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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 "element_synchronizer.hh"
			#include "sparse_matrix.hh"
			#include "static_communicator.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, 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), mass_matrix(nullptr),
			velocity_damping_matrix(nullptr), stiffness_matrix(nullptr),
			jacobian_matrix(nullptr), material_index("material index", id, memory_id),
			material_local_numbering("material local numbering", id, memory_id),
			material_selector(new DefaultMaterialSelector(material_index)),
			is_default_material_selector(true), increment_flag(false),
			are_materials_instantiated(false) { //, pbc_synch(nullptr) {
			AKANTU_DEBUG_IN();

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

			this->mesh.registerEventHandler(*this, _ehp_solid_mechanics_model);

			#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

			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();

			if (is_default_material_selector) {
			delete material_selector;
			material_selector = nullptr;
			}

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

			// delete pbc_synch;

			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::initFull(const ModelOptions & options) {
			Model::initFull(options);

			const SolidMechanicsModelOptions & smm_options =
			dynamic_cast<const SolidMechanicsModelOptions &>(options);

			this->method = smm_options.analysis_method;

			// initialize the vectors
			this->initArrays();

			if (!this->hasDefaultSolver())
			this->initNewSolver(this->method);

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

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

			//if (!smm_options.no_init_materials) {
			this->initMaterials();
			//}

			// if (increment_flag)
			this->initBC(this, displacement, displacement_increment, external_force);
			// else
			// this->initBC(this, displacement, *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;
			}
			}

			return options;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initNewSolver(const AnalysisMethod & method) {
			ID solver_name;
			TimeStepSolverType tss_type;

			this->method = method;

			switch (this->method) {
			case _explicit_lumped_mass: {
			solver_name = "explicit_lumped";
			tss_type = _tsst_dynamic_lumped;
			break;
			}
			case _explicit_consistent_mass: {
			solver_name = "explicit";
			tss_type = _tsst_dynamic;
			break;
			}
			case _static: {
			solver_name = "static";
			tss_type = _tsst_static;
			break;
			}
			case _implicit_dynamic: {
			solver_name = "implicit";
			tss_type = _tsst_dynamic;
			break;
			}
			}

			if (!this->hasSolver(solver_name)) {
			ModelSolverOptions options = this->getDefaultSolverOptions(tss_type);
			this->getNewSolver(solver_name, tss_type, options.non_linear_solver_type);
			this->setIntegrationScheme(solver_name, "displacement",
			options.integration_scheme_type["displacement"],
			options.solution_type["displacement"]);
			this->setDefaultSolver(solver_name);
			}
			}

			/* -------------------------------------------------------------------------- */
			template <typename T>
			void SolidMechanicsModel::allocNodalField(Array<T> *& array, const ID & name) {
			if (array == nullptr) {
			UInt nb_nodes = mesh.getNbNodes();
			std::stringstream sstr_disp;
			sstr_disp << id << ":" << name;

			array =
			&(alloc<T>(sstr_disp.str(), nb_nodes, Model::spatial_dimension, T()));
			}
			}

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

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

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

			if (time_step_solver_type == _tsst_dynamic \|\|
			time_step_solver_type == _tsst_static) {
			if (!dof_manager.hasMatrix("K")) {
			dof_manager.getNewMatrix("K", _symmetric);
			}

			if (!dof_manager.hasMatrix("J")) {
			dof_manager.getNewMatrix("J", "K");
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			// void SolidMechanicsModel::initParallel(MeshPartition & partition,
			// DataAccessor<Element> * data_accessor)
			// {
			// AKANTU_DEBUG_IN();

			// if (data_accessor == nullptr)
			// data_accessor = this;
			// synch_parallel = &createParallelSynch(partition, *data_accessor);

			// synch_registry->registerSynchronizer(*synch_parallel, _gst_material_id);
			// synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_mass);
			// synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_stress);
			// synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_boundary);
			// synch_registry->registerSynchronizer(*synch_parallel, _gst_for_dump);

