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solid_mechanics_model_cohesive.cc
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			/**
			* @file solid_mechanics_model_cohesive.cc
			*
			* @author Fabian Barras <fabian.barras@epfl.ch>
			* @author Mauro Corrado <mauro.corrado@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			* @author Marco Vocialta <marco.vocialta@epfl.ch>
			*
			* @date creation: Tue May 08 2012
			* @date last modification: Wed Feb 21 2018
			*
			* @brief Solid mechanics model for cohesive elements
			*
			*
			* 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 "solid_mechanics_model_cohesive.hh"
			#include "aka_iterators.hh"
			#include "cohesive_element_inserter.hh"
			#include "element_synchronizer.hh"
			#include "facet_synchronizer.hh"
			#include "fe_engine_template.hh"
			#include "global_ids_updater.hh"
			#include "integrator_gauss.hh"
			#include "material_cohesive.hh"
			#include "mesh_accessor.hh"
			#include "mesh_global_data_updater.hh"
			#include "parser.hh"
			#include "shape_cohesive.hh"
			/* -------------------------------------------------------------------------- */
			#include "dumpable_inline_impl.hh"
			#ifdef AKANTU_USE_IOHELPER
			#include "dumper_iohelper_paraview.hh"
			#endif
			/* -------------------------------------------------------------------------- */
			#include <algorithm>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			class CohesiveMeshGlobalDataUpdater : public MeshGlobalDataUpdater {
			public:
			CohesiveMeshGlobalDataUpdater(SolidMechanicsModelCohesive & model)
			: model(model), mesh(model.getMesh()),
			global_ids_updater(model.getMesh(), *model.cohesive_synchronizer) {}

			/* ------------------------------------------------------------------------ */
			std::tuple<UInt, UInt>
			updateData(NewNodesEvent & nodes_event,
			NewElementsEvent & elements_event) override {
			auto *cohesive_nodes_event =
			dynamic_cast<CohesiveNewNodesEvent *>(&nodes_event);
			if (cohesive_nodes_event == nullptr) {
			return std::make_tuple(nodes_event.getList().size(),
			elements_event.getList().size());
			}

			/// update nodes type
			auto & new_nodes = cohesive_nodes_event->getList();
			auto & old_nodes = cohesive_nodes_event->getOldNodesList();

			auto local_nb_new_nodes = new_nodes.size();
			auto nb_new_nodes = local_nb_new_nodes;

			if (mesh.isDistributed()) {
			MeshAccessor mesh_accessor(mesh);
			auto & nodes_flags = mesh_accessor.getNodesFlags();
			auto nb_old_nodes = nodes_flags.size();
			nodes_flags.resize(nb_old_nodes + local_nb_new_nodes);

			for (auto && data : zip(old_nodes, new_nodes)) {
			UInt old_node;
			UInt new_node;
			std::tie(old_node, new_node) = data;
			nodes_flags(new_node) = nodes_flags(old_node);
			}

			model.updateCohesiveSynchronizers(elements_event);
			nb_new_nodes = global_ids_updater.updateGlobalIDs(new_nodes.size());
			}

			Vector<UInt> nb_new_stuff = {nb_new_nodes, elements_event.getList().size()};
			const auto & comm = mesh.getCommunicator();
			comm.allReduce(nb_new_stuff, SynchronizerOperation::_sum);

			if (nb_new_stuff(1) > 0) {
			mesh.sendEvent(elements_event);
			}

			if (nb_new_stuff(0) > 0) {
			mesh.sendEvent(nodes_event);
			// mesh.sendEvent(global_ids_updater.getChangedNodeEvent());
			}

			return std::make_tuple(nb_new_stuff(0), nb_new_stuff(1));
			}

			private:
			SolidMechanicsModelCohesive & model;
			Mesh & mesh;
			GlobalIdsUpdater global_ids_updater;
			};

			/* -------------------------------------------------------------------------- */
			SolidMechanicsModelCohesive::SolidMechanicsModelCohesive(
			Mesh & mesh, UInt dim, const ID & id)
			: SolidMechanicsModel(mesh, dim, id,
			ModelType::_solid_mechanics_model_cohesive),
			tangents("tangents", id), facet_stress("facet_stress", id),
			facet_material("facet_material", id) {
			AKANTU_DEBUG_IN();

			registerFEEngineObject<MyFEEngineCohesiveType>("CohesiveFEEngine", mesh,
			Model::spatial_dimension);

			auto && tmp_material_selector =
			std::make_shared<DefaultMaterialCohesiveSelector>(*this);

			tmp_material_selector->setFallback(this->material_selector);
			this->material_selector = tmp_material_selector;

