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mesh.cc
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			/**
			* @file mesh.cc
			*
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Mohit Pundir <mohit.pundir@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			* @author Marco Vocialta <marco.vocialta@epfl.ch>
			*
			* @date creation: Fri Jun 18 2010
			* @date last modification: Tue Feb 09 2021
			*
			* @brief class handling meshes
			*
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2021 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 "aka_config.hh"
			/* -------------------------------------------------------------------------- */
			#include "element_class.hh"
			#include "group_manager_inline_impl.hh"
			#include "mesh.hh"
			#include "mesh_global_data_updater.hh"
			#include "mesh_io.hh"
			#include "mesh_iterators.hh"
			#include "mesh_utils.hh"
			/* -------------------------------------------------------------------------- */
			#include "communicator.hh"
			#include "element_synchronizer.hh"
			#include "facet_synchronizer.hh"
			#include "mesh_utils_distribution.hh"
			#include "node_synchronizer.hh"
			#include "periodic_node_synchronizer.hh"
			/* -------------------------------------------------------------------------- */
			#include <algorithm>
			/* -------------------------------------------------------------------------- */

			#ifdef AKANTU_USE_IOHELPER
			#include "dumper_field.hh"
			#include "dumper_internal_material_field.hh"
			#endif
			/* -------------------------------------------------------------------------- */
			#include <limits>
			#include <sstream>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			Mesh::Mesh(UInt spatial_dimension, const ID & id, Communicator & communicator)
			: GroupManager(*this, id + ":group_manager"), MeshData("mesh_data", id),
			id(id), connectivities("connectivities", id),
			ghosts_counters("ghosts_counters", id), normals("normals", id),
			spatial_dimension(spatial_dimension), size(spatial_dimension, 0.),
			bbox(spatial_dimension), bbox_local(spatial_dimension),
			communicator(&communicator) {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			Mesh::Mesh(UInt spatial_dimension, Communicator & communicator, const ID & id)
			: Mesh(spatial_dimension, id, communicator) {
			AKANTU_DEBUG_IN();

			this->nodes =
			std::make_shared<Array<Real>>(0, spatial_dimension, id + ":coordinates");
			this->nodes_flags = std::make_shared<Array<NodeFlag>>(0, 1, NodeFlag::_normal,
			id + ":nodes_flags");

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			Mesh::Mesh(UInt spatial_dimension, const ID & id)
			: Mesh(spatial_dimension, Communicator::getStaticCommunicator(), id) {}

			/* -------------------------------------------------------------------------- */
			Mesh::Mesh(UInt spatial_dimension, const std::shared_ptr<Array<Real>> & nodes,
			const ID & id)
			: Mesh(spatial_dimension, id, Communicator::getStaticCommunicator()) {
			this->nodes = nodes;

			this->nb_global_nodes = this->nodes->size();

			this->nodes_to_elements.resize(nodes->size());
			for (auto & node_set : nodes_to_elements) {
			node_set = std::make_unique<std::set<Element>>();
			}

			this->computeBoundingBox();
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::getBarycenters(Array<Real> & barycenter, ElementType type,
			GhostType ghost_type) const {
			barycenter.resize(getNbElement(type, ghost_type));
			for (auto && data : enumerate(make_view(barycenter, spatial_dimension))) {
			getBarycenter(Element{type, UInt(std::get<0>(data)), ghost_type},
			std::get<1>(data));
			}
			}

			class FacetGlobalConnectivityAccessor : public DataAccessor<Element> {
			public:
			FacetGlobalConnectivityAccessor(Mesh & mesh)
			: global_connectivity("global_connectivity",
			"facet_connectivity_synchronizer") {
			global_connectivity.initialize(
			mesh, _spatial_dimension = _all_dimensions, _with_nb_element = true,
			_with_nb_nodes_per_element = true, _element_kind = _ek_regular);
			mesh.getGlobalConnectivity(global_connectivity);
			}

