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phase_field_model.cc
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			/**
			* @file phase_field_model.cc
			*
			* @author Mohit Pundir <mohit.pundir@epfl.ch>
			*
			* @date creation: Wed Aug 01 2018
			* @date last modification: Wed Aug 01 2018
			*
			* @brief Implementation of PhaseFieldModel class
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2018 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 "phase_field_model.hh"
			#include "dumpable_inline_impl.hh"
			#include "element_synchronizer.hh"
			#include "fe_engine_template.hh"
			#include "generalized_trapezoidal.hh"
			#include "group_manager_inline_impl.cc"
			#include "integrator_gauss.hh"
			#include "mesh.hh"
			#include "parser.hh"
			#include "shape_lagrange.hh"

			#ifdef AKANTU_USE_IOHELPER
			#include "dumper_element_partition.hh"
			#include "dumper_elemental_field.hh"
			#include "dumper_internal_material_field.hh"
			#include "dumper_iohelper_paraview.hh"
			#endif

			/* -------------------------------------------------------------------------- */
			namespace akantu {


			/* -------------------------------------------------------------------------- */
			PhaseFieldModel::PhaseFieldModel(Mesh & mesh, UInt dim, const ID & id,
			const MemoryID & memory_id,
			const ModelType model_type)
			: Model(mesh, model_type, dim, id, memory_id),
			phasefield_index("phasefield index", id, memory_id),
			phasefield_local_numbering("phasefield local numbering", id, memory_id),
			BoundaryCondition<PhaseFieldModel>(),
			damage_on_qpoints("damage_on_qpoints", id),
			damage_energy_on_qpoints("damage_energy_on_qpoints", id),
			damage_energy_density_on_qpoints("damage_energy_density_on_qpoints", id),
			damage_gradient("damage_gradient", id),
			strain_on_qpoints("strain_on_qpoints", id),
			driving_force_on_qpoints("driving_force_on_qpoints", id),
			phi_history_on_qpoints("phi_history_on_qpoints", id) {

			AKANTU_DEBUG_IN();

			this->registerFEEngineObject<FEEngineType>("PhaseFieldFEEngine", mesh,
			Model::spatial_dimension);

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

			phasefield_selector = std::make_shared<DefaultPhaseFieldSelector>(phasefield_index);

			this->initDOFManager();

			this->registerDataAccessor(*this);

			if (this->mesh.isDistributed()) {
			auto & synchronizer = this->mesh.getElementSynchronizer();
			this->registerSynchronizer(synchronizer, SynchronizationTag::_pfm_damage);
			this->registerSynchronizer(synchronizer, SynchronizationTag::_pfm_driving);
			this->registerSynchronizer(synchronizer, SynchronizationTag::_pfm_history);
			this->registerSynchronizer(synchronizer, SynchronizationTag::_pfm_energy);
			}

			AKANTU_DEBUG_OUT();
			}

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

			/* -------------------------------------------------------------------------- */
			MatrixType PhaseFieldModel::getMatrixType(const ID & matrix_id) {
			if (matrix_id == "K" or matrix_id == "M") {
			return _symmetric;
			}
			return _mt_not_defined;
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::initModel() {
			auto & fem = this->getFEEngine();
			fem.initShapeFunctions(_not_ghost);
			fem.initShapeFunctions(_ghost);

			damage_on_qpoints.initialize(fem, _nb_component = 1);
			damage_energy_on_qpoints.initialize(fem, _nb_component = spatial_dimension *
			spatial_dimension);
			damage_energy_density_on_qpoints.initialize(fem, _nb_component = 1);
			damage_gradient.initialize(fem, _nb_component = spatial_dimension);
			strain_on_qpoints.initialize(fem, _nb_component =
			spatial_dimension * spatial_dimension);
			driving_force_on_qpoints.initialize(fem, _nb_component = 1);
			phi_history_on_qpoints.initialize(fem, _nb_component = 1);
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::initFullImpl(const ModelOptions & options) {
			phasefield_index.initialize(mesh, _element_kind = _ek_not_defined,
			_default_value = UInt(-1), _with_nb_element = true);
			phasefield_local_numbering.initialize(mesh, _element_kind = _ek_not_defined,
			_with_nb_element = true);

