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solid_mechanics_model_igfem.cc
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			/**
			* @file solid_mechanics_model_igfem.hh
			*
			* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
			*
			*
			* @brief solid mechanics model for IGFEM analysis
			*
			*
			* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
			* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
			*
			*/

			/* -------------------------------------------------------------------------- */
			#include "solid_mechanics_model_igfem.hh"
			#include "dumpable_inline_impl.hh"
			#include "group_manager_inline_impl.hh"
			#include "igfem_helper.hh"
			#include "material_igfem.hh"
			/* -------------------------------------------------------------------------- */
			#include "dumper_igfem_element_partition.hh"
			#include "dumper_igfem_elemental_field.hh"
			#include "dumper_igfem_material_internal_field.hh"
			#include "dumper_material_padders.hh"
			#include "dumper_paraview.hh"

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

			namespace akantu {

			const SolidMechanicsModelIGFEMOptions
			default_solid_mechanics_model_igfem_options(_static, false);

			SolidMechanicsModelIGFEM::SolidMechanicsModelIGFEM(Mesh & mesh, UInt dim,
			const ID & id)
			: SolidMechanicsModel(mesh, dim, id), IGFEMEnrichment(mesh),
			global_ids_updater(NULL) {
			AKANTU_DEBUG_IN();

			delete material_selector;
			material_selector = new DefaultMaterialIGFEMSelector(*this);

			this->registerEventHandler(*this);

			this->mesh.registerDumper<DumperParaview>("igfem elements", id);
			this->mesh.addDumpMeshToDumper("igfem elements", mesh, spatial_dimension,
			_not_ghost, _ek_igfem);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			SolidMechanicsModelIGFEM::~SolidMechanicsModelIGFEM() {
			AKANTU_DEBUG_IN();
			if (global_ids_updater)
			delete global_ids_updater;
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelIGFEM::initFull(const ModelOptions & options) {
			AKANTU_DEBUG_IN();

			/// intialize the IGFEM enrichment
			this->initialize();

			SolidMechanicsModel::initFull(options);

			// set the initial condition to 0
			real_force->clear();
			real_displacement->clear();
			real_residual->clear();

			AKANTU_DEBUG_OUT();
			}

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

			UInt nb_nodes = mesh.getNbNodes();
			std::stringstream sstr_rdisp;
			sstr_rdisp << id << ":real_displacement";
			std::stringstream sstr_rforc;
			sstr_rforc << id << ":real_force";
			std::stringstream sstr_rresi;
			sstr_rresi << id << ":real_residual";

			real_displacement = &(alloc<Real>(sstr_rdisp.str(), nb_nodes,
			spatial_dimension, REAL_INIT_VALUE));
			real_force = &(alloc<Real>(sstr_rforc.str(), nb_nodes, spatial_dimension,
			REAL_INIT_VALUE));
			real_residual = &(alloc<Real>(sstr_rresi.str(), nb_nodes, spatial_dimension,
			REAL_INIT_VALUE));

			SolidMechanicsModel::initArrays();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelIGFEM::initParallel(MeshPartition * partition,
			DataAccessor * data_accessor) {
			SolidMechanicsModel::initParallel(partition, data_accessor);
			this->intersector_sphere.setDistributedSynchronizer(synch_parallel);
			if (mesh.isDistributed())
			global_ids_updater = new GlobalIdsUpdater(mesh, synch_parallel);
			}

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

			// make sure the material are instantiated
			if (!are_materials_instantiated)
			instantiateMaterials();

			/// find the first igfem material
			UInt igfem_index = 0;

			while ((dynamic_cast<MaterialIGFEM *>(materials[igfem_index]) == NULL) &&
			igfem_index <= materials.size())
			++igfem_index;

			AKANTU_DEBUG_ASSERT(igfem_index != materials.size(),
			"No igfem materials in the material input file");

			DefaultMaterialIGFEMSelector * igfem_mat_selector =
			dynamic_cast<DefaultMaterialIGFEMSelector *>(material_selector);
			if (igfem_mat_selector != NULL)
			igfem_mat_selector->setIGFEMFallback(igfem_index);

			SolidMechanicsModel::initMaterials();

			AKANTU_DEBUG_OUT();
			}

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

			SolidMechanicsModel::initModel();

			registerFEEngineObject<MyFEEngineIGFEMType>("IGFEMFEEngine", mesh,
			spatial_dimension);
			/// insert the two feengines associated with the model in the map
			this->fe_engines_per_kind[_ek_regular] = &(this->getFEEngine());
			this->fe_engines_per_kind[_ek_igfem] = &(this->getFEEngine("IGFEMFEEngine"));

			/// add the igfem type connectivities

			for (ghost_type_t::iterator gt = ghost_type_t::begin();
			gt != ghost_type_t::end(); ++gt) {

