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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 "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 {

			// material functor can be created




			/* -------------------------------------------------------------------------- */
			PhaseFieldModel::PhaseFieldModel(Mesh & mesh, UInt dim, const ID & id,
			const MemoryID & memory_id)
			: Model(mesh, ModelType::_phase_field_model, dim, id, memory_id),
			damage_gradient("damage_gradient", id),
			damage_on_qpoints("damage_on_qpoints", id),
			strain_history_on_qpoints("strain_history_on_qpoints", id),
			displacement_on_qpoints("displacement_on_qpoints", id){

			AKANTU_DEBUG_IN();

			this->initDOFManager();

			this->registerDataAccessor(*this);

			if (this->mesh.isDistributed()) {
			auto & synchronizer = this->mesh.getElementSynchronizer();
			this->registerSynchronizer(synchronizer, _gst_pfm_damage);
			this->registerSynchronizer(synchronizer, _gst_pfm_gradient_damage);
			}

			registerFEEngineObject<FEEngineType>(id + ":fem", mesh, spatial_dimension);

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

			this->registerParam("l0", l_0, 0., _pat_parsmod, "length scale");
			this->registerParam("gc", g_c, _pat_parsmod, "critical local fracture energy density");
			this->registerParam("lambda", lame_lambda, _pat_parsmod, "lame parameter lambda");
			this->registerParam("mu", lame_mu, _pat_parsmod, "lame paramter mu");

			AKANTU_DEBUG_OUT();
			}


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

			damage_on_qpoints.initialize(fem, _nb_component = 1);
			damage_gradient.initialize(fem, _nb_component = spatial_dimension);
			displacement_on_qpoints.initialize(fem, _nb_component = spatial_dimension);
			strain_history_on_qpoints.initialize(fem, _nb_component = 1);

			}

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

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::assembleMatrix(const ID & matrix_id) {
			if (matrix_id == "K") {
			this->assembleDamageMatrix();
			} else if (matrix_id == "M" and need_to_reassemble_capacity) {
			this->assembleDamageGradMatrix();
			}
			}


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

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

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

			/*if (time_step_solver_type == _tsst_dynamic \|\|
			time_step_solver_type == _tsst_dynamic_lumped) {
			this->allocNodalField(this->damage_rate, "damage_rate");

			if (!dof_manager.hasDOFsDerivatives("damage", 1)) {
			dof_manager.registerDOFsDerivative("damage", 1,
			*this->damage_rate);
			}
			}*/
			}



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

			AKANTU_DEBUG_INFO("Assemble the new damage matrix");

			this->computeStrainHistoryOnQuadPoints(_not_ghost);

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

			switch (mesh.getSpatialDimension()) {
			case 1:
			this->assembleDamageMatrix<1>(_not_ghost);
			break;
			case 2:
			this->assembleDamageMatrix<2>(_not_ghost);
			break;
			case 3:
			this->assembleDamageMatrix<3>(_not_ghost);
			break;
			}

			AKANTU_DEBUG_OUT();
			}

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

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

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

			switch (mesh.getSpatialDimension()) {
			case 1:
			this->assembleDamageGradMatrix<1>(_not_ghost);
			break;
			case 2:
			this->assembleDamageGradMatrix<2>(_not_ghost);
			break;
			case 3:
			this->assembleDamageGradMatrix<3>(_not_ghost);
			break;
			}

			AKANTU_DEBUG_OUT();
			}


			/* -------------------------------------------------------------------------- */
			std::tuple<ID, TimeStepSolverType>
			PhaseFieldModel::getDefaultSolverID(const AnalysisMethod & method) {
			switch (method) {
			case _explicit_lumped_mass: {
			return std::make_tuple("explicit_lumped", _tsst_dynamic_lumped);
			}
			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);
			}
			}

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

			switch (type) {
			case _tsst_dynamic_lumped: {
			options.non_linear_solver_type = _nls_lumped;
			options.integration_scheme_type["damage"] = _ist_forward_euler;
			options.solution_type["damage"] = IntegrationScheme::_temperature_rate;
			break;
			}
			case _tsst_static: {
			options.non_linear_solver_type = _nls_newton_raphson;
			options.integration_scheme_type["damage"] = _ist_pseudo_time;
			options.solution_type["damage"] = 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["damage"] = _ist_forward_euler;
			options.solution_type["damage"] =
			IntegrationScheme::_temperature_rate;
			} else {
			options.non_linear_solver_type = _nls_newton_raphson;
			options.integration_scheme_type["damage"] = _ist_backward_euler;
			options.solution_type["damage"] = IntegrationScheme::_damage;
			}
			break;
			}
			default:
			AKANTU_EXCEPTION(type << " is not a valid time step solver type");
			}

			return options;
			}


			/* -------------------------------------------------------------------------- */
			template<UInt dim>
			void PhaseFieldModel::assembleDamageMatrix(const GhostType & ghost_type) {

			AKANTU_DEBUG_IN();


			auto & fem = this->getFEEngine();

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

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

			// conductivity_on_qpoints = gc*l0 = scalar
			fem.computeNtDN(conductivity_on_qpoints(type, ghost_type), *nt_d_n, type,
			ghost_type);

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

			fem.integrate(nt_d_n, K_d, nb_nodes_per_element * nb_nodes_per_element,
			type, ghost_type);

			this->getDOFManager().assembleElementalMatricesToMatrix(
			"K", "phasefield", *K_d, type, ghost_type, _symmetric);
			}

			AKANTU_DEBUG_OUT();
			}


			/* -------------------------------------------------------------------------- */
			template<UInt dim>
			void PhaseFieldModel::assembleDamageGradMatrix(const GhostType & ghost_type) {

