solid_mechanics_model_igfem.cc
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Created: Wed, Feb 19, 18:47

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
	*
	* @section LICENSE
	*
	* 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 "material_igfem.hh"
	#include "group_manager_inline_impl.cc"
	#include "igfem_helper.hh"
	#ifdef AKANTU_USE_IOHELPER
	# include "dumper_paraview.hh"
	# include "dumper_igfem_material_internal_field.hh"
	# include "dumper_igfem_element_partition.hh"
	# include "dumper_igfem_elemental_field.hh"
	# include "dumper_material_padders.hh"
	#endif

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

	__BEGIN_AKANTU__

	const SolidMechanicsModelIGFEMOptions default_solid_mechanics_model_igfem_options(_static,
	false);

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

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

	this->registerEventHandler(*this);

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


	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.clear();
	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,
	const 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();
	}

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

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

	dumper::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, dumper::IGFEMElementPartitionField>(mesh.getConnectivities(),group_name,spatial_dimension, kind);
	else if(field_name == "material_index")
	field = mesh.createElementalField<UInt, Vector, dumper::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, dumper::IGFEMInternalMaterialField>(internal_flat,
	group_name,
	spatial_dimension,kind,nb_data_per_elem);
	if (field_name == "strain"){
	dumper::ComputeStrain<false> * foo = new dumper::ComputeStrain<false>(*this);
	field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
	} else if (field_name == "Von Mises stress") {
	dumper::ComputeVonMisesStress * foo = new dumper::ComputeVonMisesStress(*this);
	field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
	} else if (field_name == "Green strain") {
	dumper::ComputeStrain<true> * foo = new dumper::ComputeStrain<true>(*this);
	field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
	} else if (field_name == "principal strain") {
	dumper::ComputePrincipalStrain<false> * foo = new dumper::ComputePrincipalStrain<false>(*this);
	field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
	} else if (field_name == "principal Green strain") {
	dumper::ComputePrincipalStrain<true> * foo = new dumper::ComputePrincipalStrain<true>(*this);
	field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
	}

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

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

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

	dumper::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;

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

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

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

	#endif
	/* -------------------------------------------------------------------------- */
	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);
	}
	}

	__END_AKANTU__

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