			GhostType type_ghost = *gt;

			Mesh::type_iterator it = mesh.firstType(spatial_dimension, type_ghost);
			Mesh::type_iterator last = mesh.lastType(spatial_dimension, type_ghost);

			for (; it != last; ++it) {
			const Array<UInt> & connectivity = mesh.getConnectivity(*it, type_ghost);
			if (connectivity.getSize() != 0) {
			ElementType type = *it;
			Vector<ElementType> types_igfem = FEEngine::getIGFEMElementTypes(type);
			for (UInt i = 0; i < types_igfem.size(); ++i)
			mesh.addConnectivityType(types_igfem(i), type_ghost);
			}
			}
			}

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

			AKANTU_DEBUG_OUT();
			}

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

			const NewIGFEMElementsEvent * igfem_event =
			dynamic_cast<const NewIGFEMElementsEvent *>(&event);
			/// insert the new and old elements in the map
			if (igfem_event != NULL) {
			this->element_map.zero();
			const Array<Element> & old_elements = igfem_event->getOldElementsList();
			for (UInt e = 0; e < elements.getSize(); ++e) {
			this->element_map[elements(e)] = old_elements(e);
			}
			}

			/// update shape functions
			getFEEngine("IGFEMFEEngine").initShapeFunctions(_not_ghost);
			getFEEngine("IGFEMFEEngine").initShapeFunctions(_ghost);

			SolidMechanicsModel::onElementsAdded(elements, event);
			this->reassignMaterial();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelIGFEM::onElementsRemoved(
			const Array<Element> & element_list,
			const ElementTypeMapArray<UInt> & new_numbering,
			const RemovedElementsEvent & event) {

			this->getFEEngine("IGFEMFEEngine").initShapeFunctions(_not_ghost);
			this->getFEEngine("IGFEMFEEngine").initShapeFunctions(_ghost);
			SolidMechanicsModel::onElementsRemoved(element_list, new_numbering, event);
			if (synch_parallel)
			synch_parallel->computeAllBufferSizes(*this);
			}

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

			const NewIGFEMNodesEvent * igfem_event =
			dynamic_cast<const NewIGFEMNodesEvent *>(&event);
			// update the node type
			if (igfem_event != NULL) {
			intersector_sphere.updateNodeType(
			nodes_list, igfem_event->getNewNodePerElem(),
			igfem_event->getElementType(), igfem_event->getGhostType());
			}

			UInt nb_nodes = mesh.getNbNodes();

			if (real_displacement)
			real_displacement->resize(nb_nodes);
			if (real_force)
			real_force->resize(nb_nodes);
			if (real_residual)
			real_residual->resize(nb_nodes);

			if (mesh.isDistributed())
			mesh.getGlobalNodesIds().resize(mesh.getNbNodes());

			if (displacement)
			displacement->resize(nb_nodes);
			if (mass)
			mass->resize(nb_nodes);
			if (velocity)
			velocity->resize(nb_nodes);
			if (acceleration)
			acceleration->resize(nb_nodes);
			if (force)
			force->resize(nb_nodes);
			if (residual)
			residual->resize(nb_nodes);
			if (blocked_dofs)
			blocked_dofs->resize(nb_nodes);

			if (previous_displacement)
			previous_displacement->resize(nb_nodes);
			if (increment_acceleration)
			increment_acceleration->resize(nb_nodes);
			if (increment)
			increment->resize(nb_nodes);

			if (current_position)
			current_position->resize(nb_nodes);

			std::vector<Material *>::iterator mat_it;
			for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			(*mat_it)->onNodesAdded(nodes_list, event);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelIGFEM::onNodesRemoved(const Array<UInt> & nodes_list,
			const Array<UInt> & new_numbering,
			const RemovedNodesEvent & event) {
			if (real_displacement)
			mesh.removeNodesFromArray(*real_displacement, new_numbering);
			if (real_force)
			mesh.removeNodesFromArray(*real_force, new_numbering);
			if (real_residual)
			mesh.removeNodesFromArray(*real_residual, new_numbering);

			// communicate global connectivity for slave nodes
			if (global_ids_updater)
			global_ids_updater->updateGlobalIDs(
			mesh.getNbNodes() - intersector_sphere.getNbStandardNodes());

			SolidMechanicsModel::onNodesRemoved(nodes_list, new_numbering, event);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelIGFEM::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();

			ElementKind _element_kind = element_kind;
			if (dumper_name == "igfem elements") {
			_element_kind = _ek_igfem;
			}

			SolidMechanicsModel::addDumpGroupFieldToDumper(
			dumper_name, field_id, group_name, _element_kind, padding_flag);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelIGFEM::onDump() {
			this->computeValuesOnEnrichedNodes();
			this->flattenAllRegisteredInternals(_ek_igfem);
			SolidMechanicsModel::onDump();
			}

