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dof_manager_petsc.cc
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/**
* @file dof_manager_petsc.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 07 2015
* @date last modification: Tue Feb 20 2018
*
* @brief DOFManaterPETSc is the PETSc implementation of the DOFManager
*
*
* 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_petsc.hh"
#include "aka_iterators.hh"
#include "communicator.hh"
#include "cppargparse.hh"
#include "non_linear_solver_petsc.hh"
#include "solver_vector_petsc.hh"
#include "sparse_matrix_petsc.hh"
#include "time_step_solver_default.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <petscis.h>
#include <petscsys.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
class PETScSingleton {
private:
PETScSingleton() {
PETSc_call(PetscInitialized, &is_initialized);
if (is_initialized == 0U) {
cppargparse::ArgumentParser & argparser = getStaticArgumentParser();
int & argc = argparser.getArgC();
char **& argv = argparser.getArgV();
PETSc_call(PetscInitialize, &argc, &argv, nullptr, nullptr);
PETSc_call(
PetscPopErrorHandler); // remove the default PETSc signal handler
PETSc_call(PetscPushErrorHandler, PetscIgnoreErrorHandler, nullptr);
}
}
public:
PETScSingleton(const PETScSingleton &) = delete;
PETScSingleton & operator=(const PETScSingleton &) = delete;
~PETScSingleton() {
if (is_initialized == 0U) {
PetscFinalize();
}
}
static PETScSingleton & getInstance() {
static PETScSingleton instance;
return instance;
}
private:
PetscBool is_initialized;
};
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFDataPETSc::DOFDataPETSc(const ID & dof_id)
: DOFData(dof_id) {}
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFManagerPETSc(const ID & id)
: DOFManager(id) {
init();
}
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFManagerPETSc(Mesh & mesh, const ID & id)
: DOFManager(mesh, id) {
init();
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::init() {
// check if the akantu types and PETSc one are consistant
static_assert(sizeof(Int) == sizeof(PetscInt),
"The integer type of Akantu does not match the one from PETSc");
static_assert(sizeof(Real) == sizeof(PetscReal),
"The integer type of Akantu does not match the one from PETSc");
#if defined(AKANTU_USE_MPI)
const auto & mpi_data =
aka::as_type<MPICommunicatorData>(communicator.getCommunicatorData());
MPI_Comm mpi_comm = mpi_data.getMPICommunicator();
this->mpi_communicator = mpi_comm;
#else
this->mpi_communicator = PETSC_COMM_SELF;
#endif
PETScSingleton & instance [[gnu::unused]] = PETScSingleton::getInstance();
}
/* -------------------------------------------------------------------------- */
auto DOFManagerPETSc::getNewDOFData(const ID & dof_id)
-> std::unique_ptr<DOFData> {
return std::make_unique<DOFDataPETSc>(dof_id);
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt, UInt>
DOFManagerPETSc::registerDOFsInternal(const ID & dof_id,
Array<Real> & dofs_array) {
dofs_ids.push_back(dof_id);
auto ret = DOFManager::registerDOFsInternal(dof_id, dofs_array);
UInt nb_dofs;
UInt nb_pure_local_dofs;
std::tie(nb_dofs, nb_pure_local_dofs, std::ignore) = ret;
auto && vector = std::make_unique<SolverVectorPETSc>(*this, id + ":solution");
auto *x = vector->getVec();
PETSc_call(VecGetLocalToGlobalMapping, x, &is_ltog_map);
// redoing the indexes based on the petsc numbering
for (auto & dof_id : dofs_ids) {
auto & dof_data = this->getDOFDataTyped<DOFDataPETSc>(dof_id);
Array<PetscInt> gidx(dof_data.local_equation_number.size());
for (auto && data : zip(dof_data.local_equation_number, gidx)) {
std::get<1>(data) = localToGlobalEquationNumber(std::get<0>(data));
}
auto & lidx = dof_data.local_equation_number_petsc;
if (is_ltog_map != nullptr) {
lidx.resize(gidx.size());
PetscInt n;
PETSc_call(ISGlobalToLocalMappingApply, is_ltog_map, IS_GTOLM_MASK,
gidx.size(), gidx.storage(), &n, lidx.storage());
}
}
residual = std::make_unique<SolverVectorPETSc>(*vector, id + ":residual");
data_cache = std::make_unique<SolverVectorPETSc>(*vector, id + ":data_cache");
solution = std::move(vector);
for (auto & mat : matrices) {
auto & A = this->getMatrix(mat.first);
A.resize();
}
return ret;
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assembleToGlobalArray(
