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solid_mechanics_model.cc
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			/**
			* @file solid_mechanics_model.cc
			*
			* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			* @author Clement Roux <clement.roux@epfl.ch>
			* @author Marco Vocialta <marco.vocialta@epfl.ch>
			*
			* @date creation: Tue Jul 27 2010
			* @date last modification: Tue Jan 19 2016
			*
			* @brief Implementation of the SolidMechanicsModel class
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2012, 2014, 2015 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 "solid_mechanics_model.hh"
			#include "integrator_gauss.hh"
			#include "shape_lagrange.hh"
			#include "solid_mechanics_model_tmpl.hh"

			#include "communicator.hh"
			#include "element_synchronizer.hh"
			#include "sparse_matrix.hh"
			#include "synchronizer_registry.hh"

			#include "dumpable_inline_impl.hh"
			#ifdef AKANTU_USE_IOHELPER
			#include "dumper_paraview.hh"
			#endif

			#include "material_non_local.hh"
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			/**
			* A solid mechanics model need a mesh and a dimension to be created. the model
			* by it self can not do a lot, the good init functions should be called in
			* order to configure the model depending on what we want to do.
			*
			* @param mesh mesh representing the model we want to simulate
			* @param dim spatial dimension of the problem, if dim = 0 (default value) the
			* dimension of the problem is assumed to be the on of the mesh
			* @param id an id to identify the model
			*/
			SolidMechanicsModel::SolidMechanicsModel(Mesh & mesh, UInt dim, const ID & id,
			const MemoryID & memory_id)
			: Model(mesh, ModelType::_solid_mechanics_model, dim, id, memory_id),
			BoundaryCondition<SolidMechanicsModel>(), f_m2a(1.0),
			displacement(nullptr), previous_displacement(nullptr),
			displacement_increment(nullptr), mass(nullptr), velocity(nullptr),
			acceleration(nullptr), external_force(nullptr), internal_force(nullptr),
			blocked_dofs(nullptr), current_position(nullptr),
			material_index("material index", id, memory_id),
			material_local_numbering("material local numbering", id, memory_id),
			increment_flag(false),
			are_materials_instantiated(false) { //, pbc_synch(nullptr) {
			AKANTU_DEBUG_IN();

			this->registerFEEngineObject<MyFEEngineType>("SolidMechanicsFEEngine", mesh,
			Model::spatial_dimension);

			#if defined(AKANTU_USE_IOHELPER)
			this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
			this->mesh.addDumpMesh(mesh, Model::spatial_dimension, _not_ghost,
			_ek_regular);
			#endif

			material_selector = std::make_shared<DefaultMaterialSelector>(material_index),

			this->initDOFManager();

			this->registerDataAccessor(*this);

			if (this->mesh.isDistributed()) {
			auto & synchronizer = this->mesh.getElementSynchronizer();
			this->registerSynchronizer(synchronizer, _gst_material_id);
			this->registerSynchronizer(synchronizer, _gst_smm_mass);
			this->registerSynchronizer(synchronizer, _gst_smm_stress);
			this->registerSynchronizer(synchronizer, _gst_smm_boundary);
			this->registerSynchronizer(synchronizer, _gst_for_dump);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			SolidMechanicsModel::~SolidMechanicsModel() {
			AKANTU_DEBUG_IN();

			for (auto & internal : this->registered_internals) {
			delete internal.second;
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::setTimeStep(Real time_step, const ID & solver_id) {
			Model::setTimeStep(time_step, solver_id);

			#if defined(AKANTU_USE_IOHELPER)
			this->mesh.getDumper().setTimeStep(time_step);
			#endif
			}

			/* -------------------------------------------------------------------------- */
			/* Initialization */
			/* -------------------------------------------------------------------------- */
			/**
			* This function groups many of the initialization in on function. For most of
			* basics case the function should be enough. The functions initialize the
			* model, the internal vectors, set them to 0, and depending on the parameters
			* it also initialize the explicit or implicit solver.
			*
			* @param material_file the file containing the materials to use
			* @param method the analysis method wanted. See the akantu::AnalysisMethod for
			* the different possibilities
			*/
			void SolidMechanicsModel::initFullImpl(const ModelOptions & options) {
			material_index.initialize(mesh, _element_kind = _ek_not_defined,
			_default_value = UInt(-1), _with_nb_element = true);
			material_local_numbering.initialize(mesh, _element_kind = _ek_not_defined,
			_with_nb_element = true);

			Model::initFullImpl(options);

			// initialize pbc
			if (this->pbc_pair.size() != 0)
			this->initPBC();

