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dof_manager.cc
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			/**
			* @file dof_manager.cc
			*
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date Wed Aug 12 09:52:30 2015
			*
			* @brief Implementation of the common parts of the DOFManagers
			*
			* @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.hh"
			#include "element_group.hh"
			#include "mesh.hh"
			#include "mesh_utils.hh"
			#include "node_group.hh"
			#include "non_linear_solver.hh"
			#include "sparse_matrix.hh"
			#include "communicator.hh"
			#include "time_step_solver.hh"
			/* -------------------------------------------------------------------------- */
			#include <memory>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			DOFManager::DOFManager(const ID & id, const MemoryID & memory_id)
			: Memory(id, memory_id), mesh(nullptr), local_system_size(0),
			pure_local_system_size(0), system_size(0),
			communicator(Communicator::getStaticCommunicator()) {}

			/* -------------------------------------------------------------------------- */
			DOFManager::DOFManager(Mesh & mesh, const ID & id, const MemoryID & memory_id)
			: Memory(id, memory_id), mesh(&mesh), local_system_size(0),
			pure_local_system_size(0), system_size(0),
			communicator(mesh.getCommunicator()) {
			this->mesh->registerEventHandler(*this, _ehp_dof_manager);
			}

			/* -------------------------------------------------------------------------- */
			DOFManager::~DOFManager() = default;

			/* -------------------------------------------------------------------------- */
			// void DOFManager::getEquationsNumbers(const ID &, Array<UInt> &) {
			// AKANTU_DEBUG_TO_IMPLEMENT();
			// }

			/* -------------------------------------------------------------------------- */
			std::vector<ID> DOFManager::getDOFIDs() const {
			std::vector<ID> keys;
			for (const auto & dof_data : this->dofs)
			keys.push_back(dof_data.first);

			return keys;
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::assembleElementalArrayLocalArray(
			const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
			const ElementType & type, const GhostType & ghost_type, Real scale_factor,
			const Array<UInt> & filter_elements) {
			AKANTU_DEBUG_IN();

			UInt nb_element;
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			UInt nb_degree_of_freedom =
			elementary_vect.getNbComponent() / nb_nodes_per_element;

			UInt * filter_it = NULL;
			if (filter_elements != empty_filter) {
			nb_element = filter_elements.size();
			filter_it = filter_elements.storage();
			} else {
			nb_element = this->mesh->getNbElement(type, ghost_type);
			}

			AKANTU_DEBUG_ASSERT(elementary_vect.size() == nb_element,
			"The vector elementary_vect("
			<< elementary_vect.getID()
			<< ") has not the good size.");

			const Array<UInt> & connectivity =
			this->mesh->getConnectivity(type, ghost_type);
			// Array<UInt>::const_vector_iterator conn_begin =
			// connectivity.begin(nb_nodes_per_element);
			// Array<UInt>::const_vector_iterator conn_it = conn_begin;

			Array<Real>::const_matrix_iterator elem_it =
			elementary_vect.begin(nb_degree_of_freedom, nb_nodes_per_element);

			for (UInt el = 0; el < nb_element; ++el, ++elem_it) {
			UInt element = el;
			if (filter_it != NULL) {
			// conn_it = conn_begin + *filter_it;
			element = *filter_it;
			}

			// const Vector<UInt> & conn = *conn_it;
			const Matrix<Real> & elemental_val = *elem_it;
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			UInt offset_node = connectivity(element, n) * nb_degree_of_freedom;
			Vector<Real> assemble(array_assembeled.storage() + offset_node,
			nb_degree_of_freedom);
			Vector<Real> elem_val = elemental_val(n);
			assemble.aXplusY(elem_val, scale_factor);
			}

			if (filter_it != NULL)
			++filter_it;
			// else
			// ++conn_it;
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::assembleElementalArrayToResidual(
			const ID & dof_id, const Array<Real> & elementary_vect,
			const ElementType & type, const GhostType & ghost_type, Real scale_factor,
			const Array<UInt> & filter_elements) {
			AKANTU_DEBUG_IN();

			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			UInt nb_degree_of_freedom =
			elementary_vect.getNbComponent() / nb_nodes_per_element;
			Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
			nb_degree_of_freedom);

			array_localy_assembeled.clear();

			this->assembleElementalArrayLocalArray(
			elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
			filter_elements);

			this->assembleToResidual(dof_id, array_localy_assembeled, 1);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::assembleElementalArrayToLumpedMatrix(
			const ID & dof_id, const Array<Real> & elementary_vect,
			const ID & lumped_mtx, const ElementType & type,
			const GhostType & ghost_type, Real scale_factor,
			const Array<UInt> & filter_elements) {
			AKANTU_DEBUG_IN();