			Model::initFullImpl(options);

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

			this->initPhaseFields();

			this->initBC(this, damage, *external_force);
			}


			/* -------------------------------------------------------------------------- */
			PhaseField &
			PhaseFieldModel::registerNewPhaseField(const ParserSection & section) {
			std::string phase_name;
			std::string phase_type = section.getName();
			std::string opt_param = section.getOption();

			try {
			std::string tmp = section.getParameter("name");
			phase_name = tmp; /** this can seam weird, but there is an ambiguous operator
			* overload that i couldn't solve. @todo remove the
			* weirdness of this code
			*/
			} catch (debug::Exception &) {
			AKANTU_ERROR("A phasefield of type \'"
			<< phase_type
			<< "\' in the input file has been defined without a name!");
			}
			PhaseField & phase = this->registerNewPhaseField(phase_name, phase_type, opt_param);

			phase.parseSection(section);

			return phase;
			}

			/* -------------------------------------------------------------------------- */
			PhaseField & PhaseFieldModel::registerNewPhaseField(const ID & phase_name,
			const ID & phase_type,
			const ID & opt_param) {
			AKANTU_DEBUG_ASSERT(phasefields_names_to_id.find(phase_name) ==
			phasefields_names_to_id.end(),
			"A phasefield with this name '"
			<< phase_name << "' has already been registered. "
			<< "Please use unique names for phasefields");

			UInt phase_count = phasefields.size();
			phasefields_names_to_id[phase_name] = phase_count;

			std::stringstream sstr_phase;
			sstr_phase << this->id << ":" << phase_count << ":" << phase_type;
			ID mat_id = sstr_phase.str();

			std::unique_ptr<PhaseField> phase = PhaseFieldFactory::getInstance().allocate(
			phase_type, spatial_dimension, opt_param, *this, mat_id);

			phasefields.push_back(std::move(phase));

			return *(phasefields.back());
			}


			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::instantiatePhaseFields() {

			ParserSection model_section;
			bool is_empty;
			std::tie(model_section, is_empty) = this->getParserSection();

			if (not is_empty) {
			auto model_phasefields = model_section.getSubSections(ParserType::_phasefield);
			for (const auto & section : model_phasefields) {
			this->registerNewPhaseField(section);
			}
			}

			auto sub_sections = this->parser.getSubSections(ParserType::_phasefield);
			for (const auto & section : sub_sections) {
			this->registerNewPhaseField(section);
			}

			if (phasefields.empty())
			AKANTU_EXCEPTION("No phasefields where instantiated for the model"
			<< getID());
			are_phasefields_instantiated = true;
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::initPhaseFields() {
			AKANTU_DEBUG_ASSERT(phasefields.size() != 0, "No phasefield to initialize !");

			if (!are_phasefields_instantiated)
			instantiatePhaseFields();

			this->assignPhaseFieldToElements();

			for (auto & phasefield : phasefields) {
			/// init internals properties
			phasefield->initPhaseField();
			}

			this->synchronize(SynchronizationTag::_smm_init_mat);
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::assignPhaseFieldToElements(
			const ElementTypeMapArray<UInt> * filter) {

			for_each_element(
			mesh,
			[&](auto && element) {
			UInt phase_index = (*phasefield_selector)(element);
			AKANTU_DEBUG_ASSERT(
			phase_index < phasefields.size(),
			"The phasefield selector returned an index that does not exists");
			phasefield_index(element) = phase_index;
			},
			_element_filter = filter, _ghost_type = _not_ghost);

			for_each_element(mesh,
			[&](auto && element) {
			auto phase_index = phasefield_index(element);
			auto index = phasefields[phase_index]->addElement(element);
			phasefield_local_numbering(element) = index;
			},
			_element_filter = filter, _ghost_type = _not_ghost);

