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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 Tue Aug 11 16:21:01 2015
*
* @brief Implementation of the default DOFManager
*
* @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 "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "element_group.hh"
#include "non_linear_solver_default.hh"
#include "sparse_matrix_aij.hh"
#include "static_communicator.hh"
#include "time_step_solver_default.hh"
#include "terms_to_assemble.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
__BEGIN_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_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_type(0, 1, std::string(id + ":dofs_type")),
data_cache(0, 1, std::string(id + ":data_cache_array")),
jacobian_release(0),
global_equation_number(0, 1, "global_equation_number"),
synchronizer(nullptr) {}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::~DOFManagerDefault() { delete synchronizer; }
/* -------------------------------------------------------------------------- */
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();
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
UInt nb_degree_of_freedoms =
array_to_assemble.getSize() * array_to_assemble.getNbComponent();
AKANTU_DEBUG_ASSERT(equation_number.getSize() == nb_degree_of_freedoms,
"The array to assemble does not have a correct size."
<< " (" << array_to_assemble.getID() << ")");
typename Array<T>::const_scalar_iterator arr_it =
array_to_assemble.begin_reinterpret(nb_degree_of_freedoms);
Array<UInt>::const_scalar_iterator equ_it = equation_number.begin();
for (UInt d = 0; d < nb_degree_of_freedoms; ++d, ++arr_it, ++equ_it) {
global_array(*equ_it) += scale_factor * (*arr_it);
}
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) {
DOFDataDefault * dofs_storage = new DOFDataDefault(dof_id);
this->dofs[dof_id] = dofs_storage;
return *dofs_storage;
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerMesh(Mesh & mesh) {
DOFManager::registerMesh(mesh);
delete synchronizer;
if(mesh.isDistributed())
synchronizer = new DOFSynchronizer(*this, this->id + ":dof_synchronizer",
this->memory_id, mesh.getCommunicator());
else synchronizer = nullptr;
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFsInternal(const ID & dof_id, UInt nb_dofs,
UInt nb_pure_local_dofs) {
// Count the number of pure local dofs per proc
StaticCommunicator & comm = mesh->getCommunicator();
UInt prank = comm.whoAmI();
UInt psize = comm.getNbProc();
Array<UInt> nb_dofs_per_proc(psize);
nb_dofs_per_proc(prank) = nb_pure_local_dofs;
comm.allGather(nb_dofs_per_proc);
UInt first_global_dofs_id = std::accumulate(
nb_dofs_per_proc.begin(), nb_dofs_per_proc.begin() + prank, 0);
DOFDataDefault & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
const DOFSupportType & support_type = dof_data.support_type;
const ID & group = dof_data.group_support;
dof_data.local_equation_number.resize(nb_dofs);
this->global_equation_number.resize(this->local_system_size);
// set the equation numbers
UInt first_dof_id = this->local_system_size - nb_dofs;
const Array<UInt> * support_nodes = nullptr;
if (group != "mesh") {
support_nodes =
&this->mesh->getElementGroup(group).getNodeGroup().getNodes();
}
if (support_type == _dst_nodal) {
dof_data.associated_nodes.resize(nb_dofs);
}
this->dofs_type.resize(local_system_size);
for (UInt d = 0; d < nb_dofs; ++d) {
UInt local_eq_num = first_dof_id + d;
dof_data.local_equation_number(d) = local_eq_num;
UInt global_eq_num = first_global_dofs_id + d;
this->global_equation_number(local_eq_num) = global_eq_num;
this->global_to_local_mapping[global_eq_num] = local_eq_num;
switch (support_type) {
case _dst_nodal: {
UInt node = d / dof_data.dof->getNbComponent();
if (support_nodes)
node = (*support_nodes)(node);
this->dofs_type(local_eq_num) = this->mesh->getNodeType(node);
dof_data.associated_nodes(d) = node;
break;
}
case _dst_generic: {
this->dofs_type(local_eq_num) = _nt_normal;
break;
}
default: { AKANTU_EXCEPTION("This type of dofs is not handled yet."); }
}
}
this->residual.resize(this->local_system_size);
this->global_solution.resize(this->local_system_size);
this->global_blocked_dofs.resize(this->local_system_size);
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;
SparseMatrix * sm = new SparseMatrixAIJ(*this, matrix_type, matrix_id);
this->registerSparseMatrix(matrix_id, *sm);
return *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);
SparseMatrix * sm = new SparseMatrixAIJ(sm_to_copy, matrix_id);
this->registerSparseMatrix(matrix_id, *sm);
return *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;
NonLinearSolver * nls = NULL;
switch (type) {
#if defined(AKANTU_IMPLICIT)
case _nls_newton_raphson:
case _nls_newton_raphson_modified: {
nls = new NonLinearSolverNewtonRaphson(*this, type, non_linear_solver_id,