			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			UInt nb_degree_of_freedom =
			elementary_vect.getNbComponent() / nb_nodes_per_element;
			Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
			nb_degree_of_freedom);

			array_localy_assembeled.clear();

			this->assembleElementalArrayLocalArray(
			elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
			filter_elements);

			this->assembleToLumpedMatrix(dof_id, array_localy_assembeled, lumped_mtx, 1);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			DOFManager::DOFData::DOFData(const ID & dof_id)
			: support_type(_dst_generic), group_support("__mesh__"), dof(NULL),
			blocked_dofs(NULL), increment(NULL), previous(NULL),
			solution(0, 1, dof_id + ":solution"),
			local_equation_number(0, 1, dof_id + ":local_equation_number") {}

			/* -------------------------------------------------------------------------- */
			DOFManager::DOFData::~DOFData() {}

			/* -------------------------------------------------------------------------- */
			DOFManager::DOFData & DOFManager::getNewDOFData(const ID & dof_id) {
			DOFStorage::iterator it = this->dofs.find(dof_id);
			if (it != this->dofs.end()) {
			AKANTU_EXCEPTION("This dof array has already been registered");
			}

			std::unique_ptr<DOFData> dofs_storage = std::make_unique<DOFData>(dof_id);
			this->dofs[dof_id] = std::move(dofs_storage);
			return *dofs_storage;
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::registerDOFsInternal(const ID & dof_id,
			Array<Real> & dofs_array) {
			DOFData & dofs_storage = this->getDOFData(dof_id);
			dofs_storage.dof = &dofs_array;

			UInt nb_local_dofs = 0;
			UInt nb_pure_local = 0;

			const DOFSupportType & support_type = dofs_storage.support_type;

			switch (support_type) {
			case _dst_nodal: {
			UInt nb_nodes = 0;
			const ID & group = dofs_storage.group_support;

			NodeGroup * node_group = NULL;
			if (group == "__mesh__") {
			nb_nodes = this->mesh->getNbNodes();
			} else {
			node_group = &this->mesh->getElementGroup(group).getNodeGroup();
			nb_nodes = node_group->size();
			}

			nb_local_dofs = nb_nodes;
			AKANTU_DEBUG_ASSERT(
			dofs_array.size() == nb_local_dofs,
			"The array of dof is too shot to be associated to nodes.");

			for (UInt n = 0; n < nb_nodes; ++n) {
			UInt node = n;
			if (node_group)
			node = node_group->getNodes()(n);

			nb_pure_local += this->mesh->isLocalOrMasterNode(node) ? 1 : 0;
			}

			nb_pure_local *= dofs_array.getNbComponent();
			nb_local_dofs *= dofs_array.getNbComponent();
			break;
			}
			case _dst_generic: {
			nb_local_dofs = nb_pure_local =
			dofs_array.size() * dofs_array.getNbComponent();
			break;
			}
			default: { AKANTU_EXCEPTION("This type of dofs is not handled yet."); }
			}

			this->pure_local_system_size += nb_pure_local;
			this->local_system_size += nb_local_dofs;

			communicator.allReduce(nb_pure_local, SynchronizerOperation::_sum);

			this->system_size += nb_pure_local;
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
			const DOFSupportType & support_type) {
			DOFData & dofs_storage = this->getNewDOFData(dof_id);
			dofs_storage.support_type = support_type;

			this->registerDOFsInternal(dof_id, dofs_array);
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
			const ID & support_group) {
			DOFData & dofs_storage = this->getNewDOFData(dof_id);
			dofs_storage.support_type = _dst_nodal;
			dofs_storage.group_support = support_group;

			this->registerDOFsInternal(dof_id, dofs_array);
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::registerDOFsPrevious(const ID & dof_id, Array<Real> & array) {
			DOFData & dof = this->getDOFData(dof_id);

			if (dof.previous != NULL) {
			AKANTU_EXCEPTION("The previous dofs array for "
			<< dof_id << " has already been registered");
			}

			dof.previous = &array;
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::registerDOFsIncrement(const ID & dof_id, Array<Real> & array) {
			DOFData & dof = this->getDOFData(dof_id);

			if (dof.increment != NULL) {
			AKANTU_EXCEPTION("The dofs increment array for "
			<< dof_id << " has already been registered");
			}

			dof.increment = &array;
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::registerDOFsDerivative(const ID & dof_id, UInt order,
			Array<Real> & dofs_derivative) {
			DOFData & dof = this->getDOFData(dof_id);
			std::vector<Array<Real> *> & derivatives = dof.dof_derivatives;