			UInt getNbData(const Array<Element> & elements,
			const SynchronizationTag & tag) const override {
			UInt size = 0;
			if (tag == SynchronizationTag::_smmc_facets_conn) {
			UInt nb_nodes = Mesh::getNbNodesPerElementList(elements);
			size += nb_nodes * sizeof(UInt);
			}
			return size;
			}

			void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
			const SynchronizationTag & tag) const override {
			if (tag == SynchronizationTag::_smmc_facets_conn) {
			for (const auto & element : elements) {
			const auto & conns =
			global_connectivity(element.type, element.ghost_type);
			for (auto n : arange(conns.getNbComponent())) {
			buffer << conns(element.element, n);
			}
			}
			}
			}

			void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
			const SynchronizationTag & tag) override {
			if (tag == SynchronizationTag::_smmc_facets_conn) {
			for (const auto & element : elements) {
			auto & conns = global_connectivity(element.type, element.ghost_type);
			for (auto n : arange(conns.getNbComponent())) {
			buffer >> conns(element.element, n);
			}
			}
			}
			}

			AKANTU_GET_MACRO(GlobalConnectivity, (global_connectivity), decltype(auto));

			protected:
			ElementTypeMapArray<UInt> global_connectivity;
			};

			/* -------------------------------------------------------------------------- */
			Mesh & Mesh::initMeshFacets(const ID & id) {
			AKANTU_DEBUG_IN();

			if (mesh_facets) {
			AKANTU_DEBUG_OUT();
			return *mesh_facets;
			}

			mesh_facets = std::make_unique<Mesh>(spatial_dimension, this->nodes,
			getID() + ":" + id);

			mesh_facets->mesh_parent = this;
			mesh_facets->is_mesh_facets = true;
			mesh_facets->nodes_flags = this->nodes_flags;
			mesh_facets->nodes_global_ids = this->nodes_global_ids;

			MeshUtils::buildAllFacets(this, mesh_facets, 0);

			if (mesh.isDistributed()) {
			mesh_facets->is_distributed = true;
			mesh_facets->element_synchronizer = std::make_unique<FacetSynchronizer>(
			*mesh_facets, mesh.getElementSynchronizer());

			FacetGlobalConnectivityAccessor data_accessor(*mesh_facets);
			/// communicate
			mesh_facets->element_synchronizer->synchronizeOnce(
			data_accessor, SynchronizationTag::_smmc_facets_conn);

			/// flip facets
			MeshUtils::flipFacets(*mesh_facets, data_accessor.getGlobalConnectivity(),
			_ghost);
			}

			/// transfers the the mesh physical names to the mesh facets
			if (not this->hasData("physical_names")) {
			AKANTU_DEBUG_OUT();
			return *mesh_facets;
			}

			auto & mesh_phys_data = this->getData<std::string>("physical_names");
			auto & phys_data = mesh_facets->getData<std::string>("physical_names");
			phys_data.initialize(*mesh_facets, _spatial_dimension = spatial_dimension - 1,
			_with_nb_element = true);

			ElementTypeMapArray<Real> barycenters(getID(), "temporary_barycenters");
			barycenters.initialize(*mesh_facets, _nb_component = spatial_dimension,
			_spatial_dimension = spatial_dimension - 1,
			_with_nb_element = true);

			for (auto && ghost_type : ghost_types) {
			for (auto && type :
			barycenters.elementTypes(spatial_dimension - 1, ghost_type)) {
			mesh_facets->getBarycenters(barycenters(type, ghost_type), type,
			ghost_type);
			}
			}

			for_each_element(
			mesh,
			[&](auto && element) {
			Vector<Real> barycenter(spatial_dimension);
			mesh.getBarycenter(element, barycenter);
			auto norm_barycenter = barycenter.norm();
			auto tolerance = Math::getTolerance();
			if (norm_barycenter > tolerance) {
			tolerance *= norm_barycenter;
			}

			Vector<Real> barycenter_facet(spatial_dimension);

			auto range = enumerate(make_view(
			barycenters(element.type, element.ghost_type), spatial_dimension));
			#ifndef AKANTU_NDEBUG
			auto min_dist = std::numeric_limits<Real>::max();
			#endif
			// this is a spacial search coded the most inefficient way.
			auto facet =
			std::find_if(range.begin(), range.end(), [&](auto && data) {
			auto norm_distance = barycenter.distance(std::get<1>(data));
			#ifndef AKANTU_NDEBUG
			min_dist = std::min(min_dist, norm_distance);
			#endif
			return (norm_distance < tolerance);
			});

			if (facet == range.end()) {
			AKANTU_DEBUG_INFO("The element "
			<< element
			<< " did not find its associated facet in the "
			"mesh_facets! Try to decrease math tolerance. "
			"The closest element was at a distance of "
			<< min_dist);
			return;
			}