const ID & dof_id, const Array<Real> & array_to_assemble,
SolverVector & global_array, Real scale_factor) {
const auto & dof_data = getDOFDataTyped<DOFDataPETSc>(dof_id);
auto & g = aka::as_type<SolverVectorPETSc>(global_array);
AKANTU_DEBUG_ASSERT(array_to_assemble.size() *
array_to_assemble.getNbComponent() ==
dof_data.local_nb_dofs,
"The array to assemble does not have the proper size");
g.addValuesLocal(dof_data.local_equation_number_petsc, array_to_assemble,
scale_factor);
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::getArrayPerDOFs(const ID & dof_id,
const SolverVector & global_array,
Array<Real> & local) {
const auto & dof_data = getDOFDataTyped<DOFDataPETSc>(dof_id);
const auto & petsc_vector = aka::as_type<SolverVectorPETSc>(global_array);
AKANTU_DEBUG_ASSERT(
local.size() * local.getNbComponent() == dof_data.local_nb_dofs,
"The array to get the values does not have the proper size");
petsc_vector.getValuesLocal(dof_data.local_equation_number_petsc, local);
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id, const Array<Real> & elementary_mat,
ElementType type, GhostType ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) {
auto & A = getMatrix(matrix_id);
DOFManager::assembleElementalMatricesToMatrix_(
A, dof_id, elementary_mat, type, ghost_type, elemental_matrix_type,
filter_elements);
A.applyModifications();
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assemblePreassembledMatrix(
const ID & dof_id_m, const ID & dof_id_n, const ID & matrix_id,
const TermsToAssemble & terms) {
auto & A = getMatrix(matrix_id);
DOFManager::assemblePreassembledMatrix_(A, dof_id_m, dof_id_n, terms);
A.applyModifications();
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assembleMatMulVectToArray(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor) {
DOFManager::assembleMatMulVectToArray_<SolverVectorPETSc>(
dof_id, A_id, x, array, scale_factor);
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::makeConsistentForPeriodicity(const ID & /*dof_id*/,
SolverVector & /*array*/) {}
/* -------------------------------------------------------------------------- */
NonLinearSolver &
DOFManagerPETSc::getNewNonLinearSolver(const ID & id,
const NonLinearSolverType & type) {
return this->registerNonLinearSolver<NonLinearSolverPETSc>(*this, id, type);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManagerPETSc::getNewTimeStepSolver(
const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, SolverCallback & callback) {
return this->registerTimeStepSolver<TimeStepSolverDefault>(
*this, id, type, non_linear_solver, callback);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerPETSc::getNewMatrix(const ID & id,
const MatrixType & matrix_type) {
return this->registerSparseMatrix<SparseMatrixPETSc>(*this, id, matrix_type);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerPETSc::getNewMatrix(const ID & id,
const ID & matrix_to_copy_id) {
return this->registerSparseMatrix<SparseMatrixPETSc>(id, matrix_to_copy_id);
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc & DOFManagerPETSc::getMatrix(const ID & id) {
auto & matrix = DOFManager::getMatrix(id);
return aka::as_type<SparseMatrixPETSc>(matrix);
}
/* -------------------------------------------------------------------------- */
SolverVector & DOFManagerPETSc::getNewLumpedMatrix(const ID & id) {
return this->registerLumpedMatrix<SolverVectorPETSc>(*this, id);
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc & DOFManagerPETSc::getSolution() {
return aka::as_type<SolverVectorPETSc>(*this->solution);
}
const SolverVectorPETSc & DOFManagerPETSc::getSolution() const {
return aka::as_type<SolverVectorPETSc>(*this->solution);
}
SolverVectorPETSc & DOFManagerPETSc::getResidual() {
return aka::as_type<SolverVectorPETSc>(*this->residual);
}
const SolverVectorPETSc & DOFManagerPETSc::getResidual() const {
return aka::as_type<SolverVectorPETSc>(*this->residual);
}
/* -------------------------------------------------------------------------- */
static bool dof_manager_is_registered [[gnu::unused]] =
DOFManagerFactory::getInstance().registerAllocator(
"petsc",
[](Mesh & mesh, const ID & id) -> std::unique_ptr<DOFManager> {
return std::make_unique<DOFManagerPETSc>(mesh, id);
});
} // namespace akantu
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