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solver_vector_petsc.cc
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rAKA akantu
solver_vector_petsc.cc
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/**
* @file solver_vector_petsc.cc
*
* @author Nicolas Richart
*
* @date creation Tue Jan 01 2019
*
* @brief A Documented file.
*
* @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 "solver_vector_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
#include <petscvec.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::SolverVectorPETSc(DOFManagerPETSc & dof_manager,
const ID & id)
: SolverVector(dof_manager, id), dof_manager(dof_manager) {
auto && mpi_comm = dof_manager.getMPIComm();
PETSc_call(VecCreate, mpi_comm, &x);
detail::PETScSetName(x, id);
PETSc_call(VecSetFromOptions, x);
auto local_system_size = dof_manager.getLocalSystemSize();
auto nb_local_dofs = dof_manager.getPureLocalSystemSize();
PETSc_call(VecSetSizes, x, nb_local_dofs, PETSC_DECIDE);
VecType vec_type;
PETSc_call(VecGetType, x, &vec_type);
if (std::string(vec_type) == std::string(VECMPI)) {
PetscInt lowest_gidx, highest_gidx;
PETSc_call(VecGetOwnershipRange, x, &lowest_gidx, &highest_gidx);
std::vector<PetscInt> ghost_idx;
for (auto && d : arange(local_system_size)) {
int gidx = dof_manager.localToGlobalEquationNumber(d);
if (gidx != -1) {
if ((gidx < lowest_gidx) or (gidx >= highest_gidx)) {
ghost_idx.push_back(gidx);
}
}
}
PETSc_call(VecMPISetGhost, x, ghost_idx.size(), ghost_idx.data());
} else {
std::vector<int> idx(nb_local_dofs);
std::iota(idx.begin(), idx.end(), 0);
ISLocalToGlobalMapping is;
PETSc_call(ISLocalToGlobalMappingCreate, PETSC_COMM_SELF, 1, idx.size(),
idx.data(), PETSC_COPY_VALUES, &is);
PETSc_call(VecSetLocalToGlobalMapping, x, is);
PETSc_call(ISLocalToGlobalMappingDestroy, &is);
}
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::SolverVectorPETSc(const SolverVectorPETSc & vector,
const ID & id)
: SolverVector(vector, id), dof_manager(vector.dof_manager) {
if (vector.x) {
PETSc_call(VecDuplicate, vector.x, &x);
PETSc_call(VecCopy, vector.x, x);
detail::PETScSetName(x, id);
}
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "SolverVectorPETSc [" << std::endl;
stream << space << " + id: " << id << std::endl;
PETSc_call(PetscViewerPushFormat, PETSC_VIEWER_STDOUT_WORLD,
PETSC_VIEWER_ASCII_INDEX);
PETSc_call(VecView, x, PETSC_VIEWER_STDOUT_WORLD);
PETSc_call(PetscViewerPopFormat, PETSC_VIEWER_STDOUT_WORLD);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::SolverVectorPETSc(Vec x, DOFManagerPETSc & dof_manager,
const ID & id)
: SolverVector(dof_manager, id), dof_manager(dof_manager) {
PETSc_call(VecDuplicate, x, &this->x);
PETSc_call(VecCopy, x, this->x);
detail::PETScSetName(x, id);
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::~SolverVectorPETSc() {
if (x) {
PETSc_call(VecDestroy, &x);
}
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::resize() {
// the arrays are destroyed and recreated in the dof manager
// resize is so not implemented
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::clear() {
PETSc_call(VecSet, x, 0.);
applyModifications();
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::applyModifications() {
PETSc_call(VecAssemblyBegin, x);
PETSc_call(VecAssemblyEnd, x);
updateGhost();
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::updateGhost() {
Vec x_ghosted{nullptr};
PETSc_call(VecGhostGetLocalForm, x, &x_ghosted);
if (x_ghosted) {
PETSc_call(VecGhostUpdateBegin, x, INSERT_VALUES, SCATTER_FORWARD);
PETSc_call(VecGhostUpdateEnd, x, INSERT_VALUES, SCATTER_FORWARD);
}
PETSc_call(VecGhostRestoreLocalForm, x, &x_ghosted);
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::getValues(const Array<Int> & idx,