			// set physical name
			auto && facet_element = Element{element.type, UInt(std::get<0>(*facet)),
			element.ghost_type};
			phys_data(facet_element) = mesh_phys_data(element);
			},
			_spatial_dimension = spatial_dimension - 1);

			mesh_facets->createGroupsFromMeshData<std::string>("physical_names");

			AKANTU_DEBUG_OUT();
			return *mesh_facets;
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::defineMeshParent(const Mesh & mesh) {
			AKANTU_DEBUG_IN();

			this->mesh_parent = &mesh;
			this->is_mesh_facets = true;

			AKANTU_DEBUG_OUT();
			}

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

			/* -------------------------------------------------------------------------- */
			void Mesh::read(const std::string & filename, const MeshIOType & mesh_io_type) {

			AKANTU_DEBUG_ASSERT(not is_distributed,
			"You cannot read a mesh that is already distributed");

			MeshIO::read(filename, *this, mesh_io_type);

			auto types =
			this->elementTypes(spatial_dimension, _not_ghost, _ek_not_defined);
			auto it = types.begin();
			auto last = types.end();
			if (it == last) {
			AKANTU_DEBUG_WARNING(
			"The mesh contained in the file "
			<< filename << " does not seem to be of the good dimension."
			<< " No element of dimension " << spatial_dimension << " were read.");
			}

			this->makeReady();
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::write(const std::string & filename,
			const MeshIOType & mesh_io_type) {
			MeshIO::write(filename, *this, mesh_io_type);
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::makeReady() {
			this->nb_global_nodes = this->nodes->size();
			this->computeBoundingBox();
			this->nodes_flags->resize(nodes->size(), NodeFlag::_normal);
			this->nodes_to_elements.resize(nodes->size());
			for (auto & node_set : nodes_to_elements) {
			node_set = std::make_unique<std::set<Element>>();
			}
			}

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

			stream << space << "Mesh [" << std::endl;
			stream << space << " + id : " << getID() << std::endl;
			stream << space << " + spatial dimension : " << this->spatial_dimension
			<< std::endl;
			stream << space << " + nodes [" << std::endl;
			nodes->printself(stream, indent + 2);
			stream << space << " + connectivities [" << std::endl;
			connectivities.printself(stream, indent + 2);
			stream << space << " ]" << std::endl;

			GroupManager::printself(stream, indent + 1);
			stream << space << "]" << std::endl;
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::computeBoundingBox() {
			AKANTU_DEBUG_IN();

			bbox_local.reset();

			for (auto & pos : make_view(*nodes, spatial_dimension)) {
			// if(!isPureGhostNode(i))
			bbox_local += pos;
			}

			if (this->is_distributed) {
			bbox = bbox_local.allSum(*communicator);
			} else {
			bbox = bbox_local;
			}

			size = bbox.size();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::initNormals() {
			normals.initialize(*this, _nb_component = spatial_dimension,
			_spatial_dimension = spatial_dimension,
			_element_kind = _ek_not_defined);
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::getGlobalConnectivity(
			ElementTypeMapArray<UInt> & global_connectivity) {
			AKANTU_DEBUG_IN();

			for (auto && ghost_type : ghost_types) {
			for (auto type :
			global_connectivity.elementTypes(_spatial_dimension = _all_dimensions,
			_element_kind = _ek_not_defined, _ghost_type = ghost_type)) {
			if (not connectivities.exists(type, ghost_type)) {
			continue;
			}

			auto & local_conn = connectivities(type, ghost_type);
			auto & g_connectivity = global_connectivity(type, ghost_type);

