solid_mechanics_model_cohesive.cc
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solid_mechanics_model_cohesive.cc
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	/**
	* @file solid_mechanics_model_cohesive.cc
	*
	* @author Marco Vocialta <marco.vocialta@epfl.ch>
	* @author Nicolas Richart <nicolas.richart@epfl.ch>
	*
	* @date creation: Tue May 08 2012
	* @date last modification: Fri Sep 05 2014
	*
	* @brief Solid mechanics model for cohesive elements
	*
	* @section LICENSE
	*
	* Copyright (©) 2014 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 <algorithm>
	#include "shape_cohesive.hh"
	#include "solid_mechanics_model_cohesive.hh"
	#include "dumpable_inline_impl.hh"
	#include "material_cohesive.hh"

	#ifdef AKANTU_USE_IOHELPER
	# include "dumper_paraview.hh"
	#endif

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

	__BEGIN_AKANTU__

	const SolidMechanicsModelCohesiveOptions default_solid_mechanics_model_cohesive_options(_explicit_lumped_mass,
	false,
	false);

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

	SolidMechanicsModelCohesive::SolidMechanicsModelCohesive(Mesh & mesh,
	UInt dim,
	const ID & id,
	const MemoryID & memory_id) :
	SolidMechanicsModel(mesh, dim, id, memory_id),
	tangents("tangents", id),
	facet_stress("facet_stress", id),
	facet_material("facet_material", id) {
	AKANTU_DEBUG_IN();

	inserter = NULL;

	#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
	facet_synchronizer = NULL;
	facet_stress_synchronizer = NULL;
	cohesive_distributed_synchronizer = NULL;
	global_connectivity = NULL;
	#endif

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

	this->registerEventHandler(*this);

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

	AKANTU_DEBUG_OUT();
	}


	/* -------------------------------------------------------------------------- */
	SolidMechanicsModelCohesive::~SolidMechanicsModelCohesive() {
	AKANTU_DEBUG_IN();

	delete inserter;

	#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
	delete cohesive_distributed_synchronizer;
	delete facet_synchronizer;
	delete facet_stress_synchronizer;
	#endif

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelCohesive::setTimeStep(Real time_step) {
	SolidMechanicsModel::setTimeStep(time_step);

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

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

	const SolidMechanicsModelCohesiveOptions & smmc_options =
	dynamic_cast<const SolidMechanicsModelCohesiveOptions &>(options);

	this->is_extrinsic = smmc_options.extrinsic;

	if (!inserter)
	inserter = new CohesiveElementInserter(mesh, is_extrinsic, synch_parallel,
	id+":cohesive_element_inserter");

	SolidMechanicsModel::initFull(options);

	#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
	if (facet_synchronizer != NULL)
	inserter->initParallel(facet_synchronizer);
	#endif

	if (is_extrinsic)
	initAutomaticInsertion();

	AKANTU_DEBUG_OUT();
	}


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

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

	/// find the first cohesive material
	UInt cohesive_index = 0;

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

	AKANTU_DEBUG_ASSERT(cohesive_index != materials.size(),
	"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
	if (is_extrinsic) {
	const Mesh & mesh_facets = inserter->getMeshFacets();
	mesh_facets.initElementTypeMapArray(facet_material, 1, spatial_dimension - 1);

	Element element;
	for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
	element.ghost_type = *gt;
	Mesh::type_iterator first = mesh_facets.firstType(spatial_dimension - 1, *gt);
	Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1, *gt);
	for(;first != last; ++first) {
	element.type = *first;
	Array<UInt> & f_material = facet_material(first, gt);
	UInt nb_element = mesh_facets.getNbElement(first, gt);
	f_material.resize(nb_element);
	f_material.set(cohesive_index);
	for (UInt el = 0; el < nb_element; ++el) {
	element.element = el;
	UInt mat_index = (*material_selector)(element);
	f_material(el) = mat_index;
	MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(*materials[mat_index]);
	mat.addFacet(element);
	}
	}
	}
	} else {
	for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
	Mesh::type_iterator first = mesh.firstType(spatial_dimension, *gt, _ek_cohesive);
	Mesh::type_iterator last = mesh.lastType(spatial_dimension, *gt, _ek_cohesive);

	for(;first != last; ++first) {
	Array<UInt> & mat_indexes = this->material_index(first, gt);
	Array<UInt> & mat_loc_num = this->material_local_numbering(first, gt);
	mat_indexes.set(cohesive_index);
	mat_loc_num.clear();
	}
	}
	}

	SolidMechanicsModel::initMaterials();

	AKANTU_DEBUG_OUT();
	}

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

	SolidMechanicsModel::initModel();

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

	/// add cohesive type connectivity
	ElementType type = _not_defined;

	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) {
	type = *it;
	ElementType type_facet = Mesh::getFacetType(type);
	ElementType 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);

	registerFEEngineObject<MyFEEngineType>("FacetsFEEngine",
	mesh.getMeshFacets(),
	spatial_dimension - 1);