			#if defined(AKANTU_USE_IOHELPER)
			this->mesh.registerDumper<DumperParaview>("cohesive elements", id);
			this->mesh.addDumpMeshToDumper("cohesive elements", mesh,
			Model::spatial_dimension, _not_ghost,
			_ek_cohesive);
			#endif

			if (this->mesh.isDistributed()) {
			/// create the distributed synchronizer for cohesive elements
			this->cohesive_synchronizer = std::make_unique<ElementSynchronizer>(
			mesh, "cohesive_distributed_synchronizer");

			auto & synchronizer = mesh.getElementSynchronizer();
			this->cohesive_synchronizer->split(synchronizer, [](auto && el) {
			return Mesh::getKind(el.type) == _ek_cohesive;
			});

			this->registerSynchronizer(*cohesive_synchronizer,
			SynchronizationTag::_material_id);
			this->registerSynchronizer(*cohesive_synchronizer,
			SynchronizationTag::_smm_stress);
			this->registerSynchronizer(*cohesive_synchronizer,
			SynchronizationTag::_smm_boundary);
			}

			this->inserter = std::make_unique<CohesiveElementInserter>(
			this->mesh, id + ":cohesive_element_inserter");

			registerFEEngineObject<MyFEEngineFacetType>(
			"FacetsFEEngine", mesh.getMeshFacets(), Model::spatial_dimension - 1);

			AKANTU_DEBUG_OUT();
			}

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

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

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

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::initFullImpl(const ModelOptions & options) {
			AKANTU_DEBUG_IN();

			const auto & smmc_options =
			aka::as_type<SolidMechanicsModelCohesiveOptions>(options);

			this->is_extrinsic = smmc_options.is_extrinsic;

			inserter->setIsExtrinsic(is_extrinsic);

			if (mesh.isDistributed()) {
			auto & mesh_facets = inserter->getMeshFacets();
			auto & synchronizer =
			aka::as_type<FacetSynchronizer>(mesh_facets.getElementSynchronizer());

			// synchronizeGhostFacetsConnectivity();

			/// create the facet synchronizer for extrinsic simulations
			if (is_extrinsic) {
			facet_stress_synchronizer = std::make_unique<ElementSynchronizer>(
			synchronizer, id + ":facet_stress_synchronizer");
			facet_stress_synchronizer->swapSendRecv();
			this->registerSynchronizer(*facet_stress_synchronizer,
			SynchronizationTag::_smmc_facets_stress);
			}
			}

			MeshAccessor mesh_accessor(mesh);
			mesh_accessor.registerGlobalDataUpdater(
			std::make_unique<CohesiveMeshGlobalDataUpdater>(*this));

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

			if (not is_empty) {
			auto inserter_section =
			section.getSubSections(ParserType::_cohesive_inserter);
			if (inserter_section.begin() != inserter_section.end()) {
			inserter->parseSection(*inserter_section.begin());
			}
			}

			SolidMechanicsModel::initFullImpl(options);

			AKANTU_DEBUG_OUT();
			} // namespace akantu

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::initMaterials() {
			AKANTU_DEBUG_IN();

			// make sure the material are instantiated
			if (not are_materials_instantiated) {
			instantiateMaterials();
			}

			/// find the first cohesive material
			UInt cohesive_index = UInt(-1);

			for (auto && material : enumerate(materials)) {
			if (dynamic_cast<MaterialCohesive *>(std::get<1>(material).get()) !=
			nullptr) {
			cohesive_index = std::get<0>(material);
			break;
			}
			}

			if (cohesive_index == UInt(-1)) {
			AKANTU_EXCEPTION("No cohesive materials in the material input file");
			}

			material_selector->setFallback(cohesive_index);

