mesh.cc
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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 Nicolas Richart <nicolas.richart@epfl.ch>
	* @author Marco Vocialta <marco.vocialta@epfl.ch>
	*
	* @date creation: Fri Jun 18 2010
	* @date last modification: Tue Feb 20 2018
	*
	* @brief class handling meshes
	*
	*
	* 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 "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)
	: EventHandlerManager<MeshEventHandler, Mesh>(*this),
	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;
	}

	const auto & element_to_facet = mesh_facets->getElementToSubelement(
	element.type, element.ghost_type);

	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 facet = std::get<0>(data);
	if (element_to_facet(facet)[1] == ElementNull) {
	return false;
	}

	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) {
	for (const auto & node : node_list) {
	for (const auto & element : *nodes_to_elements[node]) {
	elements.push_back(element);
	}
	}
	}

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

	UInt nb_nodes = nodes->size();
	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(spatial_dimension, ghost_type, _ek_not_defined)) {
	e.type = type;

	UInt nb_element = this->getNbElement(type, ghost_type);
	Array<UInt>::const_iterator<Vector<UInt>> conn_it =
	connectivities(type, ghost_type)
	.begin(Mesh::getNbNodesPerElement(type));

	for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
	e.element = el;
	const Vector<UInt> & conn = *conn_it;
	for (UInt n = 0; n < conn.size(); ++n) {
	nodes_to_elements[conn(n)]->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

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