			// initialize the materials
			if (this->parser.getLastParsedFile() != "") {
			this->instantiateMaterials();
			}

			this->initMaterials();

			this->initBC(this, displacement, displacement_increment, external_force);
			}

			/* -------------------------------------------------------------------------- */
			TimeStepSolverType SolidMechanicsModel::getDefaultSolverType() const {
			return _tsst_dynamic_lumped;
			}

			/* -------------------------------------------------------------------------- */
			ModelSolverOptions SolidMechanicsModel::getDefaultSolverOptions(
			const TimeStepSolverType & type) const {
			ModelSolverOptions options;

			switch (type) {
			case _tsst_dynamic_lumped: {
			options.non_linear_solver_type = _nls_lumped;
			options.integration_scheme_type["displacement"] = _ist_central_difference;
			options.solution_type["displacement"] = IntegrationScheme::_acceleration;
			break;
			}
			case _tsst_static: {
			options.non_linear_solver_type = _nls_newton_raphson;
			options.integration_scheme_type["displacement"] = _ist_pseudo_time;
			options.solution_type["displacement"] = IntegrationScheme::_not_defined;
			break;
			}
			case _tsst_dynamic: {
			if (this->method == _explicit_consistent_mass) {
			options.non_linear_solver_type = _nls_newton_raphson;
			options.integration_scheme_type["displacement"] = _ist_central_difference;
			options.solution_type["displacement"] = IntegrationScheme::_acceleration;
			} else {
			options.non_linear_solver_type = _nls_newton_raphson;
			options.integration_scheme_type["displacement"] = _ist_trapezoidal_rule_2;
			options.solution_type["displacement"] = IntegrationScheme::_displacement;
			}
			break;
			}
			default:
			AKANTU_EXCEPTION(type << " is not a valid time step solver type");
			}

			return options;
			}

			/* -------------------------------------------------------------------------- */
			std::tuple<ID, TimeStepSolverType>
			SolidMechanicsModel::getDefaultSolverID(const AnalysisMethod & method) {
			switch (method) {
			case _explicit_lumped_mass: {
			return std::make_tuple("explicit_lumped", _tsst_dynamic_lumped);
			}
			case _explicit_consistent_mass: {
			return std::make_tuple("explicit", _tsst_dynamic);
			}
			case _static: {
			return std::make_tuple("static", _tsst_static);
			}
			case _implicit_dynamic: {
			return std::make_tuple("implicit", _tsst_dynamic);
			}
			default:
			return std::make_tuple("unknown", _tsst_not_defined);
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initSolver(TimeStepSolverType time_step_solver_type,
			NonLinearSolverType) {
			auto & dof_manager = this->getDOFManager();

			/* ------------------------------------------------------------------------ */
			// for alloc type of solvers
			this->allocNodalField(this->displacement, spatial_dimension, "displacement");
			this->allocNodalField(this->previous_displacement, spatial_dimension,
			"previous_displacement");
			this->allocNodalField(this->displacement_increment, spatial_dimension,
			"displacement_increment");
			this->allocNodalField(this->internal_force, spatial_dimension,
			"internal_force");
			this->allocNodalField(this->external_force, spatial_dimension,
			"external_force");
			this->allocNodalField(this->blocked_dofs, spatial_dimension, "blocked_dofs");
			this->allocNodalField(this->current_position, spatial_dimension,
			"current_position");

			// initialize the current positions
			this->current_position->copy(this->mesh.getNodes());

			/* ------------------------------------------------------------------------ */
			if (!dof_manager.hasDOFs("displacement")) {
			dof_manager.registerDOFs("displacement", *this->displacement, _dst_nodal);
			dof_manager.registerBlockedDOFs("displacement", *this->blocked_dofs);
			dof_manager.registerDOFsIncrement("displacement",
			*this->displacement_increment);
			dof_manager.registerDOFsPrevious("displacement",
			*this->previous_displacement);
			}

			/* ------------------------------------------------------------------------ */
			// for dynamic
			if (time_step_solver_type == _tsst_dynamic \|\|
			time_step_solver_type == _tsst_dynamic_lumped) {
			this->allocNodalField(this->velocity, spatial_dimension, "velocity");
			this->allocNodalField(this->acceleration, spatial_dimension,
			"acceleration");

			if (!dof_manager.hasDOFsDerivatives("displacement", 1)) {
			dof_manager.registerDOFsDerivative("displacement", 1, *this->velocity);
			dof_manager.registerDOFsDerivative("displacement", 2,
			*this->acceleration);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initFEEngineBoundary() {
			FEEngine & fem_boundary = getFEEngineBoundary();
			fem_boundary.initShapeFunctions(_not_ghost);
			fem_boundary.initShapeFunctions(_ghost);

			fem_boundary.computeNormalsOnIntegrationPoints(_not_ghost);
			fem_boundary.computeNormalsOnIntegrationPoints(_ghost);
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Initialize the model,basically it pre-compute the shapes, shapes derivatives
			* and jacobian
			*/
			void SolidMechanicsModel::initModel() {
			/// \todo add the current position as a parameter to initShapeFunctions for
			/// large deformation
			getFEEngine().initShapeFunctions(_not_ghost);
			getFEEngine().initShapeFunctions(_ghost);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::assembleResidual() {
			AKANTU_DEBUG_IN();