			// set the facet information in the material in case of dynamic insertion
			// to know what material to call for stress checks

			const Mesh & mesh_facets = inserter->getMeshFacets();
			facet_material.initialize(
			mesh_facets, _spatial_dimension = spatial_dimension - 1,
			_with_nb_element = true,
			_default_value = material_selector->getFallbackValue());

			for_each_element(
			mesh_facets,
			[&](auto && element) {
			auto mat_index = (*material_selector)(element);
			auto & mat = aka::as_type<MaterialCohesive>(*materials[mat_index]);
			facet_material(element) = mat_index;
			if (is_extrinsic) {
			mat.addFacet(element);
			}
			},
			_spatial_dimension = spatial_dimension - 1, _ghost_type = _not_ghost);

			SolidMechanicsModel::initMaterials();

			if (is_extrinsic) {
			this->initAutomaticInsertion();
			} else {
			this->insertIntrinsicElements();
			}

			AKANTU_DEBUG_OUT();
			} // namespace akantu

			/* -------------------------------------------------------------------------- */
			/**
			* Initialize the model,basically it pre-compute the shapes, shapes derivatives
			* and jacobian
			*/
			void SolidMechanicsModelCohesive::initModel() {
			AKANTU_DEBUG_IN();

			SolidMechanicsModel::initModel();

			/// add cohesive type connectivity
			ElementType type = _not_defined;
			for (auto && type_ghost : ghost_types) {
			for (const auto & tmp_type :
			mesh.elementTypes(spatial_dimension, type_ghost)) {
			const auto & connectivity = mesh.getConnectivity(tmp_type, type_ghost);
			if (connectivity.empty()) {
			continue;
			}

			type = tmp_type;
			auto type_facet = Mesh::getFacetType(type);
			auto type_cohesive = FEEngine::getCohesiveElementType(type_facet);
			mesh.addConnectivityType(type_cohesive, type_ghost);
			}
			}
			AKANTU_DEBUG_ASSERT(type != _not_defined, "No elements in the mesh");

			getFEEngine("CohesiveFEEngine").initShapeFunctions(_not_ghost);
			getFEEngine("CohesiveFEEngine").initShapeFunctions(_ghost);

			if (is_extrinsic) {
			getFEEngine("FacetsFEEngine").initShapeFunctions(_not_ghost);
			getFEEngine("FacetsFEEngine").initShapeFunctions(_ghost);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::insertIntrinsicElements() {
			AKANTU_DEBUG_IN();
			inserter->insertIntrinsicElements();
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::initAutomaticInsertion() {
			AKANTU_DEBUG_IN();

			this->inserter->limitCheckFacets();
			this->updateFacetStressSynchronizer();
			this->resizeFacetStress();

			/// compute normals on facets
			this->computeNormals();

			this->initStressInterpolation();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::updateAutomaticInsertion() {
			AKANTU_DEBUG_IN();

			this->inserter->limitCheckFacets();
			this->updateFacetStressSynchronizer();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::initStressInterpolation() {
			Mesh & mesh_facets = inserter->getMeshFacets();

			/// compute quadrature points coordinates on facets
			Array<Real> & position = mesh.getNodes();

			ElementTypeMapArray<Real> quad_facets("quad_facets", id);
			quad_facets.initialize(mesh_facets, _nb_component = Model::spatial_dimension,
			_spatial_dimension = Model::spatial_dimension - 1);
			// mesh_facets.initElementTypeMapArray(quad_facets, Model::spatial_dimension,
			// Model::spatial_dimension - 1);

			getFEEngine("FacetsFEEngine")
			.interpolateOnIntegrationPoints(position, quad_facets);

			/// compute elements quadrature point positions and build
			/// element-facet quadrature points data structure
			ElementTypeMapArray<Real> elements_quad_facets("elements_quad_facets", id);

			elements_quad_facets.initialize(
			mesh, _nb_component = Model::spatial_dimension,
			_spatial_dimension = Model::spatial_dimension);
			// mesh.initElementTypeMapArray(elements_quad_facets,
			// Model::spatial_dimension,
			// Model::spatial_dimension);

			for (auto elem_gt : ghost_types) {
			for (const auto & type : mesh.elementTypes(Model::spatial_dimension, elem_gt)) {
			UInt nb_element = mesh.getNbElement(type, elem_gt);
			if (nb_element == 0) {
			continue;
			}