Array<Real> & values) const {
if (idx.size() == 0)
return;
ISLocalToGlobalMapping is_ltog_map;
PETSc_call(VecGetLocalToGlobalMapping, x, &is_ltog_map);
PetscInt n;
Array<PetscInt> lidx(idx.size());
PETSc_call(ISGlobalToLocalMappingApply, is_ltog_map, IS_GTOLM_MASK,
idx.size(), idx.storage(), &n, lidx.storage());
getValuesLocal(lidx, values);
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::getValuesLocal(const Array<Int> & idx,
Array<Real> & values) const {
if (idx.size() == 0)
return;
Vec x_ghosted{nullptr};
PETSc_call(VecGhostGetLocalForm, x, &x_ghosted);
// VecScatterBegin(scatter, x, x_local, INSERT_VALUES, SCATTER_FORWARD);
// VecScatterEnd(scatter, x, x_local, INSERT_VALUES, SCATTER_FORWARD);
if (not x_ghosted) {
const PetscScalar * array;
PETSc_call(VecGetArrayRead, x, &array);
for (auto && data : zip(idx, make_view(values))) {
auto i = std::get<0>(data);
if (i != -1) {
std::get<1>(data) = array[i];
}
}
PETSc_call(VecRestoreArrayRead, x, &array);
return;
}
PETSc_call(VecSetOption, x_ghosted, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE);
PETSc_call(VecGetValues, x_ghosted, idx.size(), idx.storage(),
values.storage());
PETSc_call(VecGhostRestoreLocalForm, x, &x_ghosted);
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::addValues(const Array<Int> & gidx,
const Array<Real> & values,
Real scale_factor) {
Real * to_add = values.storage();
Array<Real> scaled_array;
if (scale_factor != 1.) {
scaled_array.copy(values, false);
scaled_array *= scale_factor;
to_add = scaled_array.storage();
}
PETSc_call(VecSetOption, x, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE);
PETSc_call(VecSetValues, x, gidx.size(), gidx.storage(), to_add, ADD_VALUES);
applyModifications();
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::addValuesLocal(const Array<Int> & lidx,
const Array<Real> & values,
Real scale_factor) {
Vec x_ghosted{nullptr};
PETSc_call(VecGhostGetLocalForm, x, &x_ghosted);
if (not x_ghosted) {
Real * to_add = values.storage();
Array<Real> scaled_array;
if (scale_factor != 1.) {
scaled_array.copy(values, false);
scaled_array *= scale_factor;
to_add = scaled_array.storage();
}
PETSc_call(VecSetOption, x, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE);
PETSc_call(VecSetValuesLocal, x, lidx.size(), lidx.storage(), to_add,
ADD_VALUES);
return;
}
PETSc_call(VecGhostRestoreLocalForm, x, &x_ghosted);
ISLocalToGlobalMapping is_ltog_map;
PETSc_call(VecGetLocalToGlobalMapping, x, &is_ltog_map);
Array<Int> gidx(lidx.size());
PETSc_call(ISLocalToGlobalMappingApply, is_ltog_map, lidx.size(),
lidx.storage(), gidx.storage());
addValues(gidx, values, scale_factor);
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::operator const Array<Real> &() const {
const_cast<Array<Real> &>(cache).resize(local_size());
auto xl = internal::make_petsc_local_vector(x);
auto cachep = internal::make_petsc_wraped_vector(this->cache);
PETSc_call(VecCopy, cachep, xl);
return cache;
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc & SolverVectorPETSc::operator=(const SolverVectorPETSc & y) {
if (size() != y.size()) {
PETSc_call(VecDuplicate, y, &x);
}
PETSc_call(VecCopy, y.x, x);
release_ = y.release_;
return *this;
}
/* -------------------------------------------------------------------------- */
SolverVector & SolverVectorPETSc::operator=(const SolverVector & y) {
const auto & y_ = aka::as_type<SolverVectorPETSc>(y);
return operator=(y_);
}
/* -------------------------------------------------------------------------- */
SolverVector & SolverVectorPETSc::operator+(const SolverVector & y) {
auto & y_ = aka::as_type<SolverVectorPETSc>(y);
PETSc_call(VecAXPY, x, 1., y_.x);
release_ = y_.release_;
return *this;
}
} // namespace akantu
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