			// synchronize the element phasefield arrays
			this->synchronize(SynchronizationTag::_material_id);
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::assembleMatrix(const ID & matrix_id) {

			if (matrix_id == "K") {
			this->assembleStiffnessMatrix();
			} else {
			AKANTU_ERROR("Unknown Matrix ID for PhaseFieldModel : " << matrix_id);
			}
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::predictor() {
			// AKANTU_TO_IMPLEMENT();
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::corrector() {
			// AKANTU_TO_IMPLEMENT();
			}

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

			this->allocNodalField(this->damage, 1, "damage");
			this->allocNodalField(this->external_force, 1, "external_force");
			this->allocNodalField(this->internal_force, 1, "internal_force");
			this->allocNodalField(this->blocked_dofs, 1, "blocked_dofs");
			this->allocNodalField(this->previous_damage, 1, "previous_damage");
			this->allocNodalField(this->damage_increment, 1, "damage_increment");

			if (!dof_manager.hasDOFs("damage")) {
			dof_manager.registerDOFs("damage", *this->damage, _dst_nodal);
			dof_manager.registerBlockedDOFs("damage", *this->blocked_dofs);
			dof_manager.registerDOFsIncrement("damage", *this->damage_increment);
			dof_manager.registerDOFsPrevious("damage", *this->previous_damage);
			}

			if (time_step_solver_type == TimeStepSolverType::_dynamic) {
			AKANTU_TO_IMPLEMENT();
			}
			}

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

			/* -------------------------------------------------------------------------- */
			std::tuple<ID, TimeStepSolverType>
			PhaseFieldModel::getDefaultSolverID(const AnalysisMethod & method) {
			switch (method) {
			case _explicit_lumped_mass: {
			return std::make_tuple("explicit_lumped",
			TimeStepSolverType::_dynamic_lumped);
			}
			case _static: {
			return std::make_tuple("static", TimeStepSolverType::_static);
			}
			case _implicit_dynamic: {
			return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
			}
			default:
			return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
			}
			}

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

			switch (type) {
			case TimeStepSolverType::_static: {
			options.non_linear_solver_type = NonLinearSolverType::_linear;
			options.integration_scheme_type["damage"] =
			IntegrationSchemeType::_pseudo_time;
			options.solution_type["damage"] = IntegrationScheme::_not_defined;
			break;
			}
			case TimeStepSolverType::_dynamic: {
			options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
			options.integration_scheme_type["damage"] =
			IntegrationSchemeType::_backward_euler;
			options.solution_type["damage"] = IntegrationScheme::_damage;
			break;
			}
			default:
			AKANTU_EXCEPTION(type << " is not a valid time step solver type");
			}

			return options;
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::beforeSolveStep() {

			for (auto & phasefield : phasefields) {
			phasefield->beforeSolveStep();
			}

			// compute the history of local elements
			//AKANTU_DEBUG_INFO("Compute phi history");
			//this->computePhiHistoryOnQuadPoints(_not_ghost);

			// communicate the history
			//AKANTU_DEBUG_INFO("Send data for synchronization");
			//this->asynchronousSynchronize(SynchronizationTag::_pfm_history);

			// finalize communications
			//AKANTU_DEBUG_INFO("Wait distant history");
			//this->waitEndSynchronize(SynchronizationTag::_pfm_history);

			//this->computeDamageEnergyDensityOnQuadPoints(_not_ghost);

			// communicate the energy density
			//AKANTU_DEBUG_INFO("Send data for synchronization");
			//this->asynchronousSynchronize(SynchronizationTag::_pfm_energy);

			// finalize communications
			//AKANTU_DEBUG_INFO("Wait distant energy density");
			//this->waitEndSynchronize(SynchronizationTag::_pfm_energy);