			/* -------------------------------------------------------------------------- */
			dumpers::Field * SolidMechanicsModelIGFEM::createElementalField(
			const std::string & field_name, const std::string & group_name,
			bool padding_flag, const UInt & spatial_dimension, ElementKind kind) {

			dumpers::Field * field = NULL;

			if (kind != _ek_igfem)
			field = SolidMechanicsModel::createElementalField(
			field_name, group_name, padding_flag, spatial_dimension, kind);

			else {

			if (field_name == "partitions")
			field =
			mesh.createElementalField<UInt, dumpers::IGFEMElementPartitionField>(
			mesh.getConnectivities(), group_name, spatial_dimension, kind);
			else if (field_name == "material_index")
			field =
			mesh.createElementalField<UInt, Vector, dumpers::IGFEMElementalField>(
			material_index, group_name, spatial_dimension, kind);
			else {
			// this copy of field_name is used to compute derivated data such as
			// strain and von mises stress that are based on grad_u and stress
			std::string field_name_copy(field_name);

			if (field_name == "strain" \|\| field_name == "Green strain" \|\|
			field_name == "principal strain" \|\|
			field_name == "principal Green strain")
			field_name_copy = "grad_u";
			else if (field_name == "Von Mises stress")
			field_name_copy = "stress";

			bool is_internal = this->isInternal(field_name_copy, kind);

			if (is_internal) {
			ElementTypeMap<UInt> nb_data_per_elem =
			this->getInternalDataPerElem(field_name_copy, kind);
			ElementTypeMapArray<Real> & internal_flat =
			this->flattenInternal(field_name_copy, kind);
			field = mesh.createElementalField<Real,
			dumpers::IGFEMInternalMaterialField>(
			internal_flat, group_name, spatial_dimension, kind,
			nb_data_per_elem);
			if (field_name == "strain") {
			dumpers::ComputeStrain<false> * foo =
			new dumpers::ComputeStrain<false>(*this);
			field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
			} else if (field_name == "Von Mises stress") {
			dumpers::ComputeVonMisesStress * foo =
			new dumpers::ComputeVonMisesStress(*this);
			field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
			} else if (field_name == "Green strain") {
			dumpers::ComputeStrain<true> * foo =
			new dumpers::ComputeStrain<true>(*this);
			field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
			} else if (field_name == "principal strain") {
			dumpers::ComputePrincipalStrain<false> * foo =
			new dumpers::ComputePrincipalStrain<false>(*this);
			field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
			} else if (field_name == "principal Green strain") {
			dumpers::ComputePrincipalStrain<true> * foo =
			new dumpers::ComputePrincipalStrain<true>(*this);
			field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
			}

			/// treat the paddings
			if (padding_flag) {
			if (field_name == "stress") {
			if (spatial_dimension == 2) {
			dumpers::StressPadder<2> * foo =
			new dumpers::StressPadder<2>(*this);
			field =
			dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
			}
			} else if (field_name == "strain" \|\| field_name == "Green strain") {
			if (spatial_dimension == 2) {
			dumpers::StrainPadder<2> * foo =
			new dumpers::StrainPadder<2>(*this);
			field =
			dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
			}
			}
			}
			// homogenize the field
			dumpers::ComputeFunctorInterface * foo =
			dumpers::HomogenizerProxy::createHomogenizer(*field);

			field = dumpers::FieldComputeProxy::createFieldCompute(field, *foo);
			}
			}
			}
			// }
			return field;
			}

			/* -------------------------------------------------------------------------- */
			dumpers::Field *
			SolidMechanicsModelIGFEM::createNodalFieldReal(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag) {
			std::map<std::string, Array<Real> *> real_nodal_fields;
			real_nodal_fields["real_displacement"] = real_displacement;

			dumpers::Field * field = NULL;
			if (padding_flag)
			field = mesh.createNodalField(real_nodal_fields[field_name], group_name, 3);
			else
			field = mesh.createNodalField(real_nodal_fields[field_name], group_name);

			if (field == NULL)
			return SolidMechanicsModel::createNodalFieldReal(field_name, group_name,
			padding_flag);

			return field;
			}

			#else
			/* -------------------------------------------------------------------------- */
			dumpers::Field * SolidMechanicsModelIGFEM::createElementalField(
			const std::string & field_name, const std::string & group_name,
			bool padding_flag, const UInt & spatial_dimension, ElementKind kind) {
			return NULL;
			}

			/* -------------------------------------------------------------------------- */
			dumpers::Field *
			SolidMechanicsModelIGFEM::createNodalFieldReal(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag) {
			return NULL;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelIGFEM::computeValuesOnEnrichedNodes() {
			for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
			for (UInt s = 0; s < spatial_dimension; ++s)
			(real_displacement)(n, s) = (displacement)(n, s);
			}