			/* ------------------------------------------------------------------------ */
			// computes the internal forces
			this->assembleInternalForces();

			/* ------------------------------------------------------------------------ */
			this->getDOFManager().assembleToResidual("displacement",
			*this->external_force, 1);
			this->getDOFManager().assembleToResidual("displacement",
			*this->internal_force, 1);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			MatrixType SolidMechanicsModel::getMatrixType(const ID & matrix_id) {
			// \TODO check the materials to know what is the correct answer
			if (matrix_id == "C")
			return _mt_not_defined;

			return _symmetric;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::assembleMatrix(const ID & matrix_id) {
			if (matrix_id == "K") {
			this->assembleStiffnessMatrix();
			} else if (matrix_id == "M") {
			this->assembleMass();
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::assembleLumpedMatrix(const ID & matrix_id) {
			if (matrix_id == "M") {
			this->assembleMassLumped();
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::beforeSolveStep() {
			for (auto & material : materials)
			material->beforeSolveStep();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::afterSolveStep() {
			for (auto & material : materials)
			material->afterSolveStep();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::predictor() { ++displacement_release; }

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::corrector() { ++displacement_release; }

			/* -------------------------------------------------------------------------- */
			/**
			* This function computes the internal forces as F_{int} = \int_{\Omega} N
			* \sigma d\Omega@f$
			*/
			void SolidMechanicsModel::assembleInternalForces() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Assemble the internal forces");

			this->internal_force->clear();

			// compute the stresses of local elements
			AKANTU_DEBUG_INFO("Compute local stresses");
			for (auto & material : materials) {
			material->computeAllStresses(_not_ghost);
			}

			/* ------------------------------------------------------------------------ */
			/* Computation of the non local part */
			if (this->non_local_manager)
			this->non_local_manager->computeAllNonLocalStresses();

			// communicate the stresses
			AKANTU_DEBUG_INFO("Send data for residual assembly");
			this->asynchronousSynchronize(_gst_smm_stress);

			// assemble the forces due to local stresses
			AKANTU_DEBUG_INFO("Assemble residual for local elements");
			for (auto & material : materials) {
			material->assembleInternalForces(_not_ghost);
			}

			// finalize communications
			AKANTU_DEBUG_INFO("Wait distant stresses");
			this->waitEndSynchronize(_gst_smm_stress);

			// assemble the stresses due to ghost elements
			AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
			for (auto & material : materials) {
			material->assembleInternalForces(_ghost);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::assembleStiffnessMatrix() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Assemble the new stiffness matrix.");

			// Check if materials need to recompute the matrix
			bool need_to_reassemble = false;

			for (auto & material : materials) {
			need_to_reassemble \|= material->hasStiffnessMatrixChanged();
			}

			if (need_to_reassemble) {
			this->getDOFManager().getMatrix("K").clear();

			// call compute stiffness matrix on each local elements
			for (auto & material : materials) {
			material->assembleStiffnessMatrix(_not_ghost);
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updateCurrentPosition() {
			if (this->current_position_release == this->displacement_release)
			return;

			this->current_position->copy(this->mesh.getNodes());

			auto cpos_it = this->current_position->begin(Model::spatial_dimension);
			auto cpos_end = this->current_position->end(Model::spatial_dimension);
			auto disp_it = this->displacement->begin(Model::spatial_dimension);

			for (; cpos_it != cpos_end; ++cpos_it, ++disp_it) {
			cpos_it += disp_it;
			}

			this->current_position_release = this->displacement_release;
			}

			/* -------------------------------------------------------------------------- */
			const Array<Real> & SolidMechanicsModel::getCurrentPosition() {
			this->updateCurrentPosition();
			return *this->current_position;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updateDataForNonLocalCriterion(
			ElementTypeMapReal & criterion) {
			const ID field_name = criterion.getName();
			for (auto & material : materials) {
			if (!material->isInternal<Real>(field_name, _ek_regular))
			continue;

			for (auto ghost_type : ghost_types) {
			material->flattenInternal(field_name, criterion, ghost_type, _ek_regular);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			/* Information */
			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getStableTimeStep() {
			AKANTU_DEBUG_IN();