			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::afterSolveStep(bool converged) {

			if (not converged)
			return ;

			for (auto && values : zip(damage, previous_damage)) {
			auto & dam = std::get<0>(values);
			auto & prev_dam = std::get<1>(values);

			dam -= prev_dam;
			dam = std::min(1., 2 * dam - dam * dam);
			prev_dam = dam;
			}
			}

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

			AKANTU_DEBUG_INFO("Assemble the new stiffness matrix");

			if (!this->getDOFManager().hasMatrix("K")) {
			this->getDOFManager().getNewMatrix("K", getMatrixType("K"));
			}

			this->getDOFManager().clearMatrix("K");

			for (auto & phasefield : phasefields) {
			phasefield->assembleStiffnessMatrix(_not_ghost);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/*void PhaseFieldModel::assembleDamageMatrix() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Assemble the new damage matrix");

			auto & fem = this->getFEEngine();

			for (auto && type : mesh.elementTypes(spatial_dimension)) {
			auto nb_element = mesh.getNbElement(type);
			auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			auto nb_quadrature_points = fem.getNbIntegrationPoints(type);

			auto nt_b_n = std::make_unique<Array<Real>>(
			nb_element * nb_quadrature_points,
			nb_nodes_per_element * nb_nodes_per_element, "N^tbN");

			auto & damage_energy_density_on_qpoints_vect =
			damage_energy_density_on_qpoints(type);

			// damage_energy_on_qpoints = gc/l0 + phi = scalar
			fem.computeNtbN(damage_energy_density_on_qpoints_vect, *nt_b_n, 2, type);

			/// compute @f$ K_{\grad d} = \int_e \mathbf{N}^t * \mathbf{w} *
			/// \mathbf{N}@f$
			auto K_n = std::make_unique<Array<Real>>(
			nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_n");

			fem.integrate(nt_b_n, K_n, nb_nodes_per_element * nb_nodes_per_element,
			type);

			this->getDOFManager().assembleElementalMatricesToMatrix(
			"K", "damage", *K_n, type, _not_ghost, _symmetric);
			}

			AKANTU_DEBUG_OUT();

			}*/

			/* -------------------------------------------------------------------------- */
			/*void PhaseFieldModel::assembleDamageMatrix() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Assemble the new damage matrix");

			auto & fem = this->getFEEngine();

			for (auto && type : mesh.elementTypes(spatial_dimension)) {
			auto nb_element = mesh.getNbElement(type);
			auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			auto nb_quadrature_points = fem.getNbIntegrationPoints(type);

			auto nt_b_n = std::make_unique<Array<Real>>(
			nb_element * nb_quadrature_points,
			nb_nodes_per_element * nb_nodes_per_element, "N^tbN");

			auto bt_d_b = std::make_unique<Array<Real>>(
			nb_element * nb_quadrature_points,
			nb_nodes_per_element * nb_nodes_per_element, "B^tDB");

			// damage_energy_on_qpoints = gc/l0 + phi = scalar
			auto & damage_energy_density_on_qpoints_vect =
			damage_energy_density_on_qpoints(type);

			// damage_energy_on_qpoints = gc*l0 = scalar
			auto & damage_energy_on_qpoints_vect =
			damage_energy_on_qpoints(type);

			fem.computeBtDB(damage_energy_on_qpoints_vect, *bt_d_b, 2, type);

			fem.computeNtbN(damage_energy_density_on_qpoints_vect, *nt_b_n, 2, type);

			/// compute @f$ K_{\grad d} = \int_e \mathbf{N}^t * \mathbf{w} *
			/// \mathbf{N}@f$
			auto K_n = std::make_unique<Array<Real>>(
			nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_n");

			fem.integrate(nt_b_n, K_n, nb_nodes_per_element * nb_nodes_per_element,
			type);

			this->getDOFManager().assembleElementalMatricesToMatrix(
			"K", "damage", *K_n, type, _not_ghost, _symmetric);

