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rAKA/src/solver/sparse_matrix.cc
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sparse_matrix.cc
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/**
* @file sparse_matrix.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Mon Sep 15 2014
*
* @brief implementation of the SparseMatrix class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 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 <fstream>
/* -------------------------------------------------------------------------- */
#include "sparse_matrix.hh"
#include "static_communicator.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(UInt size,
const SparseMatrixType & sparse_matrix_type,
const ID & id,
const MemoryID & memory_id) :
Memory(id, memory_id),
sparse_matrix_type(sparse_matrix_type),
size(size),
nb_non_zero(0),
irn(0,1,"irn"), jcn(0,1,"jcn"), a(0,1,"A"), offset(1) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
nb_proc = comm.getNbProc();
dof_synchronizer = NULL;
irn_save = NULL;
jcn_save = NULL;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(const SparseMatrix & matrix,
const ID & id,
const MemoryID & memory_id) :
Memory(id, memory_id),
sparse_matrix_type(matrix.sparse_matrix_type),
size(matrix.size),
nb_proc(matrix.nb_proc),
nb_non_zero(matrix.nb_non_zero),
irn(matrix.irn, true), jcn(matrix.jcn, true), a(matrix.getA(), true),
irn_jcn_k(matrix.irn_jcn_k), offset(1) {
AKANTU_DEBUG_IN();
size_save = 0;
irn_save = NULL;
jcn_save = NULL;
dof_synchronizer = matrix.dof_synchronizer;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrix::~SparseMatrix() {
AKANTU_DEBUG_IN();
// if (irn_jcn_to_k) delete irn_jcn_to_k;
if(irn_save) delete irn_save;
if(jcn_save) delete jcn_save;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrix::buildProfile(const Mesh & mesh, const DOFSynchronizer & dof_synchronizer, UInt nb_degree_of_freedom) {
AKANTU_DEBUG_IN();
// if(irn_jcn_to_k) delete irn_jcn_to_k;
// irn_jcn_to_k = new std::map<std::pair<UInt, UInt>, UInt>;
clearProfile();
this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
coordinate_list_map::iterator irn_jcn_k_it;
Int * eq_nb_val = dof_synchronizer.getGlobalDOFEquationNumbers().storage();
Mesh::type_iterator it = mesh.firstType(mesh.getSpatialDimension(), _not_ghost, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType (mesh.getSpatialDimension(), _not_ghost, _ek_not_defined);
for(; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom;
UInt * conn_val = mesh.getConnectivity(*it, _not_ghost).storage();
Int * local_eq_nb_val = new Int[nb_degree_of_freedom * nb_nodes_per_element];
for (UInt e = 0; e < nb_element; ++e) {
Int * tmp_local_eq_nb_val = local_eq_nb_val;
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
UInt n = conn_val[i];
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
*tmp_local_eq_nb_val++ = eq_nb_val[n * nb_degree_of_freedom + d];
}
// memcpy(tmp_local_eq_nb_val, eq_nb_val + n * nb_degree_of_freedom, nb_degree_of_freedom * sizeof(Int));
// tmp_local_eq_nb_val += nb_degree_of_freedom;
}
for (UInt i = 0; i < size_mat; ++i) {
UInt c_irn = local_eq_nb_val[i];
if(c_irn < this->size) {