			AKANTU_DEBUG_IN();


			auto & fem = this->getFEEngine();

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

			// conductivity_on_qpoints = gc*l0 = scalar
			fem.computeBtDB(conductivity_on_qpoints(type, ghost_type), *bt_d_b, type,
			ghost_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, ghost_type);

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

			AKANTU_DEBUG_OUT();
			}


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

			for (auto & type : mesh.elementType(spatial_dimension, ghost_type)) {
			auto & displacement_interpolated = displacement_on_qpoints(type, ghost_type);

			// compute the strain on quadrature points
			this->getFEEngine().interpolateOnIntegrationPoints(
			*displacement, displacement_interpolated, , type, ghost_type);

			auto & strain_history = strain_history_on_qpoints(type, ghost_type);
			for (auto && tuple :
			zip(make_view(strain_history, spatial_dimension, spatial_dimension),
			displacement_interpolated)) {

			// compute strain on quad from displacement_interpolated
			// commpute matrix sigma_plus and sigma_minus using
			// lame_lambda and lame_mu

			// compute phi_plus
			// updated strain_history


			}
			}

			}

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

			this->internal_force->clear();

			this->synchronize(_gst_pfm_damage);
			auto & fem = this->getFFEngine();

			for (auto ghost_type: ghost_types) {

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

			auto & strain_history_on_qpoints_vect = strain_history_on_qpoints(type, ghost_type);

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

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

			fem.integrate(nt_strain_history, int_nt_srain_history, nb_nodes_per_element, type,
			ghost_type);

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

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::readMaterials() {
			auto sect = this->getParserSection();

			if (not std::get<1>(sect)) {
			const auto & section = std::get<0>(sect);
			this->parseSection(section);
			}

			gc_on_qpoints.set(g_c);
			}

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::initFullImpl(const ModelOptions & options) {
			Model::initFullImpl(options);

			readMaterials();
			}

			/* -------------------------------------------------------------------------- */
			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 _gst_material_id: {
			size += elements.size() * sizeof(UInt);
			break;
			}
			case _gst_pfm_damage: {
			size += nb_nodes_per_element * sizeof(Real); // damage
			break;
			}
			case _gst_pfm_gradient_damage: {
			size += getNbIntegrationPoints(elements) * spatial_dimension * sizeof(Real);
			size += nb_nodes_per_element * 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 _gst_pfm_damage: {
			packNodalDataHelper(*damage, buffer, elements, mesh);
			break;
			}
			case _gst_htm_gradient_damage: {
			packElementalDataHelper(damage_gradient, buffer, elements, true,
			getFEEngine());
			packNodalDataHelper(*damage, buffer, elements, mesh);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}
			}

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

			switch (tag) {
			case _gst_pfm_damage: {
			unpackNodalDataHelper(*damage, buffer, elements, mesh);
			break;
			}
			case _gst_pfm_gradient_damage: {
			unpackElementalDataHelper(damage_gradient, buffer, elements, true,
			getFEEngine());
			unpackNodalDataHelper(*damage, buffer, elements, mesh);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}

			}

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

			AKANTU_DEBUG_IN();

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

			switch (tag) {
			case _gst_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 _gst_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 Synchronization & tag) {

			AKANTU_DEBUG_IN();

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

			AKANTU_DEBUG_OUT();
			}

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

			dumper::Field * PhaseFieldModel::createNodalFieldBool(
			const std::string & field_name, const std::string & group_name,
			__attribute__((unused)) bool padding_flag ) {

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

			dumper::Field * field = nullptr;
			field = mesh.createNodalFieldBool(uint_nodal_fields[field_name], group_name);
			return field;
			}

			/* -------------------------------------------------------------------------- */
			dumper::Field * PhaseFieldModel::createNodalFieldReal(
			const std::string & field_name, const std::string & group_name,
			__attribute__((unused)) 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;

			dumper::Field * field =
			mesh.createNodalField(real_nodal_fields[field_name], group_name);

			return field;
			}

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

			dumper::Field * field = nullptr;

			if (field_name == "partitions")
			field = 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, element_kind);

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

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

			return field;
			}

			/* -------------------------------------------------------------------------- */
			#else
			/* -------------------------------------------------------------------------- */
			dumper::Field * HeatTransferModel::createElementalField(
			__attribute__((unused)) const std::string & field_name,
			__attribute__((unused)) const std::string & group_name,
			__attribute__((unused)) bool padding_flag,
			__attribute__((unused)) const ElementKind & element_kind) {
			return nullptr;
			}

			/* -------------------------------------------------------------------------- */
			dumper::Field * HeatTransferModel::createNodalFieldBool(
			__attribute__((unused)) const std::string & field_name,
			__attribute__((unused)) const std::string & group_name,
			__attribute__((unused)) bool padding_flag) {
			return nullptr;
			}

			/* -------------------------------------------------------------------------- */
			dumper::Field * HeatTransferModel::createNodalFieldReal(
			__attribute__((unused)) const std::string & field_name,
			__attribute__((unused)) const std::string & group_name,
			__attribute__((unused)) bool padding_flag) {
			return nullptr;
			}
			#endif

			/* -------------------------------------------------------------------------- */
			void PhaseFieldModel::dump(conts 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); }

			/* -------------------------------------------------------------------------- */
			} // akantu

rAKA/src/model/phase_field/phase_field_model.cc6fb268b4807bbugfixes/access_PBC_sla…

phase_field_model.ccView Options

rAKA/src/model/phase_field/phase_field_model.cc
6fb268b4807bbugfixes/access_PBC_sla…

phase_field_model.cc
View Options