			/// compute @f$ K_{\grad d} = \int_e \mathbf{B}^t * \mathbf{W} *
			/// \mathbf{B}@f$
			auto K_b = std::make_unique<Array<Real>>(
			nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_b");

			fem.integrate(bt_d_b, K_b, nb_nodes_per_element * nb_nodes_per_element,
			type);

			this->getDOFManager().assembleElementalMatricesToMatrix(
			"K", "damage", *K_b, type, _not_ghost, _symmetric);
			}

			AKANTU_DEBUG_OUT();
			}*/

			/* -------------------------------------------------------------------------- */
			/*void PhaseFieldModel::assembleDamageGradMatrix() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Assemble the new damage gradient matrix");

			auto & fem = this->getFEEngine();

			for (auto && type : mesh.elementTypes(spatial_dimension)) {
			auto nb_element = mesh.getNbElement(type);
			auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			auto nb_quadrature_points = fem.getNbIntegrationPoints(type);

			auto bt_d_b = std::make_unique<Array<Real>>(
			nb_element * nb_quadrature_points,
			nb_nodes_per_element * nb_nodes_per_element, "B^tDB");

			auto & damage_energy_on_qpoints_vect =
			damage_energy_on_qpoints(type);

			// damage_energy_on_qpoints = gc*l0 = scalar
			fem.computeBtDB(damage_energy_on_qpoints_vect, *bt_d_b, 2, type);

			/// compute @f$ K_{\grad d} = \int_e \mathbf{B}^t * \mathbf{W} *
			/// \mathbf{B}@f$
			auto K_b = std::make_unique<Array<Real>>(
			nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_b");

			fem.integrate(bt_d_b, K_b, nb_nodes_per_element * nb_nodes_per_element,
			type);

			this->getDOFManager().assembleElementalMatricesToMatrix(
			"K", "damage", *K_b, type, _not_ghost, _symmetric);
			}


			AKANTU_DEBUG_OUT();
			}*/

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::assembleResidual() {

			AKANTU_DEBUG_IN();

			this->assembleInternalForces();

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

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::assembleInternalForces() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Assemble the internal forces");

			this->internal_force->clear();

			// compute the driving forces of local elements
			AKANTU_DEBUG_INFO("Compute local driving forces");
			for (auto & phasefield : phasefields) {
			phasefield->computeAllDrivingForces(_not_ghost);
			}

			// communicate the driving forces
			AKANTU_DEBUG_INFO("Send data for residual assembly");
			this->asynchronousSynchronize(SynchronizationTag::_pfm_driving);

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

			// finalize communications
			AKANTU_DEBUG_INFO("Wait distant driving forces");
			this->waitEndSynchronize(SynchronizationTag::_pfm_driving);

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

			AKANTU_DEBUG_OUT();
			}


			/* -------------------------------------------------------------------------- */
			/*void PhaseFieldModel::assembleInternalForces(const GhostType & ghost_type) {
			AKANTU_DEBUG_IN();

			this->synchronize(SynchronizationTag::_pfm_damage);
			auto & fem = this->getFEEngine();

			for (auto type : mesh.elementTypes(spatial_dimension, ghost_type)) {
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			auto & driving_force_on_qpoints_vect =
			driving_force_on_qpoints(type, ghost_type);

			UInt nb_quad_points = driving_force_on_qpoints_vect.size();
			Array<Real> nt_driving_force(nb_quad_points, nb_nodes_per_element);
			fem.computeNtb(driving_force_on_qpoints_vect, nt_driving_force, type,
			ghost_type);

			UInt nb_elements = mesh.getNbElement(type, ghost_type);
			Array<Real> int_nt_driving_force(nb_elements, nb_nodes_per_element);

			fem.integrate(nt_driving_force, int_nt_driving_force,
			nb_nodes_per_element, type, ghost_type);

			this->getDOFManager().assembleElementalArrayLocalArray(
			int_nt_driving_force, *this->internal_force, type, ghost_type, 1);
			}
			AKANTU_DEBUG_OUT();
			}*/