UInt j_start = (sparse_matrix_type == _symmetric) ? i : 0;
for (UInt j = j_start; j < size_mat; ++j) {
UInt c_jcn = local_eq_nb_val[j];
if(c_jcn < this->size) {
KeyCOO irn_jcn = key(c_irn, c_jcn);
irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
if (irn_jcn_k_it == irn_jcn_k.end()) {
irn_jcn_k[irn_jcn] = nb_non_zero;
irn.push_back(c_irn + 1);
jcn.push_back(c_jcn + 1);
nb_non_zero++;
}
}
}
}
}
conn_val += nb_nodes_per_element;
}
delete [] local_eq_nb_val;
}
/// for pbc @todo correct it for parallel
if(StaticCommunicator::getStaticCommunicator().getNbProc() == 1) {
for (UInt i = 0; i < size; ++i) {
KeyCOO irn_jcn = key(i, i);
irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
if(irn_jcn_k_it == irn_jcn_k.end()) {
irn_jcn_k[irn_jcn] = nb_non_zero;
irn.push_back(i + 1);
jcn.push_back(i + 1);
nb_non_zero++;
}
}
}
else { // for pbc in parallel
for (UInt n=0; n<mesh.getNbNodes(); ++n) {
for (UInt d=0; d<nb_degree_of_freedom; ++d) {
if (mesh.isLocalOrMasterNode(n)) {
UInt i = mesh.getNodeGlobalId(n) * nb_degree_of_freedom + d;
KeyCOO irn_jcn = key(i, i);
irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
if(irn_jcn_k_it == irn_jcn_k.end()) {
irn_jcn_k[irn_jcn] = nb_non_zero;
irn.push_back(i + 1);
jcn.push_back(i + 1);
nb_non_zero++;
}
}
}
}
}
a.resize(nb_non_zero);
AKANTU_DEBUG_OUT();
}
///* -------------------------------------------------------------------------- */
//void SparseMatrix::applyBoundaryNormal(Array<bool> & boundary_normal, Array<Real> & EulerAngles, Array<Real> & rhs, const Array<Real> & matrix, Array<Real> & rhs_rotated) {
// AKANTU_DEBUG_IN();
//
//
// const UInt dim = nb_degree_of_freedom;
// const UInt nb_nodes = boundary_normal.getSize();
// Matrix<Real> Ti(dim, dim);
// Matrix<Real> Tj(dim, dim);
// Matrix<Real> small_matrix(dim, dim);
// Matrix<Real> Ti_small_matrix(dim, dim);
// Matrix<Real> Ti_small_matrix_Tj(dim, dim);
// Matrix<Real> small_rhs(dim, 1);
// Matrix<Real> Ti_small_rhs(dim, 1);
// //Transformation matrix based on euler angles X_1Y_2Z_3
//
// const DOFSynchronizer::GlobalEquationNumberMap & local_eq_num_to_global = dof_synchronizer->getGlobalEquationNumberToLocal();
//
// Int * irn_val = irn.storage();
// Int * jcn_val = jcn.storage();
// Int * eq_nb_val = dof_synchronizer->getGlobalDOFEquationNumbers().storage();
// Int * eq_nb_rhs_val = dof_synchronizer->getLocalDOFEquationNumbers().storage();
//
// Array<bool> * nodes_rotated = new Array<bool > (nb_nodes, dim, "nodes_rotated");
// nodes_rotated->clear();
//
// Array<Int> * local_eq_nb_val_node_i = new Array<Int > (1, nb_degree_of_freedom, "local_eq_nb_val_node_i");
// local_eq_nb_val_node_i->clear();
// Array<Int> * local_eq_nb_val_node_j = new Array<Int > (1, nb_degree_of_freedom, "local_eq_nb_val_node_j");
// local_eq_nb_val_node_j->clear();
//
// for (UInt i = 0; i < nb_non_zero; ++i) {
// UInt ni = local_eq_num_to_global.find(*irn_val - 1)->second;
// UInt node_i = (ni - ni % nb_degree_of_freedom) / nb_degree_of_freedom;
// UInt nj = local_eq_num_to_global.find(*jcn_val - 1)->second;
// UInt node_j = (nj - nj % nb_degree_of_freedom) / nb_degree_of_freedom;
// bool constrain_ij = false;
// for (UInt j = 0; j < dim; j++){