			Real min_dt = getStableTimeStep(_not_ghost);

			/// reduction min over all processors
			mesh.getCommunicator().allReduce(min_dt, SynchronizerOperation::_min);

			AKANTU_DEBUG_OUT();
			return min_dt;
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getStableTimeStep(const GhostType & ghost_type) {
			AKANTU_DEBUG_IN();

			Real min_dt = std::numeric_limits<Real>::max();

			this->updateCurrentPosition();

			Element elem;
			elem.ghost_type = ghost_type;

			for (auto type :
			mesh.elementTypes(Model::spatial_dimension, ghost_type, _ek_regular)) {
			elem.type = type;
			UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
			UInt nb_element = mesh.getNbElement(type);

			auto mat_indexes = material_index(type, ghost_type).begin();
			auto mat_loc_num = material_local_numbering(type, ghost_type).begin();

			Array<Real> X(0, nb_nodes_per_element * Model::spatial_dimension);
			FEEngine::extractNodalToElementField(mesh, *current_position, X, type,
			_not_ghost);

			auto X_el = X.begin(Model::spatial_dimension, nb_nodes_per_element);

			for (UInt el = 0; el < nb_element;
			++el, ++X_el, ++mat_indexes, ++mat_loc_num) {
			elem.element = *mat_loc_num;
			Real el_h = getFEEngine().getElementInradius(*X_el, type);
			Real el_c = this->materials[*mat_indexes]->getCelerity(elem);
			Real el_dt = el_h / el_c;

			min_dt = std::min(min_dt, el_dt);
			}
			}

			AKANTU_DEBUG_OUT();
			return min_dt;
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getKineticEnergy() {
			AKANTU_DEBUG_IN();

			Real ekin = 0.;
			UInt nb_nodes = mesh.getNbNodes();

			if (this->getDOFManager().hasLumpedMatrix("M")) {
			auto m_it = this->mass->begin(Model::spatial_dimension);
			auto m_end = this->mass->end(Model::spatial_dimension);
			auto v_it = this->velocity->begin(Model::spatial_dimension);

			for (UInt n = 0; m_it != m_end; ++n, ++m_it, ++v_it) {
			const Vector<Real> & v = *v_it;
			const Vector<Real> & m = *m_it;

			Real mv2 = 0;
			bool is_local_node = mesh.isLocalOrMasterNode(n);
			// bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
			bool count_node = is_local_node; // && is_not_pbc_slave_node;
			if (count_node) {
			for (UInt i = 0; i < Model::spatial_dimension; ++i) {
			if (m(i) > std::numeric_limits<Real>::epsilon())
			mv2 += v(i) * v(i) * m(i);
			}
			}

			ekin += mv2;
			}
			} else if (this->getDOFManager().hasMatrix("M")) {
			Array<Real> Mv(nb_nodes, Model::spatial_dimension);
			this->getDOFManager().getMatrix("M").matVecMul(*this->velocity, Mv);

			auto mv_it = Mv.begin(Model::spatial_dimension);
			auto mv_end = Mv.end(Model::spatial_dimension);
			auto v_it = this->velocity->begin(Model::spatial_dimension);

			for (; mv_it != mv_end; ++mv_it, ++v_it) {
			ekin += v_it->dot(*mv_it);
			}
			} else {
			AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
			}

			mesh.getCommunicator().allReduce(ekin, SynchronizerOperation::_sum);

			AKANTU_DEBUG_OUT();
			return ekin * .5;
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getKineticEnergy(const ElementType & type,
			UInt index) {
			AKANTU_DEBUG_IN();

			UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);

			Array<Real> vel_on_quad(nb_quadrature_points, Model::spatial_dimension);
			Array<UInt> filter_element(1, 1, index);

			getFEEngine().interpolateOnIntegrationPoints(*velocity, vel_on_quad,
			Model::spatial_dimension, type,
			_not_ghost, filter_element);

			Array<Real>::vector_iterator vit =
			vel_on_quad.begin(Model::spatial_dimension);
			Array<Real>::vector_iterator vend = vel_on_quad.end(Model::spatial_dimension);

			Vector<Real> rho_v2(nb_quadrature_points);

			Real rho = materials[material_index(type)(index)]->getRho();

			for (UInt q = 0; vit != vend; ++vit, ++q) {
			rho_v2(q) = rho * vit->dot(*vit);
			}