			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::assembleLumpedMatrix(const ID & /matrix_id/) {}

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

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

			/* -------------------------------------------------------------------------- */
			/*void PhaseFieldModel::computeDrivingForce(const GhostType & ghost_type) {

			for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {

			for (auto && values :
			zip(make_view(phi_history_on_qpoints(type, ghost_type)),
			make_view(driving_force_on_qpoints(type, ghost_type)))) {
			auto & phi_history = std::get<0>(values);
			auto & driving_force = std::get<1>(values);

			driving_force = 2.0 * phi_history;
			}
			}

			AKANTU_DEBUG_OUT();
			}*/


			/* -------------------------------------------------------------------------- */
			/*void PhaseFieldModel::computeDamageEnergyDensityOnQuadPoints(
			const GhostType & ghost_type) {

			AKANTU_DEBUG_IN();

			for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {
			for (auto && values :
			zip(make_view(damage_energy_density_on_qpoints(type, ghost_type)),
			make_view(phi_history_on_qpoints(type, ghost_type)))) {

			auto & dam_energy_density = std::get<0>(values);
			auto & phi_history = std::get<1>(values);
			dam_energy_density = g_c / l_0 + 2.0 * phi_history;
			}
			}

			AKANTU_DEBUG_OUT();
			}*/

			/* -------------------------------------------------------------------------- */
			/*void PhaseFieldModel::computePhiHistoryOnQuadPoints(
			const GhostType & ghost_type) {

			Matrix<Real> strain_plus(spatial_dimension, spatial_dimension);
			Matrix<Real> strain_minus(spatial_dimension, spatial_dimension);
			Matrix<Real> strain_dir(spatial_dimension, spatial_dimension);
			Matrix<Real> strain_diag_plus(spatial_dimension, spatial_dimension);
			Matrix<Real> strain_diag_minus(spatial_dimension, spatial_dimension);

			Vector<Real> strain_values(spatial_dimension);

			Real trace_plus, trace_minus, phi_plus;

			for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {

			for (auto && values :
			zip(make_view(strain_on_qpoints(type, ghost_type), spatial_dimension,
			spatial_dimension),
			make_view(phi_history_on_qpoints(type, ghost_type)))) {

			auto & strain = std::get<0>(values);
			auto & phi_history = std::get<1>(values);

			strain_plus.clear();
			strain_minus.clear();
			strain_dir.clear();
			strain_values.clear();
			strain_diag_plus.clear();
			strain_diag_minus.clear();

			strain.eig(strain_values, strain_dir);

			for (UInt i = 0; i < spatial_dimension; i++) {
			strain_diag_plus(i, i) = std::max(Real(0.), strain_values(i));
			strain_diag_minus(i, i) = std::min(Real(0.), strain_values(i));
			}

			Matrix<Real> mat_tmp(spatial_dimension, spatial_dimension);
			Matrix<Real> sigma_plus(spatial_dimension, spatial_dimension);
			Matrix<Real> sigma_minus(spatial_dimension, spatial_dimension);

			mat_tmp.mul<false, true>(strain_diag_plus, strain_dir);
			strain_plus.mul<false, false>(strain_dir, mat_tmp);
			mat_tmp.mul<false, true>(strain_diag_minus, strain_dir);
			strain_minus.mul<false, true>(strain_dir, mat_tmp);

			trace_plus = std::max(Real(0.), strain.trace());
			trace_minus = std::min(Real(0.), strain.trace());

			for (UInt i = 0; i < spatial_dimension; i++) {
			for (UInt j = 0; j < spatial_dimension; j++) {
			sigma_plus(i, j) =
			(i == j) * lambda * trace_plus + 2 * mu * strain_plus(i, j);
			sigma_minus(i, j) =
			(i == j) * lambda * trace_minus + 2 * mu * strain_minus(i, j);
			}
			}

			phi_plus = 1. / 2 * sigma_plus.doubleDot(strain);

			if (phi_plus > phi_history) {
			phi_history = phi_plus;
			}
			}
			}
			}*/

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::computeDamageOnQuadPoints(const GhostType & ghost_type) {