// if ( (boundary_normal(node_i, j) || boundary_normal(node_j, j)) ) {
// constrain_ij = true;
// break;
// }
// }
//
// if(constrain_ij){
// if(dim==2){
// Real Theta=EulerAngles(node_i,0);
// Ti(0,0)=cos(Theta);
// Ti(0,1)=-sin(Theta);
// Ti(1,1)=cos(Theta);
// Ti(1,0)=sin(Theta);
//
// Theta=EulerAngles(node_j,0);
// Tj(0,0)=cos(Theta);
// Tj(0,1)=-sin(Theta);
// Tj(1,1)=cos(Theta);
// Tj(1,0)=sin(Theta);
// }
// else if(dim==3){
// Real Theta_x=EulerAngles(node_i,0);
// Real Theta_y=EulerAngles(node_i,1);
// Real Theta_z=EulerAngles(node_i,2);
//
// Ti(0,0)=cos(Theta_y)*cos(Theta_z);
// Ti(0,1)=-cos(Theta_y)*sin(Theta_z);
// Ti(0,2)=sin(Theta_y);
// Ti(1,0)=cos(Theta_x)*sin(Theta_z)+cos(Theta_z)*sin(Theta_x)*sin(Theta_y);
// Ti(1,1)=cos(Theta_x)*cos(Theta_z)-sin(Theta_x)*sin(Theta_y)*sin(Theta_z);
// Ti(1,2)=-cos(Theta_y)*sin(Theta_x);
// Ti(2,0)=sin(Theta_x)*sin(Theta_z)-cos(Theta_x)*cos(Theta_z)*sin(Theta_y);
// Ti(2,1)=cos(Theta_z)*sin(Theta_x)+cos(Theta_x)*sin(Theta_y)*sin(Theta_z);
// Ti(2,2)=cos(Theta_x)*cos(Theta_y);
//
// Theta_x=EulerAngles(node_j,0);
// Theta_y=EulerAngles(node_j,1);
// Theta_z=EulerAngles(node_j,2);
//
// Tj(0,0)=cos(Theta_y)*cos(Theta_z);
// Tj(0,1)=-cos(Theta_y)*sin(Theta_z);
// Tj(0,2)=sin(Theta_y);
// Tj(1,0)=cos(Theta_x)*sin(Theta_z)+cos(Theta_z)*sin(Theta_x)*sin(Theta_y);
// Tj(1,1)=cos(Theta_x)*cos(Theta_z)-sin(Theta_x)*sin(Theta_y)*sin(Theta_z);
// Tj(1,2)=-cos(Theta_y)*sin(Theta_x);
// Tj(2,0)=sin(Theta_x)*sin(Theta_z)-cos(Theta_x)*cos(Theta_z)*sin(Theta_y);
// Tj(2,1)=cos(Theta_z)*sin(Theta_x)+cos(Theta_x)*sin(Theta_y)*sin(Theta_z);
// Tj(2,2)=cos(Theta_x)*cos(Theta_y);
// }
// for (UInt j = 0; j < nb_degree_of_freedom; ++j){
// local_eq_nb_val_node_i->storage()[j] = eq_nb_val[node_i * nb_degree_of_freedom + j];
// local_eq_nb_val_node_j->storage()[j] = eq_nb_val[node_j * nb_degree_of_freedom + j];
// }
// for (UInt j = 0; j < nb_degree_of_freedom; ++j) {
// for (UInt k = 0; k < nb_degree_of_freedom; ++k) {
// KeyCOO jcn_irn = key(local_eq_nb_val_node_i->storage()[j], local_eq_nb_val_node_j->storage()[k]);
// coordinate_list_map::iterator irn_jcn_k_it = irn_jcn_k.find(jcn_irn);
// small_matrix(j, k) = matrix.storage()[irn_jcn_k_it->second];
// }
// small_rhs(j,0)=rhs.storage()[eq_nb_rhs_val[node_i*dim+j]];
// }
//
// Ti_small_matrix.mul < false, false > (Ti, small_matrix);
// Ti_small_matrix_Tj.mul < false, true> (Ti_small_matrix, Tj);
// Ti_small_rhs.mul<false, false>(Ti, small_rhs);
//
// /*for (UInt j = 0; j < nb_degree_of_freedom; ++j) {
// for (UInt k = 0; k < nb_degree_of_freedom; ++k) {
// KeyCOO jcn_irn = key(local_eq_nb_val_node_i->storage()[j], local_eq_nb_val_node_j->storage()[k]);
// coordinate_list_map::iterator irn_jcn_k_it = irn_jcn_k.find(jcn_irn);
// a.storage()[irn_jcn_k_it->second] = T_small_matrix_T(j,k);
// }
// if(node_constrain==node_i && !( nodes_rotated->storage()[node_i]))
// rhs.storage()[eq_nb_rhs_val[node_i*dim+j]]=T_small_rhs(j,0);
// }*/
// KeyCOO jcn_irn = key(ni, nj);
// coordinate_list_map::iterator irn_jcn_k_it = irn_jcn_k.find(jcn_irn);
// a.storage()[irn_jcn_k_it->second] = Ti_small_matrix_Tj(ni % nb_degree_of_freedom, nj % nb_degree_of_freedom);