			AKANTU_DEBUG_OUT();

			return .5 * getFEEngine().integrate(rho_v2, type, index);
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getExternalWork() {
			AKANTU_DEBUG_IN();

			auto ext_force_it = external_force->begin(Model::spatial_dimension);
			auto int_force_it = internal_force->begin(Model::spatial_dimension);
			auto boun_it = blocked_dofs->begin(Model::spatial_dimension);

			decltype(ext_force_it) incr_or_velo_it;
			if (this->method == _static) {
			incr_or_velo_it =
			this->displacement_increment->begin(Model::spatial_dimension);
			} else {
			incr_or_velo_it = this->velocity->begin(Model::spatial_dimension);
			}

			Real work = 0.;

			UInt nb_nodes = this->mesh.getNbNodes();

			for (UInt n = 0; n < nb_nodes;
			++n, ++ext_force_it, ++int_force_it, ++boun_it, ++incr_or_velo_it) {
			const auto & int_force = *int_force_it;
			const auto & ext_force = *ext_force_it;
			const auto & boun = *boun_it;
			const auto & incr_or_velo = *incr_or_velo_it;

			bool is_local_node = this->mesh.isLocalOrMasterNode(n);
			// bool is_not_pbc_slave_node = !this->isPBCSlaveNode(n);
			bool count_node = is_local_node; // && is_not_pbc_slave_node;

			if (count_node) {
			for (UInt i = 0; i < Model::spatial_dimension; ++i) {
			if (boun(i))
			work -= int_force(i) * incr_or_velo(i);
			else
			work += ext_force(i) * incr_or_velo(i);
			}
			}
			}

			mesh.getCommunicator().allReduce(work, SynchronizerOperation::_sum);

			if (this->method != _static)
			work *= this->getTimeStep();

			AKANTU_DEBUG_OUT();
			return work;
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getEnergy(const std::string & energy_id) {
			AKANTU_DEBUG_IN();

			if (energy_id == "kinetic") {
			return getKineticEnergy();
			} else if (energy_id == "external work") {
			return getExternalWork();
			}

			Real energy = 0.;
			for (auto & material : materials)
			energy += material->getEnergy(energy_id);

			/// reduction sum over all processors
			mesh.getCommunicator().allReduce(energy, SynchronizerOperation::_sum);

			AKANTU_DEBUG_OUT();
			return energy;
			}
			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getEnergy(const std::string & energy_id,
			const ElementType & type, UInt index) {
			AKANTU_DEBUG_IN();

			if (energy_id == "kinetic") {
			return getKineticEnergy(type, index);
			}

			UInt mat_index = this->material_index(type, _not_ghost)(index);
			UInt mat_loc_num = this->material_local_numbering(type, _not_ghost)(index);
			Real energy =
			this->materials[mat_index]->getEnergy(energy_id, type, mat_loc_num);

			AKANTU_DEBUG_OUT();
			return energy;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::onElementsAdded(const Array<Element> & element_list,
			const NewElementsEvent & event) {
			AKANTU_DEBUG_IN();

			this->material_index.initialize(mesh, _element_kind = _ek_not_defined,
			_default_value = UInt(-1));
			this->material_local_numbering.initialize(
			mesh, _element_kind = _ek_not_defined, _default_value = UInt(-1));

			ElementTypeMapArray<UInt> filter("new_element_filter", this->getID(),
			this->getMemoryID());

			for (auto & elem : element_list) {
			if (!filter.exists(elem.type, elem.ghost_type))
			filter.alloc(0, 1, elem.type, elem.ghost_type);
			filter(elem.type, elem.ghost_type).push_back(elem.element);
			}

			this->assignMaterialToElements(&filter);

			for (auto & material : materials)
			material->onElementsAdded(element_list, event);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::onElementsRemoved(
			const Array<Element> & element_list,
			const ElementTypeMapArray<UInt> & new_numbering,
			const RemovedElementsEvent & event) {
			for (auto & material : materials) {
			material->onElementsRemoved(element_list, new_numbering, event);
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::onNodesAdded(const Array<UInt> & nodes_list,
			const NewNodesEvent & event) {
			AKANTU_DEBUG_IN();
			UInt nb_nodes = mesh.getNbNodes();

			if (displacement) {
			displacement->resize(nb_nodes, 0.);
			++displacement_release;
			}
			if (mass)
			mass->resize(nb_nodes, 0.);
			if (velocity)
			velocity->resize(nb_nodes, 0.);
			if (acceleration)
			acceleration->resize(nb_nodes, 0.);
			if (external_force)
			external_force->resize(nb_nodes, 0.);
			if (internal_force)
			internal_force->resize(nb_nodes, 0.);
			if (blocked_dofs)
			blocked_dofs->resize(nb_nodes, 0.);
			if (current_position)
			current_position->resize(nb_nodes, 0.);