this->memory_id);
break;
}
case _nls_linear: {
nls = new NonLinearSolverLinear(*this, type, non_linear_solver_id,
this->memory_id);
break;
}
#endif
case _nls_lumped: {
nls = new 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");
}
this->registerNonLinearSolver(non_linear_solver_id, *nls);
return *nls;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver &
DOFManagerDefault::getNewTimeStepSolver(const ID & id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) {
ID time_step_solver_id = this->id + ":tss:" + id;
TimeStepSolver * tss = new TimeStepSolverDefault(
*this, type, non_linear_solver, time_step_solver_id, this->memory_id);
this->registerTimeStepSolver(time_step_solver_id, *tss);
return *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() {
DOFStorage::iterator it = this->dofs.begin();
DOFStorage::iterator 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) {
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.getSize();
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::getEquationsNumbers(const ID & dof_id,
Array<UInt> & equation_numbers) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->global_equation_number, equation_numbers);
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, const Array<Real> & array_to_assemble,
Real scale_factor) {
AKANTU_DEBUG_IN();
this->assembleToGlobalArray(dof_id, array_to_assemble, this->residual,
scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleToLumpedMatrix(
const ID & dof_id, const Array<Real> & array_to_assemble,
const ID & lumped_mtx, Real scale_factor) {
AKANTU_DEBUG_IN();
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.);
A.matVecMul(data_cache, this->residual, scale_factor, 1.);
}
/* -------------------------------------------------------------------------- */
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);
Array<Real>::const_scalar_iterator A_it = A.begin();
Array<Real>::const_scalar_iterator A_end = A.end();
Array<Real>::const_scalar_iterator x_it = data_cache.begin();
Array<Real>::scalar_iterator 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();
this->addToProfile(matrix_id, dof_id, type, ghost_type);
DOFData & dof_data = this->getDOFData(dof_id);
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
UInt nb_element;
if (ghost_type == _not_ghost) {
nb_element = this->mesh->getNbElement(type);
} else {
AKANTU_DEBUG_TO_IMPLEMENT();
}
UInt * filter_it = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
filter_it = filter_elements.storage();
} else {
if (dof_data.group_support != "mesh") {
const Array<UInt> & group_elements =
this->mesh->getElementGroup(dof_data.group_support).getElements(type, ghost_type);
nb_element = group_elements.getSize();
filter_it = group_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
}
AKANTU_DEBUG_ASSERT(elementary_mat.getSize() == 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);
this->localToGlobalEquationNumber(element_eq_nb);
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.getSize());
else
this->addUnsymmetricElementalMatrixToSymmetric(
A, *el_mat_it, element_eq_nb, A.getSize());
else
this->addElementalMatrixToUnsymmetric(A, *el_mat_it, element_eq_nb,
A.getSize());
}
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) {
A.addToMatrix(equation_number_m(term.i()),
equation_number_n(term.j()),
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 Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
UInt size = A.getSize();
UInt 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.getSize();
UInt * ge_it = nullptr;
if (dof_data.group_support != "mesh") {
const Array<UInt> & group_elements =
this->mesh->getElementGroup(dof_data.group_support)
.getElements(type, ghost_type);
ge_it = group_elements.storage();
nb_elements = group_elements.getSize();
}
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);
this->localToGlobalEquationNumber(element_eq_nb);
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.addToProfile(c_irn, c_jcn);
}
}
}
}
}
this->matrix_profiled_dofs[mat_dof].push_back(type_pair);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::applyBoundary() {
this->updateGlobalBlockedDofs();
SparseMatrixAIJ & J = this->getMatrix("J");
if (this->jacobian_release == J.getValueRelease()) {
Array<bool>::const_scalar_iterator it = global_blocked_dofs.begin();
Array<bool>::const_scalar_iterator end = global_blocked_dofs.end();
Array<bool>::const_scalar_iterator pit =
previous_global_blocked_dofs.begin();
for (; it != end && *it == *pit; ++it, ++pit)
;
if (it != end)
J.applyBoundary();
} else {
J.applyBoundary();
}
this->jacobian_release = J.getValueRelease();
}
/* -------------------------------------------------------------------------- */
__END_AKANTU__
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