// //this->saveMatrix("stiffness_partial.out");
// if (!(nodes_rotated->storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]])) {
// rhs_rotated.storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]] = Ti_small_rhs(ni % nb_degree_of_freedom, 0);
// nodes_rotated->storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]] = true;
// }
// }
// else{
// if (!(nodes_rotated->storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]])) {
// rhs_rotated.storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]] = rhs.storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]];
// nodes_rotated->storage()[eq_nb_rhs_val[node_i * dim + ni % nb_degree_of_freedom]] = true;
// }
// }
// irn_val++;
// jcn_val++;
// }
//
// delete local_eq_nb_val_node_i;
// delete local_eq_nb_val_node_j;
// delete nodes_rotated;
// this->saveMatrix("stiffness_rotated.out");
// applyBoundary(boundary_normal);
//
// /*Real norm = 0;
// UInt n_zeros = 0;
// for (UInt j = 0; j < nb_degree_of_freedom; ++j) {
// norm += Normal.storage()[j] * Normal.storage()[j];
// if (std::abs(Normal.storage()[j]) < Math::getTolerance())
// n_zeros++;
// }
// norm = sqrt(norm);
// AKANTU_DEBUG_ASSERT(norm > Math::getTolerance(), "The normal is not right");
// for (UInt j = 0; j < nb_degree_of_freedom; ++j)
// Normal.storage()[j] /= norm;
//
// if (n_zeros == nb_degree_of_freedom - 1) {
// UInt nb_nodes = boundary_normal.getSize();
// for (UInt i = 0; i < nb_nodes; ++i) {
// if (boundary_normal(i, 0))
// for (UInt j = 0; j < nb_degree_of_freedom; ++j)
// boundary(i, j) += Normal(0, j);
// }
// } else {
//
// const DOFSynchronizer::GlobalEquationNumberMap & local_eq_num_to_global = dof_synchronizer->getGlobalEquationNumberToLocal();
//
// Int * irn_val = irn.storage();
// Int * eq_nb_val = dof_synchronizer->getGlobalDOFEquationNumbers().storage();
// Array<Int> * local_eq_nb_val = new Array<Int > (1, nb_degree_of_freedom, "local_eq_nb_val");
// local_eq_nb_val->clear();
// UInt nb_nodes = boundary_normal.getSize();
// Array<bool> * node_set = new Array<bool > (nb_nodes, 1, "node_set");
// node_set->clear();
//
// for (UInt i = 0; i < nb_non_zero; ++i) {
// UInt ni = local_eq_num_to_global.find(*irn_val - 1)->second;
// UInt node_i = (ni - ni % nb_degree_of_freedom) / nb_degree_of_freedom;
// if (boundary_normal.storage()[ni]) {
// if ((!number.storage()[ni]) && (!node_set->storage()[node_i])) {
// UInt normal_component_i = ni % nb_degree_of_freedom; //DOF of node node_i to be removed
// if (std::abs(Normal.storage()[normal_component_i]) > Math::getTolerance()) {
// for (UInt j = 0; j < nb_degree_of_freedom; ++j)
// local_eq_nb_val->storage()[j] = eq_nb_val[node_i * nb_degree_of_freedom + j];
//
// UInt DOF_remove = local_eq_nb_val->storage()[normal_component_i];
// KeyCOO jcn_irn = key(DOF_remove, DOF_remove);
// coordinate_list_map::iterator irn_jcn_k_it = irn_jcn_k.find(jcn_irn);
//
// Real aii = a.storage()[irn_jcn_k_it->second];
// Real normal_constant = (1 - aii) / (Normal.storage()[normal_component_i] * Normal.storage()[normal_component_i]);
//
// for (UInt j = 0; j < nb_degree_of_freedom; ++j) {
// UInt line_j = local_eq_nb_val->storage()[j];