			// AKANTU_DEBUG_OUT();
			// }

			/* -------------------------------------------------------------------------- */
			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);
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Allocate all the needed vectors. By default their are not necessarily set to
			* 0
			*/
			void SolidMechanicsModel::initArrays() {
			AKANTU_DEBUG_IN();

			for (auto ghost_type : ghost_types) {
			for (auto type : mesh.elementTypes(Model::spatial_dimension, ghost_type,
			_ek_not_defined)) {
			UInt nb_element = mesh.getNbElement(type, ghost_type);
			this->material_index.alloc(nb_element, 1, type, ghost_type);
			this->material_local_numbering.alloc(nb_element, 1, type, ghost_type);
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/**
			* 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::initPBC() {
			// Model::initPBC();
			// registerPBCSynchronizer();

			// // as long as there are ones on the diagonal of the matrix, we can put
			// // boudandary true for slaves
			// std::map<UInt, UInt>::iterator it = pbc_pair.begin();
			// std::map<UInt, UInt>::iterator end = pbc_pair.end();
			// UInt dim = mesh.getSpatialDimension();
			// while (it != end) {
			// for (UInt i = 0; i < dim; ++i)
			// (blocked_dofs)((it).first, i) = true;
			// ++it;
			// }
			// }

			// /* --------------------------------------------------------------------------
			// */
			// void SolidMechanicsModel::registerPBCSynchronizer() {
			// pbc_synch = new PBCSynchronizer(pbc_pair);
			// synch_registry->registerSynchronizer(*pbc_synch, _gst_smm_uv);
			// synch_registry->registerSynchronizer(*pbc_synch, _gst_smm_mass);
			// synch_registry->registerSynchronizer(*pbc_synch, _gst_smm_res);
			// synch_registry->registerSynchronizer(*pbc_synch, _gst_for_dump);
			// // changeLocalEquationNumberForPBC(pbc_pair, mesh.getSpatialDimension());
			// }

			/* -------------------------------------------------------------------------- */
			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();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::assembleJacobian() {
			this->assembleStiffnessMatrix();
			}

			/* -------------------------------------------------------------------------- */
			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);
			}

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

			// 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::initializeUpdateResidualData() {
			// AKANTU_DEBUG_IN();
			// UInt nb_nodes = mesh.getNbNodes();
			// internal_force->resize(nb_nodes);

			// /// copy the forces in residual for boundary conditions
			// this->getDOFManager().assembleToResidual("displacement",
			// *this->external_force);

			// // start synchronization
			// this->asynchronousSynchronize(_gst_smm_uv);
			// this->waitEndSynchronize(_gst_smm_uv);

			// this->updateCurrentPosition();

			// AKANTU_DEBUG_OUT();
			// }

			/* -------------------------------------------------------------------------- */
			/* Explicit scheme */
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			// void SolidMechanicsModel::computeStresses() {
			// if (isExplicit()) {
			// // start synchronization
			// this->asynchronousSynchronize(_gst_smm_uv);
			// this->waitEndSynchronize(_gst_smm_uv);

			// // compute stresses on all local elements for each materials
			// std::vector<Material *>::iterator mat_it;
			// for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			// Material & mat = **mat_it;
			// mat.computeAllStresses(_not_ghost);
			// }

			// #ifdef AKANTU_DAMAGE_NON_LOCAL
			// /* Computation of the non local part */
			// this->non_local_manager->computeAllNonLocalStresses();
			// #endif
			// } else {
			// std::vector<Material *>::iterator mat_it;
			// for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			// Material & mat = **mat_it;
			// mat.computeAllStressesFromTangentModuli(_not_ghost);
			// }
			// }
			// }

			/* -------------------------------------------------------------------------- */
			/* Implicit scheme */
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			// /**
			// * Initialize the solver and create the sparse matrices needed.
			// *
			// */
			// void SolidMechanicsModel::initSolver(__attribute__((unused))
			// SolverOptions & options) {
			// UInt nb_global_nodes = mesh.getNbGlobalNodes();

			// jacobian_matrix = &(this->getDOFManager().getNewMatrix("jacobian",
			// _symmetric));

			// // jacobian_matrix->buildProfile(mesh, *dof_synchronizer,
			// spatial_dimension);

			// if (!isExplicit()) {
			// delete stiffness_matrix;
			// std::stringstream sstr_sti;
			// sstr_sti << id << ":stiffness_matrix";