			if (derivatives.size() < order) {
			derivatives.resize(order, NULL);
			} else {
			if (derivatives[order - 1] != NULL) {
			AKANTU_EXCEPTION("The dof derivatives of order "
			<< order << " already been registered for this dof ("
			<< dof_id << ")");
			}
			}

			derivatives[order - 1] = &dofs_derivative;
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::registerBlockedDOFs(const ID & dof_id,
			Array<bool> & blocked_dofs) {
			DOFData & dof = this->getDOFData(dof_id);

			if (dof.blocked_dofs != NULL) {
			AKANTU_EXCEPTION("The blocked dofs array for "
			<< dof_id << " has already been registered");
			}

			dof.blocked_dofs = &blocked_dofs;
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::splitSolutionPerDOFs() {
			DOFStorage::iterator it = this->dofs.begin();
			DOFStorage::iterator end = this->dofs.end();

			for (; it != end; ++it) {
			DOFData & dof_data = *it->second;
			dof_data.solution.resize(dof_data.dof->size() *
			dof_data.dof->getNbComponent());
			this->getSolutionPerDOFs(it->first, dof_data.solution);
			}
			}

			/* -------------------------------------------------------------------------- */
			SparseMatrix &
			DOFManager::registerSparseMatrix(const ID & matrix_id,
			std::unique_ptr<SparseMatrix> & matrix) {
			SparseMatricesMap::const_iterator it = this->matrices.find(matrix_id);
			if (it != this->matrices.end()) {
			AKANTU_EXCEPTION("The matrix " << matrix_id << " already exists in "
			<< this->id);
			}

			SparseMatrix & ret = *matrix;
			this->matrices[matrix_id] = std::move(matrix);
			return ret;
			}

			/* -------------------------------------------------------------------------- */
			/// Get an instance of a new SparseMatrix
			Array<Real> & DOFManager::getNewLumpedMatrix(const ID & id) {
			ID matrix_id = this->id + ":lumped_mtx:" + id;
			LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
			if (it != this->lumped_matrices.end()) {
			AKANTU_EXCEPTION("The lumped matrix " << matrix_id << " already exists in "
			<< this->id);
			}

			auto mtx =
			std::make_unique<Array<Real>>(this->local_system_size, 1, matrix_id);
			this->lumped_matrices[matrix_id] = std::move(mtx);
			return *this->lumped_matrices[matrix_id];
			}

			/* -------------------------------------------------------------------------- */
			NonLinearSolver & DOFManager::registerNonLinearSolver(
			const ID & non_linear_solver_id,
			std::unique_ptr<NonLinearSolver> & non_linear_solver) {
			NonLinearSolversMap::const_iterator it =
			this->non_linear_solvers.find(non_linear_solver_id);
			if (it != this->non_linear_solvers.end()) {
			AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
			<< " already exists in "
			<< this->id);
			}

			NonLinearSolver & ret = *non_linear_solver;
			this->non_linear_solvers[non_linear_solver_id] = std::move(non_linear_solver);

			return ret;
			}

			/* -------------------------------------------------------------------------- */
			TimeStepSolver & DOFManager::registerTimeStepSolver(
			const ID & time_step_solver_id,
			std::unique_ptr<TimeStepSolver> & time_step_solver) {
			TimeStepSolversMap::const_iterator it =
			this->time_step_solvers.find(time_step_solver_id);
			if (it != this->time_step_solvers.end()) {
			AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
			<< " already exists in "
			<< this->id);
			}

			TimeStepSolver & ret = *time_step_solver;
			this->time_step_solvers[time_step_solver_id] = std::move(time_step_solver);
			return ret;
			}

			/* -------------------------------------------------------------------------- */
			SparseMatrix & DOFManager::getMatrix(const ID & id) {
			ID matrix_id = this->id + ":mtx:" + id;
			SparseMatricesMap::const_iterator it = this->matrices.find(matrix_id);
			if (it == this->matrices.end()) {
			AKANTU_SILENT_EXCEPTION("The matrix " << matrix_id << " does not exists in "
			<< this->id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			bool DOFManager::hasMatrix(const ID & id) const {
			ID mtx_id = this->id + ":mtx:" + id;
			SparseMatricesMap::const_iterator it = this->matrices.find(mtx_id);
			return it != this->matrices.end();
			}

			/* -------------------------------------------------------------------------- */
			Array<Real> & DOFManager::getLumpedMatrix(const ID & id) {
			ID matrix_id = this->id + ":lumped_mtx:" + id;
			LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
			if (it == this->lumped_matrices.end()) {
			AKANTU_SILENT_EXCEPTION("The lumped matrix "
			<< matrix_id << " does not exists in " << this->id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			const Array<Real> & DOFManager::getLumpedMatrix(const ID & id) const {
			ID matrix_id = this->id + ":lumped_mtx:" + id;
			LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
			if (it == this->lumped_matrices.end()) {
			AKANTU_SILENT_EXCEPTION("The lumped matrix "
			<< matrix_id << " does not exists in " << this->id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			bool DOFManager::hasLumpedMatrix(const ID & id) const {
			ID mtx_id = this->id + ":lumped_mtx:" + id;
			LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(mtx_id);
			return it != this->lumped_matrices.end();
			}