			if (previous_displacement)
			previous_displacement->resize(nb_nodes, 0.);
			if (displacement_increment)
			displacement_increment->resize(nb_nodes, 0.);

			for (auto & material : materials) {
			material->onNodesAdded(nodes_list, event);
			}

			need_to_reassemble_lumped_mass = true;
			need_to_reassemble_mass = true;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::onNodesRemoved(const Array<UInt> & /element_list/,
			const Array<UInt> & new_numbering,
			const RemovedNodesEvent & /event/) {
			if (displacement) {
			mesh.removeNodesFromArray(*displacement, new_numbering);
			++displacement_release;
			}
			if (mass)
			mesh.removeNodesFromArray(*mass, new_numbering);
			if (velocity)
			mesh.removeNodesFromArray(*velocity, new_numbering);
			if (acceleration)
			mesh.removeNodesFromArray(*acceleration, new_numbering);
			if (internal_force)
			mesh.removeNodesFromArray(*internal_force, new_numbering);
			if (external_force)
			mesh.removeNodesFromArray(*external_force, new_numbering);
			if (blocked_dofs)
			mesh.removeNodesFromArray(*blocked_dofs, new_numbering);

			// if (increment_acceleration)
			// mesh.removeNodesFromArray(*increment_acceleration, new_numbering);
			if (displacement_increment)
			mesh.removeNodesFromArray(*displacement_increment, new_numbering);

			if (previous_displacement)
			mesh.removeNodesFromArray(*previous_displacement, new_numbering);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::printself(std::ostream & stream, int indent) const {
			std::string space;
			for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
			;

			stream << space << "Solid Mechanics Model [" << std::endl;
			stream << space << " + id : " << id << std::endl;
			stream << space << " + spatial dimension : " << Model::spatial_dimension
			<< std::endl;
			stream << space << " + fem [" << std::endl;
			getFEEngine().printself(stream, indent + 2);
			stream << space << AKANTU_INDENT << "]" << std::endl;
			stream << space << " + nodals information [" << std::endl;
			displacement->printself(stream, indent + 2);
			if (velocity)
			velocity->printself(stream, indent + 2);
			if (acceleration)
			acceleration->printself(stream, indent + 2);
			if (mass)
			mass->printself(stream, indent + 2);
			external_force->printself(stream, indent + 2);
			internal_force->printself(stream, indent + 2);
			blocked_dofs->printself(stream, indent + 2);
			stream << space << AKANTU_INDENT << "]" << std::endl;

			stream << space << " + material information [" << std::endl;
			material_index.printself(stream, indent + 2);
			stream << space << AKANTU_INDENT << "]" << std::endl;

			stream << space << " + materials [" << std::endl;
			for (auto & material : materials) {
			material->printself(stream, indent + 1);
			}
			stream << space << AKANTU_INDENT << "]" << std::endl;

			stream << space << "]" << std::endl;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initializeNonLocal() {
			this->non_local_manager->synchronize(*this, _gst_material_id);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::insertIntegrationPointsInNeighborhoods(
			const GhostType & ghost_type) {
			for (auto & mat : materials) {
			MaterialNonLocalInterface * mat_non_local;
			if ((mat_non_local =
			dynamic_cast<MaterialNonLocalInterface *>(mat.get())) == nullptr)
			continue;

			ElementTypeMapArray<Real> quadrature_points_coordinates(
			"quadrature_points_coordinates_tmp_nl", this->id, this->memory_id);
			quadrature_points_coordinates.initialize(this->getFEEngine(),
			_nb_component = spatial_dimension,
			_ghost_type = ghost_type);

			for (auto & type : quadrature_points_coordinates.elementTypes(
			Model::spatial_dimension, ghost_type)) {
			this->getFEEngine().computeIntegrationPointsCoordinates(
			quadrature_points_coordinates(type, ghost_type), type, ghost_type);
			}

			mat_non_local->initMaterialNonLocal();

			mat_non_local->insertIntegrationPointsInNeighborhoods(
			ghost_type, quadrature_points_coordinates);
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::computeNonLocalStresses(
			const GhostType & ghost_type) {
			for (auto & mat : materials) {
			if (dynamic_cast<MaterialNonLocalInterface *>(mat.get()) == nullptr)
			continue;

			auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
			mat_non_local.computeNonLocalStresses(ghost_type);
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updateLocalInternal(
			ElementTypeMapReal & internal_flat, const GhostType & ghost_type,
			const ElementKind & kind) {
			const ID field_name = internal_flat.getName();
			for (auto & material : materials) {
			if (material->isInternal<Real>(field_name, kind))
			material->flattenInternal(field_name, internal_flat, ghost_type, kind);
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updateNonLocalInternal(
			ElementTypeMapReal & internal_flat, const GhostType & ghost_type,
			const ElementKind & kind) {

			const ID field_name = internal_flat.getName();

			for (auto & mat : materials) {
			if (dynamic_cast<MaterialNonLocalInterface *>(mat.get()) == nullptr)
			continue;

			auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
			mat_non_local.updateNonLocalInternals(internal_flat, field_name, ghost_type,
			kind);
			}
			}