			UInt nb_nodes = local_conn.size() * local_conn.getNbComponent();

			std::transform(local_conn.begin_reinterpret(nb_nodes),
			local_conn.end_reinterpret(nb_nodes),
			g_connectivity.begin_reinterpret(nb_nodes),
			[&](UInt l) -> UInt { return this->getNodeGlobalId(l); });
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			DumperIOHelper & Mesh::getGroupDumper(const std::string & dumper_name,
			const std::string & group_name) {
			if (group_name == "all") {
			return this->getDumper(dumper_name);
			}
			return element_groups[group_name]->getDumper(dumper_name);
			}

			/* -------------------------------------------------------------------------- */
			template <typename T>
			ElementTypeMap<UInt> Mesh::getNbDataPerElem(ElementTypeMapArray<T> & arrays) {
			ElementTypeMap<UInt> nb_data_per_elem;

			for (auto type : arrays.elementTypes(_element_kind = _ek_not_defined)) {
			UInt nb_elements = this->getNbElement(type);
			auto & array = arrays(type);

			nb_data_per_elem(type) = array.getNbComponent() * array.size();
			nb_data_per_elem(type) /= nb_elements;
			}

			return nb_data_per_elem;
			}

			/* -------------------------------------------------------------------------- */
			template ElementTypeMap<UInt>
			Mesh::getNbDataPerElem(ElementTypeMapArray<Real> & array);

			template ElementTypeMap<UInt>
			Mesh::getNbDataPerElem(ElementTypeMapArray<UInt> & array);

			/* -------------------------------------------------------------------------- */
			#ifdef AKANTU_USE_IOHELPER
			template <typename T>
			std::shared_ptr<dumpers::Field>
			Mesh::createFieldFromAttachedData(const std::string & field_id,
			const std::string & group_name,
			ElementKind element_kind) {

			std::shared_ptr<dumpers::Field> field;
			ElementTypeMapArray<T> * internal = nullptr;
			try {
			internal = &(this->getData<T>(field_id));
			} catch (...) {
			return nullptr;
			}

			ElementTypeMap<UInt> nb_data_per_elem = this->getNbDataPerElem(*internal);

			field = this->createElementalField<T, dumpers::InternalMaterialField>(
			*internal, group_name, this->spatial_dimension, element_kind,
			nb_data_per_elem);

			return field;
			}

			template std::shared_ptr<dumpers::Field>
			Mesh::createFieldFromAttachedData<Real>(const std::string & field_id,
			const std::string & group_name,
			ElementKind element_kind);

			template std::shared_ptr<dumpers::Field>
			Mesh::createFieldFromAttachedData<UInt>(const std::string & field_id,
			const std::string & group_name,
			ElementKind element_kind);
			#endif

			/* -------------------------------------------------------------------------- */
			void Mesh::distributeImpl(
			Communicator & communicator,
			const std::function<Int(const Element &, const Element &)> &
			edge_weight_function [[gnu::unused]],
			const std::function<Int(const Element &)> & vertex_weight_function
			[[gnu::unused]]) {
			AKANTU_DEBUG_ASSERT(is_distributed == false,
			"This mesh is already distribute");
			this->communicator = &communicator;

			this->element_synchronizer = std::make_unique<ElementSynchronizer>(
			*this, this->getID() + ":element_synchronizer", true);

			this->node_synchronizer = std::make_unique<NodeSynchronizer>(
			*this, this->getID() + ":node_synchronizer", true);

			Int psize = this->communicator->getNbProc();

			if (psize > 1) {
			#ifdef AKANTU_USE_SCOTCH
			Int prank = this->communicator->whoAmI();
			if (prank == 0) {
			MeshPartitionScotch partition(*this, spatial_dimension);
			partition.partitionate(psize, edge_weight_function,
			vertex_weight_function);

			MeshUtilsDistribution::distributeMeshCentralized(*this, 0, partition);
			} else {
			MeshUtilsDistribution::distributeMeshCentralized(*this, 0);
			}
			#else
			if (psize > 1) {
			AKANTU_ERROR("Cannot distribute a mesh without a partitioning tool");
			}
			#endif
			}