			/// compute elements' quadrature points and list of facet
			/// quadrature points positions by element
			const auto & facet_to_element =
			mesh_facets.getSubelementToElement(type, elem_gt);
			auto & el_q_facet = elements_quad_facets(type, elem_gt);

			auto facet_type = Mesh::getFacetType(type);
			auto nb_quad_per_facet =
			getFEEngine("FacetsFEEngine").getNbIntegrationPoints(facet_type);
			auto nb_facet_per_elem = facet_to_element.getNbComponent();

			// small hack in the loop to skip boundary elements, they are silently
			// initialized to NaN to see if this causes problems
			el_q_facet.resize(nb_element * nb_facet_per_elem * nb_quad_per_facet,
			std::numeric_limits<Real>::quiet_NaN());

			for (auto && data :
			zip(make_view(facet_to_element),
			make_view(el_q_facet, spatial_dimension, nb_quad_per_facet))) {
			const auto & global_facet = std::get<0>(data);
			auto & el_q = std::get<1>(data);

			if (global_facet == ElementNull) {
			continue;
			}

			Matrix<Real> quad_f =
			make_view(quad_facets(global_facet.type, global_facet.ghost_type),
			spatial_dimension, nb_quad_per_facet)
			.begin()[global_facet.element];

			el_q = quad_f;

			// for (UInt q = 0; q < nb_quad_per_facet; ++q) {
			// for (UInt s = 0; s < Model::spatial_dimension; ++s) {
			// el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
			// f * nb_quad_per_facet + q,
			// s) = quad_f(global_facet * nb_quad_per_facet + q,
			// s);
			// }
			// }
			//}
			}
			}
			}

			/// loop over non cohesive materials
			for (auto && material : materials) {
			if (aka::is_of_type<MaterialCohesive>(material)) {
			continue;
			}
			/// initialize the interpolation function
			material->initElementalFieldInterpolation(elements_quad_facets);
			}

			AKANTU_DEBUG_OUT();
			}

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

			// f_int += f_int_cohe
			for (auto & material : this->materials) {
			try {
			auto & mat = aka::as_type<MaterialCohesive>(*material);
			mat.computeTraction(_not_ghost);
			} catch (std::bad_cast & bce) {
			}
			}

			SolidMechanicsModel::assembleInternalForces();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::computeNormals() {
			AKANTU_DEBUG_IN();

			Mesh & mesh_facets = this->inserter->getMeshFacets();
			this->getFEEngine("FacetsFEEngine")
			.computeNormalsOnIntegrationPoints(_not_ghost);

			/**
			* @todo store tangents while computing normals instead of
			* recomputing them as follows:
			*/
			/* ------------------------------------------------------------------------ */
			UInt tangent_components =
			Model::spatial_dimension * (Model::spatial_dimension - 1);

			tangents.initialize(mesh_facets, _nb_component = tangent_components,
			_spatial_dimension = Model::spatial_dimension - 1);
			// mesh_facets.initElementTypeMapArray(tangents, tangent_components,
			// Model::spatial_dimension - 1);

			for (auto facet_type :
			mesh_facets.elementTypes(Model::spatial_dimension - 1)) {
			const Array<Real> & normals =
			this->getFEEngine("FacetsFEEngine")
			.getNormalsOnIntegrationPoints(facet_type);

			Array<Real> & tangents = this->tangents(facet_type);

			Math::compute_tangents(normals, tangents);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::interpolateStress() {
			ElementTypeMapArray<Real> by_elem_result("temporary_stress_by_facets", id);

			for (auto & material : materials) {
			if (not aka::is_of_type<MaterialCohesive>(material)) {
			/// interpolate stress on facet quadrature points positions
			material->interpolateStressOnFacets(facet_stress, by_elem_result);
			}
			}

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

			/* -------------------------------------------------------------------------- */
			UInt SolidMechanicsModelCohesive::checkCohesiveStress() {
			AKANTU_DEBUG_IN();

			if (not is_extrinsic) {
			AKANTU_EXCEPTION(
			"This function can only be used for extrinsic cohesive elements");
			}

			interpolateStress();

			for (auto & mat : materials) {
			if (aka::is_of_type<MaterialCohesive>(mat)) {
			/// check which not ghost cohesive elements are to be created
			auto * mat_cohesive = aka::as_type<MaterialCohesive>(mat.get());
			mat_cohesive->checkInsertion();
			}
			}

			/// communicate data among processors
			// this->synchronize(SynchronizationTag::_smmc_facets);

			/// insert cohesive elements
			UInt nb_new_elements = inserter->insertElements();