			AKANTU_DEBUG_IN();

			auto & fem = this->getFEEngine();

			for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {
			auto & damage_on_qpoints_vect = damage_on_qpoints(type, ghost_type);
			fem.interpolateOnIntegrationPoints(*damage, damage_on_qpoints_vect, 1, type,
			ghost_type);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			UInt PhaseFieldModel::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 SynchronizationTag::_pfm_damage: {
			size += nb_nodes_per_element * sizeof(Real); // damage
			break;
			}
			case SynchronizationTag::_pfm_driving: {
			size += getNbIntegrationPoints(elements) * sizeof(Real);
			break;
			}
			case SynchronizationTag::_pfm_history: {
			size += getNbIntegrationPoints(elements) * sizeof(Real);
			break;
			}
			case SynchronizationTag::_pfm_energy: {
			size += getNbIntegrationPoints(elements) * sizeof(Real);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}

			AKANTU_DEBUG_OUT();
			return size;
			}

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

			switch (tag) {
			case SynchronizationTag::_pfm_damage: {
			packNodalDataHelper(*damage, buffer, elements, mesh);
			break;
			}
			case SynchronizationTag::_pfm_driving: {
			packElementalDataHelper(driving_force_on_qpoints, buffer, elements, true, getFEEngine());
			break;
			}
			case SynchronizationTag::_pfm_history: {
			packElementalDataHelper(phi_history_on_qpoints, buffer, elements, true, getFEEngine());
			break;
			}
			case SynchronizationTag::_pfm_energy: {
			packElementalDataHelper(damage_energy_density_on_qpoints, buffer, elements, true, getFEEngine());
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}
			}

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

			switch (tag) {
			case SynchronizationTag::_pfm_damage: {
			unpackNodalDataHelper(*damage, buffer, elements, mesh);
			break;
			}
			case SynchronizationTag::_pfm_driving: {
			unpackElementalDataHelper(driving_force_on_qpoints, buffer, elements, true, getFEEngine());
			break;
			}
			case SynchronizationTag::_pfm_history: {
			unpackElementalDataHelper(phi_history_on_qpoints, buffer, elements, true, getFEEngine());
			break;
			}
			case SynchronizationTag::_pfm_energy: {
			unpackElementalDataHelper(damage_energy_density_on_qpoints, buffer, elements, true, getFEEngine());
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}
			}

			/* -------------------------------------------------------------------------- */
			UInt PhaseFieldModel::getNbData(const Array<UInt> & indexes,
			const SynchronizationTag & tag) const {

			AKANTU_DEBUG_IN();

			UInt size = 0;
			UInt nb_nodes = indexes.size();

			switch (tag) {
			case SynchronizationTag::_pfm_damage: {
			size += nb_nodes * sizeof(Real);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}

			AKANTU_DEBUG_OUT();
			return size;
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::packData(CommunicationBuffer & buffer,
			const Array<UInt> & indexes,
			const SynchronizationTag & tag) const {

			AKANTU_DEBUG_IN();

			for (auto index : indexes) {
			switch (tag) {
			case SynchronizationTag::_pfm_damage: {
			buffer << (*damage)(index);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::unpackData(CommunicationBuffer & buffer,
			const Array<UInt> & indexes,
			const SynchronizationTag & tag) {