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

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelCohesive::limitInsertion(BC::Axis axis,
	Real first_limit,
	Real second_limit) {
	AKANTU_DEBUG_IN();
	inserter->setLimit(axis, first_limit, second_limit);
	AKANTU_DEBUG_OUT();
	}

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

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

	#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
	if (facet_stress_synchronizer != NULL) {
	DataAccessor * data_accessor = this;
	const ElementTypeMapArray<UInt> & rank_to_element = synch_parallel->getPrankToElement();

	facet_stress_synchronizer->updateFacetStressSynchronizer(*inserter,
	rank_to_element,
	*data_accessor);
	}
	#endif

	inserter->getMeshFacets().initElementTypeMapArray(facet_stress,
	2 * spatial_dimension * spatial_dimension,
	spatial_dimension - 1);

	resizeFacetStress();

	/// compute normals on facets
	computeNormals();

	initStressInterpolation();
	}

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

	inserter->limitCheckFacets();

	#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
	if (facet_stress_synchronizer != NULL) {
	DataAccessor * data_accessor = this;
	const ElementTypeMapArray<UInt> & rank_to_element = synch_parallel->getPrankToElement();

	facet_stress_synchronizer->updateFacetStressSynchronizer(*inserter,
	rank_to_element,
	*data_accessor);
	}
	#endif

	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);
	mesh_facets.initElementTypeMapArray(quad_facets,
	spatial_dimension, spatial_dimension - 1);

	getFEEngine("FacetsFEEngine").interpolateOnQuadraturePoints(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);

	mesh.initElementTypeMapArray(elements_quad_facets,
	spatial_dimension,
	spatial_dimension);

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

	GhostType elem_gt = *gt;

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

	for (; it != last; ++it) {
	ElementType type = *it;
	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
	Array<Element> & facet_to_element = mesh_facets.getSubelementToElement(type,
	elem_gt);
	UInt nb_facet_per_elem = facet_to_element.getNbComponent();

	Array<Real> & el_q_facet = elements_quad_facets(type, elem_gt);

	ElementType facet_type = Mesh::getFacetType(type);

	UInt nb_quad_per_facet =
	getFEEngine("FacetsFEEngine").getNbQuadraturePoints(facet_type);

	el_q_facet.resize(nb_element * nb_facet_per_elem * nb_quad_per_facet);

	for (UInt el = 0; el < nb_element; ++el) {
	for (UInt f = 0; f < nb_facet_per_elem; ++f) {
	Element global_facet_elem = facet_to_element(el, f);
	UInt global_facet = global_facet_elem.element;
	GhostType facet_gt = global_facet_elem.ghost_type;
	const Array<Real> & quad_f = quad_facets(facet_type, facet_gt);

	for (UInt q = 0; q < nb_quad_per_facet; ++q) {
	for (UInt s = 0; s < 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 (UInt m = 0; m < materials.size(); ++m) {
	try {
	MaterialCohesive & mat __attribute__((unused)) =
	dynamic_cast<MaterialCohesive &>(*materials[m]);
	} catch(std::bad_cast&) {
	/// initialize the interpolation function
	materials[m]->initElementalFieldInterpolation(elements_quad_facets);
	}
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelCohesive::updateResidual(bool need_initialize) {
	AKANTU_DEBUG_IN();

	if (need_initialize) initializeUpdateResidualData();

	// f -= fint
	std::vector<Material *>::iterator mat_it;
	for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
	try {
	MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(**mat_it);
	mat.computeTraction(_not_ghost);
	} catch (std::bad_cast & bce) { }
	}

	SolidMechanicsModel::updateResidual(false);

	for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
	try {
	MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(**mat_it);
	mat.computeEnergies();
	} catch (std::bad_cast & bce) { }
	}


	AKANTU_DEBUG_OUT();
	}

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

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

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

	mesh_facets.initElementTypeMapArray(tangents,
	tangent_components,
	spatial_dimension - 1);

	Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1);
	Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1);

	for (; it != last; ++it) {
	ElementType facet_type = *it;

	const Array<Real> & normals =
	getFEEngine("FacetsFEEngine").getNormalsOnQuadPoints(facet_type);

	UInt nb_quad = normals.getSize();

	Array<Real> & tang = tangents(facet_type);
	tang.resize(nb_quad);

	Real * normal_it = normals.storage();
	Real * tangent_it = tang.storage();

	/// compute first tangent
	for (UInt q = 0; q < nb_quad; ++q) {

	/// if normal is orthogonal to xy plane, arbitrarly define tangent
	if ( Math::are_float_equal(Math::norm2(normal_it), 0) )
	tangent_it[0] = 1;
	else
	Math::normal2(normal_it, tangent_it);

	normal_it += spatial_dimension;
	tangent_it += tangent_components;
	}

	/// compute second tangent (3D case)
	if (spatial_dimension == 3) {
	normal_it = normals.storage();
	tangent_it = tang.storage();

	for (UInt q = 0; q < nb_quad; ++q) {
	Math::normal3(normal_it, tangent_it, tangent_it + spatial_dimension);
	normal_it += spatial_dimension;
	tangent_it += tangent_components;
	}
	}
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelCohesive::interpolateStress() {
	for (UInt m = 0; m < materials.size(); ++m) {
	try {
	MaterialCohesive & mat __attribute__((unused)) =
	dynamic_cast<MaterialCohesive &>(*materials[m]);
	} catch(std::bad_cast&) {
	/// interpolate stress on facet quadrature points positions
	materials[m]->interpolateStressOnFacets(facet_stress);
	}
	}