			Element element;
			Vector<Real> real_coords(spatial_dimension);
			Vector<Real> interpolated(spatial_dimension);
			Array<Real>::const_vector_iterator r_displ_it =
			this->real_displacement->begin(spatial_dimension);

			for (ghost_type_t::iterator gt = ghost_type_t::begin();
			gt != ghost_type_t::end(); ++gt) {
			element.ghost_type = *gt;
			Mesh::type_iterator it = mesh.firstType(spatial_dimension, *gt, _ek_igfem);
			Mesh::type_iterator last = mesh.lastType(spatial_dimension, *gt, _ek_igfem);
			for (; it != last; ++it) {
			element.type = *it;
			UInt nb_element = mesh.getNbElement(it, gt);
			if (!nb_element)
			continue;
			UInt * elem_val = mesh.getConnectivity(it, gt).storage();
			UInt nb_nodes_per_element = mesh.getNbNodesPerElement(*it);
			Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
			Matrix<Real> displ_val(spatial_dimension, nb_nodes_per_element);

			UInt nb_enriched_nodes = IGFEMHelper::getNbEnrichedNodes(*it);
			UInt nb_parent_nodes = IGFEMHelper::getNbParentNodes(*it);
			for (UInt el = 0; el < nb_element; ++el) {
			element.element = el;
			/// get the node coordinates of the element
			mesh.extractNodalValuesFromElement(
			mesh.getNodes(), nodes_coord.storage(),
			elem_val + el * nb_nodes_per_element, nb_nodes_per_element,
			spatial_dimension);

			/// get the displacement values at the nodes of the element
			mesh.extractNodalValuesFromElement(
			*(this->displacement), displ_val.storage(),
			elem_val + el * nb_nodes_per_element, nb_nodes_per_element,
			spatial_dimension);

			for (UInt i = 0; i < nb_enriched_nodes; ++i) {
			/// coordinates of enriched node
			real_coords = nodes_coord(nb_parent_nodes + i);
			/// global index of the enriched node
			UInt idx = elem_val[el * nb_nodes_per_element + nb_parent_nodes + i];
			/// compute the real displacement value
			this->getFEEngine("IGFEMFEEngine")
			.interpolate(real_coords, displ_val, interpolated, element);
			r_displ_it[idx] = interpolated;
			}
			}
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelIGFEM::transferInternalValues(
			const ID & internal, std::vector<Element> & new_elements,
			Array<Real> & added_quads, Array<Real> & internal_values) {

			/// @todo sort the new elements by their corresponding old element type and
			/// old material!!!

			/// get the number of elements for which iternals need to be transfered
			UInt nb_new_elements = new_elements.size();
			UInt nb_new_quads = added_quads.getSize() / nb_new_elements;

			Array<Real>::const_matrix_iterator quad_coords =
			added_quads.begin_reinterpret(this->spatial_dimension, nb_new_quads,
			nb_new_elements);
			UInt nb_internal_component = internal_values.getNbComponent();
			Array<Real>::matrix_iterator internal_val = internal_values.begin_reinterpret(
			nb_internal_component, nb_new_quads, nb_new_elements);
			Vector<Real> default_values(nb_internal_component, 0.);

			for (UInt e = 0; e < nb_new_elements; ++e, ++quad_coords, ++internal_val) {
			Element new_element = new_elements[e];
			Element old_element = this->element_map[new_element];
			UInt mat_idx = (this->material_index(
			old_element.type, old_element.ghost_type))(old_element.element);
			Material & old_material = *(this->materials[mat_idx]);
			old_material.extrapolateInternal(internal, old_element, *quad_coords,
			*internal_val);
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModelIGFEM::applyEigenGradU(
			const Matrix<Real> & prescribed_eigen_grad_u, const ID & material_name,
			const GhostType ghost_type) {

			AKANTU_DEBUG_ASSERT(prescribed_eigen_grad_u.size() ==
			spatial_dimension * spatial_dimension,
			"The prescribed grad_u is not of the good size");
			std::vector<Material *>::iterator mat_it;
			for (mat_it = this->materials.begin(); mat_it != this->materials.end();
			++mat_it) {
			MaterialIGFEM * mat_igfem = dynamic_cast<MaterialIGFEM >(mat_it);
			if (mat_igfem != NULL)
			mat_igfem->applyEigenGradU(prescribed_eigen_grad_u, material_name,
			ghost_type);
			else if ((*mat_it)->getName() == material_name)
			(*mat_it)->applyEigenGradU(prescribed_eigen_grad_u, ghost_type);
			}
			}

			} // namespace akantu

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rAKA/extra_packages/igfem/src/solid_mechanics_model_igfem.cc
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solid_mechanics_model_igfem.cc
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