			// stiffness_matrix = &(this->getDOFManager().getNewMatrix("stiffness",
			// _symmetric));
			// }

			// if (solver) solver->initialize(options);
			// }

			// /* --------------------------------------------------------------------------
			// */
			// void SolidMechanicsModel::initJacobianMatrix() {
			// // @todo make it more flexible: this is an ugly patch to treat the case of
			// non
			// // fix profile of the K matrix
			// delete jacobian_matrix;

			// jacobian_matrix = &(this->getDOFManager().getNewMatrix("jacobian",
			// "stiffness"));

			// std::stringstream sstr_solv; sstr_solv << id << ":solver";
			// delete solver;
			// solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
			// if(solver)
			// solver->initialize(_solver_no_options);
			// }

			/* -------------------------------------------------------------------------- */
			/**
			* Initialize the implicit solver, either for dynamic or static cases,
			*
			* @param dynamic
			*/
			// void SolidMechanicsModel::initImplicit(bool dynamic) {
			// AKANTU_DEBUG_IN();

			// method = dynamic ? _implicit_dynamic : _static;

			// if (!increment)
			// setIncrementFlagOn();

			// initSolver();

			// // if(method == _implicit_dynamic) {
			// // if(integrator) delete integrator;
			// // integrator = new TrapezoidalRule2();
			// // }

			// AKANTU_DEBUG_OUT();
			// }

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

			/* -------------------------------------------------------------------------- */
			// SparseMatrix & SolidMechanicsModel::initVelocityDampingMatrix() {
			// return this->getDOFManager().getNewMatrix("velocity_damping", "jacobian");
			// }

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

			// if(previous_displacement) previous_displacement->copy(*displacement);

			// if(method == _implicit_dynamic)
			// integrator->integrationSchemePred(time_step,
			// *displacement,
			// *velocity,
			// *acceleration,
			// *blocked_dofs);

			// AKANTU_DEBUG_OUT();
			// }

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

			// if(method == _implicit_dynamic) {
			// integrator->integrationSchemeCorrDispl(time_step,
			// *displacement,
			// *velocity,
			// *acceleration,
			// *blocked_dofs,
			// *increment);
			// } else {
			// UInt nb_nodes = displacement->getSize();
			// UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;

			// Real * incr_val = increment->storage();
			// Real * disp_val = displacement->storage();
			// bool * boun_val = blocked_dofs->storage();

			// for (UInt j = 0; j < nb_degree_of_freedom; ++j, ++disp_val, ++incr_val,
			// ++boun_val){
			// incr_val = (1. - *boun_val);
			// disp_val += incr_val;
			// }
			// }

			// AKANTU_DEBUG_OUT();
			// }

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

			// auto incr_it = this->displacement_increment->begin(spatial_dimension);
			// auto incr_end = this->displacement_increment->end(spatial_dimension);
			// auto disp_it = this->displacement->begin(spatial_dimension);
			// auto prev_disp_it = this->previous_displacement->begin(spatial_dimension);

			// for (; incr_it != incr_end; ++incr_it) {
			// incr_it = disp_it;
			// incr_it -= prev_disp_it;
			// }

			// AKANTU_DEBUG_OUT();
			// }

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

			// AKANTU_DEBUG_ASSERT(
			// previous_displacement,
			// "The previous displacement has to be initialized."
			// << " Are you working with Finite or Ineslactic deformations?");

			// previous_displacement->copy(*displacement);

			// AKANTU_DEBUG_OUT();
			// }

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

			/* -------------------------------------------------------------------------- */
			// void SolidMechanicsModel::synchronizeBoundaries() {
			// AKANTU_DEBUG_IN();
			// this->synchronize(_gst_smm_boundary);
			// AKANTU_DEBUG_OUT();
			// }

			// /* --------------------------------------------------------------------------
			// */ void SolidMechanicsModel::synchronizeResidual() {
			// AKANTU_DEBUG_IN();
			// this->synchronize(_gst_smm_res);
			// AKANTU_DEBUG_OUT();
			// }

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

			// if (!displacement_increment) {
			// this->allocNodalField(displacement_increment, spatial_dimension,
			// "displacement_increment");