			// if (psize > 1)
			this->is_distributed = true;

			this->computeBoundingBox();
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::getAssociatedElements(const Array<UInt> & node_list,
			Array<Element> & elements) const {
			for (const auto & node : node_list) {
			for (const auto & element : *nodes_to_elements[node]) {
			elements.push_back(element);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::getAssociatedElements(const UInt & node,
			Array<Element> & elements) const {
			for (const auto & element : *nodes_to_elements[node]) {
			elements.push_back(element);
			}
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::fillNodesToElements(UInt dimension) {
			Element e;

			UInt nb_nodes = nodes->size();
			this->nodes_to_elements.resize(nb_nodes);

			for (UInt n = 0; n < nb_nodes; ++n) {
			if (this->nodes_to_elements[n]) {
			this->nodes_to_elements[n]->clear();
			} else {
			this->nodes_to_elements[n] = std::make_unique<std::set<Element>>();
			}
			}

			for (auto ghost_type : ghost_types) {
			e.ghost_type = ghost_type;
			for (const auto & type :
			elementTypes(dimension, ghost_type, _ek_not_defined)) {
			e.type = type;

			UInt nb_element = this->getNbElement(type, ghost_type);
			auto connectivity = connectivities(type, ghost_type);
			auto conn_it = connectivity.begin(connectivity.getNbComponent());

			for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
			e.element = el;
			const Vector<UInt> & conn = *conn_it;
			for (auto node : conn) {
			nodes_to_elements[node]->insert(e);
			}
			}
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			std::tuple<UInt, UInt>
			Mesh::updateGlobalData(NewNodesEvent & nodes_event,
			NewElementsEvent & elements_event) {
			if (global_data_updater) {
			return this->global_data_updater->updateData(nodes_event, elements_event);
			}
			return std::make_tuple(nodes_event.getList().size(),
			elements_event.getList().size());
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::registerGlobalDataUpdater(
			std::unique_ptr<MeshGlobalDataUpdater> && global_data_updater) {
			this->global_data_updater = std::move(global_data_updater);
			}

			/* -------------------------------------------------------------------------- */
			void Mesh::eraseElements(const Array<Element> & elements) {
			ElementTypeMap<UInt> last_element;

			RemovedElementsEvent event(*this, "new_numbering", AKANTU_CURRENT_FUNCTION);
			auto & remove_list = event.getList();
			auto & new_numbering = event.getNewNumbering();

			for (auto && el : elements) {
			if (el.ghost_type != _not_ghost) {
			auto & count = ghosts_counters(el);
			--count;
			if (count > 0) {
			continue;
			}
			}

			remove_list.push_back(el);
			if (not new_numbering.exists(el.type, el.ghost_type)) {
			auto nb_element = mesh.getNbElement(el.type, el.ghost_type);
			auto & numbering =
			new_numbering.alloc(nb_element, 1, el.type, el.ghost_type);
			for (auto && pair : enumerate(numbering)) {
			std::get<1>(pair) = std::get<0>(pair);
			}
			}

			new_numbering(el) = UInt(-1);
			}

			auto find_last_not_deleted = [](auto && array, Int start) -> Int {
			do {
			--start;
			} while (start >= 0 and array[start] == UInt(-1));

			return start;
			};

			auto find_first_deleted = [](auto && array, Int start) -> Int {
			auto begin = array.begin();
			auto it = std::find_if(begin + start, array.end(),
			[](auto & el) { return el == UInt(-1); });
			return Int(it - begin);
			};

			for (auto ghost_type : ghost_types) {
			for (auto type : new_numbering.elementTypes(_ghost_type = ghost_type)) {
			auto & numbering = new_numbering(type, ghost_type);
			auto last_not_delete = find_last_not_deleted(numbering, numbering.size());

			if (last_not_delete < 0) {
			continue;
			}

			auto pos = find_first_deleted(numbering, 0);

			while (pos < last_not_delete) {
			std::swap(numbering[pos], numbering[last_not_delete]);
			last_not_delete = find_last_not_deleted(numbering, last_not_delete);
			pos = find_first_deleted(numbering, pos + 1);
			}
			}
			}
			this->sendEvent(event);
			}

			} // namespace akantu

rAKA/src/mesh/mesh.ccaf0351339c8fbugfixes/32-python…

mesh.ccView Options

rAKA/src/mesh/mesh.cc
af0351339c8fbugfixes/32-python…

mesh.cc
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