// for (UInt k = 0; k < nb_degree_of_freedom; ++k) {
// UInt column_k = local_eq_nb_val->storage()[k];
// jcn_irn = key(line_j, column_k);
// if ((line_j == column_k) && (line_j == DOF_remove))
// a.storage()[irn_jcn_k_it->second] = 1;
// else
// a.storage()[irn_jcn_k_it->second] += Normal.storage()[j] * Normal.storage()[k] * normal_constant;
// }
// }
//
// number.storage()[ni]++;
// node_set->storage()[node_i] = false;
// }
// }
// }
// irn_val++;
// }
//
// delete local_eq_nb_val;
// delete node_set;
// }*/
// AKANTU_DEBUG_OUT();
//}
/* -------------------------------------------------------------------------- */
void SparseMatrix::applyBoundary(const Array<bool> & boundary, Real block_val) {
AKANTU_DEBUG_IN();
const DOFSynchronizer::GlobalEquationNumberMap & local_eq_num_to_global = dof_synchronizer->getGlobalEquationNumberToLocal();
Int * irn_val = irn.storage();
Int * jcn_val = jcn.storage();
Real * a_val = a.storage();
for (UInt i = 0; i < nb_non_zero; ++i) {
/// @todo fix this hack, put here for the implementation of augmented
/// lagrangian contact
if (local_eq_num_to_global.find(*irn_val - 1) == local_eq_num_to_global.end())
continue;
if (local_eq_num_to_global.find(*jcn_val - 1) == local_eq_num_to_global.end())
continue;
UInt ni = local_eq_num_to_global.find(*irn_val - 1)->second;
UInt nj = local_eq_num_to_global.find(*jcn_val - 1)->second;
if(boundary.storage()[ni] || boundary.storage()[nj]) {
if (*irn_val != *jcn_val) {
*a_val = 0;
} else {
if(dof_synchronizer->getDOFTypes()(ni) >= 0) {
*a_val = 0;
} else {
*a_val = block_val;
}
}
}
irn_val++; jcn_val++; a_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrix::saveProfile(const std::string & filename) const {
AKANTU_DEBUG_IN();
std::ofstream outfile;
outfile.open(filename.c_str());
outfile << "%%MatrixMarket matrix coordinate pattern";
if(sparse_matrix_type == _symmetric) outfile << " symmetric";
else outfile << " general";
outfile << std::endl;
UInt m = size;
outfile << m << " " << m << " " << nb_non_zero << std::endl;
for (UInt i = 0; i < nb_non_zero; ++i) {
outfile << irn.storage()[i] << " " << jcn.storage()[i] << " 1" << std::endl;
}
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrix::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
std::ofstream outfile;
outfile.precision(std::numeric_limits<Real>::digits10);
outfile.open(filename.c_str());
outfile << "%%MatrixMarket matrix coordinate real";
if(sparse_matrix_type == _symmetric) outfile << " symmetric";
else outfile << " general";
outfile << std::endl;
outfile << size << " " << size << " " << nb_non_zero << std::endl;
for (UInt i = 0; i < nb_non_zero; ++i) {
outfile << irn(i) << " " << jcn(i) << " " << a(i) << std::endl;
}
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Array<Real> & operator*=(Array<Real> & vect, const SparseMatrix & mat) {
AKANTU_DEBUG_IN();
// AKANTU_DEBUG_ASSERT((vect.getSize()*vect.getNbComponent() == mat.getSize()) &&
// (vect.getNbComponent() == mat.getNbDegreOfFreedom()),
// "The size of the matrix and the vector do not match");
const SparseMatrixType & sparse_matrix_type = mat.getSparseMatrixType();