			/* -------------------------------------------------------------------------- */
			FEEngine & SolidMechanicsModel::getFEEngineBoundary(const ID & name) {
			return dynamic_cast<FEEngine &>(
			getFEEngineClassBoundary<MyFEEngineType>(name));
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::splitElementByMaterial(
			const Array<Element> & elements,
			std::vector<Array<Element>> & elements_per_mat) const {
			ElementType current_element_type = _not_defined;
			GhostType current_ghost_type = _casper;
			const Array<UInt> * mat_indexes = nullptr;
			const Array<UInt> * mat_loc_num = nullptr;

			for (auto && el : elements) {
			if (el.type != current_element_type \|\|
			el.ghost_type != current_ghost_type) {
			current_element_type = el.type;
			current_ghost_type = el.ghost_type;
			mat_indexes = &(this->material_index(el.type, el.ghost_type));
			mat_loc_num = &(this->material_local_numbering(el.type, el.ghost_type));
			}

			UInt old_id = el.element;
			el.element = (*mat_loc_num)(old_id);
			elements_per_mat[(*mat_indexes)(old_id)].push_back(el);
			}
			}

			/* -------------------------------------------------------------------------- */
			UInt SolidMechanicsModel::getNbData(const Array<Element> & elements,
			const SynchronizationTag & tag) const {
			AKANTU_DEBUG_IN();

			UInt size = 0;
			UInt nb_nodes_per_element = 0;

			for (const Element & el : elements) {
			nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
			}

			switch (tag) {
			case _gst_material_id: {
			size += elements.size() * sizeof(UInt);
			break;
			}
			case _gst_smm_mass: {
			size += nb_nodes_per_element * sizeof(Real) *
			Model::spatial_dimension; // mass vector
			break;
			}
			case _gst_smm_for_gradu: {
			size += nb_nodes_per_element * Model::spatial_dimension *
			sizeof(Real); // displacement
			break;
			}
			case _gst_smm_boundary: {
			// force, displacement, boundary
			size += nb_nodes_per_element * Model::spatial_dimension *
			(2 * sizeof(Real) + sizeof(bool));
			break;
			}
			case _gst_for_dump: {
			// displacement, velocity, acceleration, residual, force
			size += nb_nodes_per_element * Model::spatial_dimension * sizeof(Real) * 5;
			break;
			}
			default: {}
			}

			if (tag != _gst_material_id) {
			splitByMaterial(elements, [&](auto && mat, auto && elements) {
			size += mat.getNbData(elements, tag);
			});
			}

			AKANTU_DEBUG_OUT();
			return size;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const SynchronizationTag & tag) const {
			AKANTU_DEBUG_IN();

			switch (tag) {
			case _gst_material_id: {
			this->packElementalDataHelper(material_index, buffer, elements, false,
			getFEEngine());
			break;
			}
			case _gst_smm_mass: {
			packNodalDataHelper(*mass, buffer, elements, mesh);
			break;
			}
			case _gst_smm_for_gradu: {
			packNodalDataHelper(*displacement, buffer, elements, mesh);
			break;
			}
			case _gst_for_dump: {
			packNodalDataHelper(*displacement, buffer, elements, mesh);
			packNodalDataHelper(*velocity, buffer, elements, mesh);
			packNodalDataHelper(*acceleration, buffer, elements, mesh);
			packNodalDataHelper(*internal_force, buffer, elements, mesh);
			packNodalDataHelper(*external_force, buffer, elements, mesh);
			break;
			}
			case _gst_smm_boundary: {
			packNodalDataHelper(*external_force, buffer, elements, mesh);
			packNodalDataHelper(*velocity, buffer, elements, mesh);
			packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
			break;
			}
			default: {}
			}

			if (tag != _gst_material_id) {
			splitByMaterial(elements, [&](auto && mat, auto && elements) {
			mat.packData(buffer, elements, tag);
			});
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const SynchronizationTag & tag) {
			AKANTU_DEBUG_IN();

			switch (tag) {
			case _gst_material_id: {
			for (auto && element : elements) {
			UInt recv_mat_index;
			buffer >> recv_mat_index;
			UInt & mat_index = material_index(element);
			if (mat_index != UInt(-1))
			continue;