			// if (nb_new_elements > 0) {
			// this->reinitializeSolver();
			// }

			AKANTU_DEBUG_OUT();

			return nb_new_elements;
			}

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

			SolidMechanicsModel::onElementsAdded(element_list, event);

			if (is_extrinsic) {
			resizeFacetStress();
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::onNodesAdded(const Array<UInt> & new_nodes,
			const NewNodesEvent & event) {
			AKANTU_DEBUG_IN();

			SolidMechanicsModel::onNodesAdded(new_nodes, event);

			const CohesiveNewNodesEvent * cohesive_event;
			if ((cohesive_event = dynamic_cast<const CohesiveNewNodesEvent *>(&event)) ==
			nullptr) {
			return;
			}

			const auto & old_nodes = cohesive_event->getOldNodesList();

			auto copy = [this, &new_nodes, &old_nodes](auto & arr) {
			UInt new_node;
			UInt old_node;

			auto view = make_view(arr, spatial_dimension);
			auto begin = view.begin();

			for (auto && pair : zip(new_nodes, old_nodes)) {
			std::tie(new_node, old_node) = pair;

			auto old_ = begin + old_node;
			auto new_ = begin + new_node;

			new_ = old_;
			}
			};

			copy(*displacement);
			copy(*blocked_dofs);

			if (velocity) {
			copy(*velocity);
			}

			if (acceleration) {
			copy(*acceleration);
			}

			if (current_position) {
			copy(*current_position);
			}

			if (previous_displacement) {
			copy(*previous_displacement);
			}

			// if (external_force)
			// copy(*external_force);
			// if (internal_force)
			// copy(*internal_force);

			if (displacement_increment) {
			copy(*displacement_increment);
			}

			copy(getDOFManager().getSolution("displacement"));
			// this->assembleMassLumped();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::afterSolveStep(bool converged) {
			AKANTU_DEBUG_IN();

			/*
			* This is required because the Cauchy stress is the stress measure that
			* is used to check the insertion of cohesive elements
			*/
			if (converged) {
			for (auto & mat : materials) {
			if (mat->isFiniteDeformation()) {
			mat->computeAllCauchyStresses(_not_ghost);
			}
			}
			}

			SolidMechanicsModel::afterSolveStep(converged);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::printself(std::ostream & stream,
			int indent) const {
			std::string space(indent, AKANTU_INDENT);

			stream << space << "SolidMechanicsModelCohesive ["
			<< "\n";
			SolidMechanicsModel::printself(stream, indent + 2);
			stream << space << "]" << std::endl;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::resizeFacetStress() {
			AKANTU_DEBUG_IN();

			this->facet_stress.initialize(getFEEngine("FacetsFEEngine"),
			_nb_component =
			2 * spatial_dimension * spatial_dimension,
			_spatial_dimension = spatial_dimension - 1);

			// for (auto && ghost_type : ghost_types) {
			// for (const const auto & type :
			// mesh_facets.elementTypes(spatial_dimension - 1, ghost_type)) {
			// UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);

			// UInt nb_quadrature_points = getFEEngine("FacetsFEEngine")
			// .getNbIntegrationPoints(type,
			// ghost_type);

			// UInt new_size = nb_facet * nb_quadrature_points;

			// facet_stress(type, ghost_type).resize(new_size);
			// }
			// }

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelCohesive::addDumpGroupFieldToDumper(
			const std::string & dumper_name, const std::string & field_id,
			const std::string & group_name, ElementKind element_kind,
			bool padding_flag) {
			AKANTU_DEBUG_IN();

			UInt spatial_dimension = Model::spatial_dimension;
			ElementKind _element_kind = element_kind;
			if (dumper_name == "cohesive elements") {
			_element_kind = _ek_cohesive;
			} else if (dumper_name == "facets") {
			spatial_dimension = Model::spatial_dimension - 1;
			}
			SolidMechanicsModel::addDumpGroupFieldToDumper(dumper_name, field_id,
			group_name, spatial_dimension,
			_element_kind, padding_flag);

			AKANTU_DEBUG_OUT();
			}

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

			void SolidMechanicsModelCohesive::onDump() {
			this->flattenAllRegisteredInternals(_ek_cohesive);
			SolidMechanicsModel::onDump();
			}

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

			} // namespace akantu

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rAKA/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
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