			// this->getDOFManager().registerDOFsIncrement("displacement",
			// *this->displacement_increment);
			// }

			// increment_flag = true;

			// AKANTU_DEBUG_OUT();
			// }

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

			Real min_dt = getStableTimeStep(_not_ghost);

			/// reduction min over all processors
			StaticCommunicator::getStaticCommunicator().allReduce(min_dt, _so_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;
			elem.kind = _ek_regular;

			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.");
			}

			StaticCommunicator::getStaticCommunicator().allReduce(ekin, _so_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 incr_or_velo_it = this->velocity->begin(Model::spatial_dimension);
			if (this->method == _static) {
			incr_or_velo_it =
			this->displacement_increment->begin(Model::spatial_dimension);
			}

			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);

			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);
			}
			}
			}

			StaticCommunicator::getStaticCommunicator().allReduce(work, _so_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
			StaticCommunicator::getStaticCommunicator().allReduce(energy, _so_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();

			for (auto ghost_type : ghost_types) {
			for (auto type : mesh.elementTypes(Model::spatial_dimension, ghost_type,
			_ek_not_defined)) {
			UInt nb_element = this->mesh.getNbElement(type, ghost_type);

			if (!material_index.exists(type, ghost_type)) {
			this->material_index.alloc(nb_element, 1, type, ghost_type);
			this->material_local_numbering.alloc(nb_element, 1, type, ghost_type);
			} else {
			this->material_index(type, ghost_type).resize(nb_element);
			this->material_local_numbering(type, ghost_type).resize(nb_element);
			}
			}
			}

			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(
			__attribute__((unused)) const Array<Element> & element_list,
			const ElementTypeMapArray<UInt> & new_numbering,
			const RemovedElementsEvent & event) {
			this->getFEEngine().initShapeFunctions(_not_ghost);
			this->getFEEngine().initShapeFunctions(_ghost);

			for (auto & material : materials) {
			material->onElementsRemoved(element_list, new_numbering, event);
			}
			}

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

			if (displacement)
			displacement->resize(nb_nodes, 0.);
			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);
			}

			if(this->getDOFManager().hasMatrix("M")) {
			this->assembleMass(nodes_list);
			}

			if(this->getDOFManager().hasLumpedMatrix("M")) {
			this->assembleMassLumped(nodes_list);
			}


			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::onNodesRemoved(__attribute__((unused))
			const Array<UInt> & element_list,
			const Array<UInt> & new_numbering,
			__attribute__((unused))
			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);

			// if (method != _explicit_lumped_mass) {
			// this->initSolver();
			// }
			}

			/* -------------------------------------------------------------------------- */
			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);
			mass->printself(stream, indent + 2);
			velocity->printself(stream, indent + 2);
			acceleration->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::insertIntegrationPointsInNeighborhoods(
			const GhostType & ghost_type) {
			for (auto & mat : materials) {
			try {
			ElementTypeMapArray<Real> quadrature_points_coordinates(
			"quadrature_points_coordinates_tmp_nl", this->id, this->memory_id);
			quadrature_points_coordinates.initialize(
			this->getFEEngine(), _spatial_dimension = Model::spatial_dimension,
			_nb_component = Model::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);
			}

			auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
			mat_non_local.insertIntegrationPointsInNeighborhoods(
			ghost_type, quadrature_points_coordinates);
			} catch (std::bad_cast &) {
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::computeNonLocalStresses(
			const GhostType & ghost_type) {
			for (auto & mat : materials) {
			try {
			auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
			mat_non_local.computeNonLocalStresses(ghost_type);
			} catch (std::bad_cast &) {
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			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) {
			try {
			auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
			mat_non_local.updateNonLocalInternals(internal_flat, field_name,
			ghost_type, kind);
			} catch (std::bad_cast &) {
			}
			}
			}

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

			} // namespace akantu

rAKA/src/model/solid_mechanics/solid_mechanics_model.ccd5ad37a502b4bugfixes/64-building…

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rAKA/src/model/solid_mechanics/solid_mechanics_model.cc
d5ad37a502b4bugfixes/64-building…

solid_mechanics_model.cc
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