DOFSynchronizer * dof_synchronizer = mat.getDOFSynchronizerPointer();
UInt nb_non_zero = mat.getNbNonZero();
Real * tmp = new Real [vect.getNbComponent() * vect.getSize()];
std::fill_n(tmp, vect.getNbComponent() * vect.getSize(), 0);
Int * i_val = mat.getIRN().storage();
Int * j_val = mat.getJCN().storage();
Real * a_val = mat.getA().storage();
Real * vect_val = vect.storage();
for (UInt k = 0; k < nb_non_zero; ++k) {
UInt i = *(i_val++);
UInt j = *(j_val++);
Real a = *(a_val++);
UInt local_i = i - 1;
UInt local_j = j - 1;
if(dof_synchronizer) {
local_i = dof_synchronizer->getDOFLocalID(local_i);
local_j = dof_synchronizer->getDOFLocalID(local_j);
}
tmp[local_i] += a * vect_val[local_j];
if((sparse_matrix_type == _symmetric) && (local_i != local_j))
tmp[local_j] += a * vect_val[local_i];
}
memcpy(vect_val, tmp, vect.getNbComponent() * vect.getSize() * sizeof(Real));
delete [] tmp;
if(dof_synchronizer)
dof_synchronizer->reduceSynchronize<AddOperation>(vect);
AKANTU_DEBUG_OUT();
return vect;
}
/* -------------------------------------------------------------------------- */
void SparseMatrix::copyContent(const SparseMatrix & matrix) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(nb_non_zero == matrix.getNbNonZero(),
"The to matrix don't have the same profiles");
memcpy(a.storage(), matrix.getA().storage(), nb_non_zero * sizeof(Real));
AKANTU_DEBUG_OUT();
}
///* -------------------------------------------------------------------------- */
//void SparseMatrix::copyProfile(const SparseMatrix & matrix) {
// AKANTU_DEBUG_IN();
// irn = matrix.irn;
// jcn = matrix.jcn;
// nb_non_zero = matrix.nb_non_zero;
// irn_jcn_k = matrix.irn_jcn_k;
// a.resize(nb_non_zero);
// AKANTU_DEBUG_OUT();
//}
/* -------------------------------------------------------------------------- */
void SparseMatrix::add(const SparseMatrix & matrix, Real alpha) {
AKANTU_DEBUG_ASSERT(nb_non_zero == matrix.getNbNonZero(),
"The to matrix don't have the same profiles");
Real * a_val = a.storage();
Real * b_val = matrix.a.storage();
for (UInt n = 0; n < nb_non_zero; ++n) {
*a_val++ += alpha * *b_val++;
}
}
/* -------------------------------------------------------------------------- */
void SparseMatrix::lump(Array<Real> & lumped) {
AKANTU_DEBUG_IN();
UInt vect_size = size / lumped.getNbComponent();
if(dof_synchronizer) vect_size = dof_synchronizer->getNbDOFs() / lumped.getNbComponent();
lumped.resize(vect_size);
lumped.clear();
Int * i_val = irn.storage();
Int * j_val = jcn.storage();
Real * a_val = a.storage();
Real * vect_val = lumped.storage();
for (UInt k = 0; k < nb_non_zero; ++k) {
UInt i = *(i_val++);
UInt j = *(j_val++);
Real a = *(a_val++);
UInt local_i = i - 1;
UInt local_j = j - 1;
if(dof_synchronizer) {
local_i = dof_synchronizer->getDOFLocalID(local_i);
local_j = dof_synchronizer->getDOFLocalID(local_j);
}
vect_val[local_i] += a;
if(sparse_matrix_type == _symmetric && (i != j))
vect_val[local_j] += a;
}
if(dof_synchronizer)
dof_synchronizer->reduceSynchronize<AddOperation>(lumped);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrix::clear() {
memset(a.storage(), 0, nb_non_zero*sizeof(Real));
}
__END_AKANTU__
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