			AKANTU_DEBUG_IN();

			for (auto index : indexes) {
			switch (tag) {
			case SynchronizationTag::_pfm_damage: {
			buffer >> (*damage)(index);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			#ifdef AKANTU_USE_IOHELPER

			std::shared_ptr<dumper::Field>
			PhaseFieldModel::createNodalFieldBool(const std::string & field_name,
			const std::string & group_name,
			bool /padding_flag/) {

			std::map<std::string, Array<bool> *> uint_nodal_fields;
			uint_nodal_fields["blocked_dofs"] = blocked_dofs;

			return mesh.createNodalField(uint_nodal_fields[field_name], group_name);

			std::shared_ptr<dumper::Field> field;
			return field;
			}

			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumper::Field>
			PhaseFieldModel::createNodalFieldReal(const std::string & field_name,
			const std::string & group_name,
			bool /padding_flag/) {

			if (field_name == "capacity_lumped") {
			AKANTU_EXCEPTION(
			"Capacity lumped is a nodal field now stored in the DOF manager."
			"Therefore it cannot be used by a dumper anymore");
			}

			std::map<std::string, Array<Real> *> real_nodal_fields;
			real_nodal_fields["damage"] = damage;
			real_nodal_fields["external_force"] = external_force;
			real_nodal_fields["internal_force"] = internal_force;

			return mesh.createNodalField(real_nodal_fields[field_name], group_name);

			std::shared_ptr<dumper::Field> field;
			return field;
			}

			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumper::Field> PhaseFieldModel::createElementalField(
			const std::string & field_name, const std::string & group_name,
			bool /padding_flag/, const UInt & /spatial_dimension/,
			const ElementKind & element_kind) {

			if (field_name == "partitions") {
			return mesh.createElementalField<UInt, dumper::ElementPartitionField>(
			mesh.getConnectivities(), group_name, this->spatial_dimension,
			element_kind);
			} else if (field_name == "damage_gradient") {
			ElementTypeMap<UInt> nb_data_per_elem =
			this->mesh.getNbDataPerElem(damage_gradient);

			return mesh.createElementalField<Real, dumper::InternalMaterialField>(
			damage_gradient, group_name, this->spatial_dimension, element_kind,
			nb_data_per_elem);
			} else if (field_name == "damage_energy") {
			ElementTypeMap<UInt> nb_data_per_elem =
			this->mesh.getNbDataPerElem(damage_energy_on_qpoints);

			return mesh.createElementalField<Real, dumper::InternalMaterialField>(
			damage_energy_on_qpoints, group_name, this->spatial_dimension,
			element_kind, nb_data_per_elem);
			}

			std::shared_ptr<dumper::Field> field;
			return field;
			}

			/* -------------------------------------------------------------------------- */
			#else
			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumper::Field> PhaseFieldModel::createElementalField(
			const std::string & /field_name/, const std::string & /group_name/,
			bool /padding_flag/, const ElementKind & /element_kind/) {
			return nullptr;
			}

			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumper::Field>
			PhaseFieldModel::createNodalFieldBool(const std::string & /field_name/,
			const std::string & /group_name/,
			bool /padding_flag/) {
			return nullptr;
			}

			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumper::Field>
			PhaseFieldModel::createNodalFieldReal(const std::string & /field_name/,
			const std::string & /group_name/,
			bool /padding_flag/) {
			return nullptr;
			}
			#endif

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::dump(const std::string & dumper_name) {
			mesh.dump(dumper_name);
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::dump(const std::string & dumper_name, UInt step) {
			mesh.dump(dumper_name, step);
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::dump(const std::string & dumper_name, Real time,
			UInt step) {
			mesh.dump(dumper_name, time, step);
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::dump() { mesh.dump(); }

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::dump(UInt step) { mesh.dump(step); }

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::dump(Real time, UInt step) { mesh.dump(time, step); }

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

			stream << space << "Phase Field 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;
			damage->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 << " + phasefield information [" << std::endl;
			stream << space << AKANTU_INDENT << "]" << std::endl;

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

			} // namespace akantu

rAKA/src/model/phase_field/phase_field_model.cc8070a024e3e5bugfixes/akantu-as…

phase_field_model.ccView Options

rAKA/src/model/phase_field/phase_field_model.cc
8070a024e3e5bugfixes/akantu-as…

phase_field_model.cc
View Options