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test_petsc_matrix_diagonal.cc
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rAKA akantu
test_petsc_matrix_diagonal.cc
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/**
* @file test_petsc_matrix_diagonal.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Sun Oct 19 2014
* @date last modification: Wed Nov 08 2017
*
* @brief test the connectivity is correctly represented in the PETScMatrix
*
*
* @section LICENSE
*
* Copyright (©) 2015-2021 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 <iostream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_csr.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "dumper_paraview.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_partition_scotch.hh"
#include "mesh_utils.hh"
#include "petsc_matrix.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if (prank == 0) {
/// creation mesh
mesh.read("triangle.msh");
MeshPartitionScotch * partition =
new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
// DumperParaview mesh_dumper("mesh_dumper");
// mesh_dumper.registerMesh(mesh, spatial_dimension, _not_ghost);
// mesh_dumper.dump();
/// initialize the FEEngine and the dof_synchronizer
FEEngine * fem =
new FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular>(
mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// construct an Akantu sparse matrix, build the profile and fill the matrix
// for the given mesh
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K_akantu(nb_global_nodes * spatial_dimension, _unsymmetric);
K_akantu.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// use as elemental matrices a matrix with values equal to 1 every where
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1.);
Array<Real> K_e =
Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it =
K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end =
K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for (; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K_akantu, spatial_dimension, element_type,
ghost_type);
/// construct a PETSc matrix
PETScMatrix K_petsc(nb_global_nodes * spatial_dimension, _unsymmetric);
/// build the profile of the PETSc matrix for the mesh of this example
K_petsc.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// add an Akantu sparse matrix to a PETSc sparse matrix
K_petsc.add(K_akantu, 1);
/// check to how many elements each node is connected
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem, spatial_dimension);
/// test the diagonal of the PETSc matrix: the diagonal entries
/// of the PETSc matrix correspond to the number of elements
/// connected to the node of the dof. Note: for an Akantu matrix this is only
/// true for the serial case
Real error = 0.;
/// loop over all diagonal values of the matrix
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
UInt dof = i * spatial_dimension + j;
/// for PETSc matrix only DOFs on the processor and be accessed
if (dof_synchronizer.isLocalOrMasterDOF(dof)) {
UInt global_dof = dof_synchronizer.getDOFGlobalID(dof);
std::cout << "Number of elements connected: "
<< node_to_elem.getNbCols(i) << std::endl;
std::cout << "K_petsc(" << global_dof << "," << global_dof
<< ")=" << K_petsc(dof, dof) << std::endl;
error += std::abs(K_petsc(dof, dof) - node_to_elem.getNbCols(i));
}
}
}
if (error > Math::getTolerance()) {
std::cout << "error in the stiffness matrix!!!" << std::endl;
finalize();
return EXIT_FAILURE;
}
delete communicator;
finalize();
return EXIT_SUCCESS;
}
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