	#if defined(AKANTU_DEBUG_TOOLS)
	debug::element_manager.printData(debug::_dm_model_cohesive,
	"Interpolated stresses before",
	facet_stress);
	#endif

	synch_registry->synchronize(_gst_smmc_facets_stress);

	#if defined(AKANTU_DEBUG_TOOLS)
	debug::element_manager.printData(debug::_dm_model_cohesive,
	"Interpolated stresses",
	facet_stress);
	#endif
	}

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

	for (UInt m = 0; m < materials.size(); ++m) {
	try {
	MaterialCohesive & mat_cohesive = dynamic_cast<MaterialCohesive &>(*materials[m]);
	/// check which not ghost cohesive elements are to be created
	mat_cohesive.checkInsertion();
	} catch(std::bad_cast&) { }
	}

	/* if(static and extrinsic) {
	check max mean stresses
	and change inserter.getInsertionFacets(type_facet);
	}
	*/

	/// communicate data among processors
	synch_registry->synchronize(_gst_smmc_facets);

	/// insert cohesive elements
	return inserter->insertElements();
	}

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

	#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
	updateCohesiveSynchronizers();
	#endif

	SolidMechanicsModel::onElementsAdded(element_list, event);

	#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
	if (cohesive_distributed_synchronizer != NULL)
	cohesive_distributed_synchronizer->computeAllBufferSizes(*this);
	#endif

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

	if (is_extrinsic) resizeFacetStress();

	AKANTU_DEBUG_OUT();
	}

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

	UInt nb_new_nodes = doubled_nodes.getSize();
	Array<UInt> nodes_list(nb_new_nodes);

	for (UInt n = 0; n < nb_new_nodes; ++n)
	nodes_list(n) = doubled_nodes(n, 1);

	SolidMechanicsModel::onNodesAdded(nodes_list, event);

	for (UInt n = 0; n < nb_new_nodes; ++n) {

	UInt old_node = doubled_nodes(n, 0);
	UInt new_node = doubled_nodes(n, 1);

	for (UInt dim = 0; dim < spatial_dimension; ++dim) {
	(displacement)(new_node, dim) = (displacement)(old_node, dim);
	(velocity) (new_node, dim) = (velocity) (old_node, dim);
	(acceleration)(new_node, dim) = (acceleration)(old_node, dim);
	(blocked_dofs)(new_node, dim) = (blocked_dofs)(old_node, dim);

	if (current_position)
	(current_position)(new_node, dim) = (current_position)(old_node, dim);

	if (increment_acceleration)
	(*increment_acceleration)(new_node, dim)
	= (*increment_acceleration)(old_node, dim);

	if (increment)
	(increment)(new_node, dim) = (increment)(old_node, dim);

	if (previous_displacement)
	(*previous_displacement)(new_node, dim)
	= (*previous_displacement)(old_node, dim);
	}
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelCohesive::onEndSolveStep(const AnalysisMethod & method) {

	AKANTU_DEBUG_IN();

	/******************************************************************************
	This is required because the Cauchy stress is the stress measure that is used
	to check the insertion of cohesive elements
	******************************************************************************/

	std::vector<Material *>::iterator mat_it;
	for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
	Material & mat = **mat_it;
	if(mat.isFiniteDeformation())
	mat.computeAllCauchyStresses(_not_ghost);
	}

	AKANTU_DEBUG_OUT();
	}


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

	stream << space << "SolidMechanicsModelCohesive [" << std::endl;

	SolidMechanicsModel::printself(stream, indent + 1);

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

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

	Mesh & mesh_facets = inserter->getMeshFacets();

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

	Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, ghost_type);
	Mesh::type_iterator end = mesh_facets.lastType(spatial_dimension - 1, ghost_type);
	for(; it != end; ++it) {
	ElementType type = *it;

	UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);

	UInt nb_quadrature_points =
	getFEEngine("FacetsFEEngine").getNbQuadraturePoints(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,
	const ElementKind & element_kind,
	bool padding_flag) {
	AKANTU_DEBUG_IN();

	ElementKind _element_kind = element_kind;
	if (dumper_name == "cohesive elements") {
	_element_kind = _ek_cohesive;
	}
	SolidMechanicsModel::addDumpGroupFieldToDumper(dumper_name,
	field_id,
	group_name,
	_element_kind,
	padding_flag);

	AKANTU_DEBUG_OUT();
	}

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

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

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



	__END_AKANTU__

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