			/* -------------------------------------------------------------------------- */
			NonLinearSolver & DOFManager::getNonLinearSolver(const ID & id) {
			ID non_linear_solver_id = this->id + ":nls:" + id;
			NonLinearSolversMap::const_iterator it =
			this->non_linear_solvers.find(non_linear_solver_id);
			if (it == this->non_linear_solvers.end()) {
			AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
			<< " does not exists in "
			<< this->id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			bool DOFManager::hasNonLinearSolver(const ID & id) const {
			ID solver_id = this->id + ":nls:" + id;
			NonLinearSolversMap::const_iterator it =
			this->non_linear_solvers.find(solver_id);
			return it != this->non_linear_solvers.end();
			}

			/* -------------------------------------------------------------------------- */
			TimeStepSolver & DOFManager::getTimeStepSolver(const ID & id) {
			ID time_step_solver_id = this->id + ":tss:" + id;
			TimeStepSolversMap::const_iterator it =
			this->time_step_solvers.find(time_step_solver_id);
			if (it == this->time_step_solvers.end()) {
			AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
			<< " does not exists in "
			<< this->id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			bool DOFManager::hasTimeStepSolver(const ID & solver_id) const {
			ID time_step_solver_id = this->id + ":tss:" + solver_id;
			TimeStepSolversMap::const_iterator it =
			this->time_step_solvers.find(time_step_solver_id);
			return it != this->time_step_solvers.end();
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::savePreviousDOFs(const ID & dofs_id) {
			this->getPreviousDOFs(dofs_id).copy(this->getDOFs(dofs_id));
			}

			/* -------------------------------------------------------------------------- */
			/* Mesh Events */
			/* -------------------------------------------------------------------------- */
			std::pair<UInt, UInt>
			DOFManager::updateNodalDOFs(const ID & dof_id, const Array<UInt> & nodes_list) {
			auto & dof_data = this->getDOFData(dof_id);
			UInt nb_new_local_dofs = 0;
			UInt nb_new_pure_local = 0;

			nb_new_local_dofs = nodes_list.size();
			for (const auto & node : nodes_list) {
			nb_new_pure_local += this->mesh->isLocalOrMasterNode(node) ? 1 : 0;
			}

			const auto & dof_array = *dof_data.dof;
			nb_new_pure_local *= dof_array.getNbComponent();
			nb_new_local_dofs *= dof_array.getNbComponent();

			this->pure_local_system_size += nb_new_pure_local;
			this->local_system_size += nb_new_local_dofs;

			UInt nb_new_global = nb_new_pure_local;
			communicator.allReduce(nb_new_global, SynchronizerOperation::_sum);

			this->system_size += nb_new_global;

			return std::make_pair(nb_new_local_dofs, nb_new_pure_local);
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::onNodesAdded(const Array<UInt> & nodes_list,
			const NewNodesEvent &) {
			for (auto & pair : this->dofs) {
			const auto & dof_id = pair.first;
			auto & dof_data = this->getDOFData(dof_id);
			if (dof_data.support_type != _dst_nodal)
			continue;

			const auto & group = dof_data.group_support;

			if (group == "__mesh__") {
			this->updateNodalDOFs(dof_id, nodes_list);
			} else {
			const auto & node_group =
			this->mesh->getElementGroup(group).getNodeGroup();
			Array<UInt> new_nodes_list;
			for (const auto & node : nodes_list) {
			if (node_group.find(node) != UInt(-1))
			new_nodes_list.push_back(node);
			}

			this->updateNodalDOFs(dof_id, new_nodes_list);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void DOFManager::onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
			const RemovedNodesEvent &) {}

			/* -------------------------------------------------------------------------- */
			void DOFManager::onElementsAdded(const Array<Element> &,
			const NewElementsEvent &) {}

			/* -------------------------------------------------------------------------- */
			void DOFManager::onElementsRemoved(const Array<Element> &,
			const ElementTypeMapArray<UInt> &,
			const RemovedElementsEvent &) {}

			/* -------------------------------------------------------------------------- */
			void DOFManager::onElementsChanged(const Array<Element> &,
			const Array<Element> &,
			const ElementTypeMapArray<UInt> &,
			const ChangedElementsEvent &) {}

			/* -------------------------------------------------------------------------- */

			} // namespace akantu

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dof_manager.cc
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