			// add ghosts element to the correct material
			mat_index = recv_mat_index;
			UInt index = materials[mat_index]->addElement(element);
			material_local_numbering(element) = index;
			}
			break;
			}
			case _gst_smm_mass: {
			unpackNodalDataHelper(*mass, buffer, elements, mesh);
			break;
			}
			case _gst_smm_for_gradu: {
			unpackNodalDataHelper(*displacement, buffer, elements, mesh);
			break;
			}
			case _gst_for_dump: {
			unpackNodalDataHelper(*displacement, buffer, elements, mesh);
			unpackNodalDataHelper(*velocity, buffer, elements, mesh);
			unpackNodalDataHelper(*acceleration, buffer, elements, mesh);
			unpackNodalDataHelper(*internal_force, buffer, elements, mesh);
			unpackNodalDataHelper(*external_force, buffer, elements, mesh);
			break;
			}
			case _gst_smm_boundary: {
			unpackNodalDataHelper(*external_force, buffer, elements, mesh);
			unpackNodalDataHelper(*velocity, buffer, elements, mesh);
			unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
			break;
			}
			default: {}
			}

			if (tag != _gst_material_id) {
			splitByMaterial(elements, [&](auto && mat, auto && elements) {
			mat.unpackData(buffer, elements, tag);
			});
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			UInt SolidMechanicsModel::getNbData(const Array<UInt> & dofs,
			const SynchronizationTag & tag) const {
			AKANTU_DEBUG_IN();

			UInt size = 0;
			// UInt nb_nodes = mesh.getNbNodes();

			switch (tag) {
			case _gst_smm_uv: {
			size += sizeof(Real) * Model::spatial_dimension * 2;
			break;
			}
			case _gst_smm_res: {
			size += sizeof(Real) * Model::spatial_dimension;
			break;
			}
			case _gst_smm_mass: {
			size += sizeof(Real) * Model::spatial_dimension;
			break;
			}
			case _gst_for_dump: {
			size += sizeof(Real) * Model::spatial_dimension * 5;
			break;
			}
			default: {
			AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
			}
			}

			AKANTU_DEBUG_OUT();
			return size * dofs.size();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
			const Array<UInt> & dofs,
			const SynchronizationTag & tag) const {
			AKANTU_DEBUG_IN();

			switch (tag) {
			case _gst_smm_uv: {
			packDOFDataHelper(*displacement, buffer, dofs);
			packDOFDataHelper(*velocity, buffer, dofs);
			break;
			}
			case _gst_smm_res: {
			packDOFDataHelper(*internal_force, buffer, dofs);
			break;
			}
			case _gst_smm_mass: {
			packDOFDataHelper(*mass, buffer, dofs);
			break;
			}
			case _gst_for_dump: {
			packDOFDataHelper(*displacement, buffer, dofs);
			packDOFDataHelper(*velocity, buffer, dofs);
			packDOFDataHelper(*acceleration, buffer, dofs);
			packDOFDataHelper(*internal_force, buffer, dofs);
			packDOFDataHelper(*external_force, buffer, dofs);
			break;
			}
			default: {
			AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
			const Array<UInt> & dofs,
			const SynchronizationTag & tag) {
			AKANTU_DEBUG_IN();

			switch (tag) {
			case _gst_smm_uv: {
			unpackDOFDataHelper(*displacement, buffer, dofs);
			unpackDOFDataHelper(*velocity, buffer, dofs);
			break;
			}
			case _gst_smm_res: {
			unpackDOFDataHelper(*internal_force, buffer, dofs);
			break;
			}
			case _gst_smm_mass: {
			unpackDOFDataHelper(*mass, buffer, dofs);
			break;
			}
			case _gst_for_dump: {
			unpackDOFDataHelper(*displacement, buffer, dofs);
			unpackDOFDataHelper(*velocity, buffer, dofs);
			unpackDOFDataHelper(*acceleration, buffer, dofs);
			unpackDOFDataHelper(*internal_force, buffer, dofs);
			unpackDOFDataHelper(*external_force, buffer, dofs);
			break;
			}
			default: {
			AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
			}
			}

			AKANTU_DEBUG_OUT();
			}

			} // namespace akantu

rAKA/src/model/solid_mechanics/solid_mechanics_model.ccd1ebb2778129features/30-implementin…

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rAKA/src/model/solid_mechanics/solid_mechanics_model.cc
d1ebb2778129features/30-implementin…

solid_mechanics_model.cc
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