local_eq_num);
if (is_local_dof) {
this->global_equation_number(local_eq_num) = first_global_dof_id;
this->global_to_local_mapping[first_global_dof_id] = local_eq_num;
++first_global_dof_id;
} else {
this->global_equation_number(local_eq_num) = UInt(-1);
}
if (is_periodic_master) {
auto node = getNode(d / dof_data.dof->getNbComponent());
auto dof = d % dof_data.dof->getNbComponent();
masters_dofs.insert(
std::make_pair(std::make_pair(node, dof), local_eq_num));
}
++local_eq_num;
}
// correct periodic slave equation numbers
if (this->mesh->isPeriodic()) {
auto assoc_begin = dof_data.associated_nodes.begin();
for (auto d : arange(nb_local_dofs_added)) {
auto node = dof_data.associated_nodes(first_dof_pos + d);
if (not this->mesh->isPeriodicSlave(node))
continue;
auto master_node = this->mesh->getPeriodicMaster(node);
auto dof = d % dof_data.dof->getNbComponent();
dof_data.local_equation_number(first_dof_pos + d) =
masters_dofs[std::make_pair(master_node, dof)];
}
}
// synchronize the global numbering for slaves
if (this->synchronizer) {
GlobalDOFInfoDataAccessor data_accessor(dof_data, *this);
if (this->mesh->isPeriodic()) {
mesh->getPeriodicNodeSynchronizer().synchronizeOnce(data_accessor,
_gst_giu_global_conn);
}
auto & node_synchronizer = this->mesh->getNodeSynchronizer();
node_synchronizer.synchronizeOnce(data_accessor, _gst_ask_nodes);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::updateDOFsData(DOFDataDefault & dof_data,
UInt nb_new_local_dofs,
UInt nb_new_pure_local) {
resizeGlobalArrays();
dof_data.local_equation_number.reserve(dof_data.local_equation_number.size() +
nb_new_local_dofs);
UInt first_local_dof_id, first_global_dof_id;
std::tie(first_local_dof_id, first_global_dof_id) =
computeFirstDOFIDs(nb_new_local_dofs, nb_new_pure_local);
// update per dof info
for (auto _[[gnu::unused]] : arange(nb_new_local_dofs)) {
// update equation numbers
this->dofs_flag(first_local_dof_id) = NodeFlag::_normal;
;
dof_data.local_equation_number.push_back(first_local_dof_id);
this->global_equation_number(first_local_dof_id) = first_global_dof_id;
this->global_to_local_mapping[first_global_dof_id] = first_local_dof_id;
++first_global_dof_id;
++first_local_dof_id;
}
}
/* -------------------------------------------------------------------------- */
// 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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