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mesh_utils.cc
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			/**
			* @file mesh_utils.cc
			*
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author Dana Christen <dana.christen@epfl.ch>
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
			* @author Marco Vocialta <marco.vocialta@epfl.ch>
			*
			* @date creation: Fri Aug 20 2010
			* @date last modification: Wed Feb 21 2018
			*
			* @brief All mesh utils necessary for various tasks
			*
			*
			* 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 "element_synchronizer.hh"
			#include "fe_engine.hh"
			#include "mesh_accessor.hh"
			#include "mesh_iterators.hh"
			#include "mesh_utils.hh"
			/* -------------------------------------------------------------------------- */
			#include <limits>
			#include <numeric>
			#include <queue>
			#include <set>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			void MeshUtils::buildNode2Elements(const Mesh & mesh,
			CSR<Element> & node_to_elem,
			UInt spatial_dimension) {
			AKANTU_DEBUG_IN();
			if (spatial_dimension == _all_dimensions) {
			spatial_dimension = mesh.getSpatialDimension();
			}

			/// count number of occurrence of each node
			UInt nb_nodes = mesh.getNbNodes();

			/// array for the node-element list
			node_to_elem.resizeRows(nb_nodes);
			node_to_elem.clearRows();

			for_each_element(
			mesh,
			[&](auto && element) {
			Vector<UInt> conn = mesh.getConnectivity(element);
			for (auto && node : conn) {
			++node_to_elem.rowOffset(node);
			}
			},
			_spatial_dimension = spatial_dimension, _element_kind = _ek_not_defined);

			node_to_elem.countToCSR();
			node_to_elem.resizeCols();

			/// rearrange element to get the node-element list
			// Element e;
			node_to_elem.beginInsertions();

			for_each_element(
			mesh,
			[&](auto && element) {
			Vector<UInt> conn = mesh.getConnectivity(element);
			for (auto && node : conn) {
			node_to_elem.insertInRow(node, element);
			}
			},
			_spatial_dimension = spatial_dimension, _element_kind = _ek_not_defined);

			node_to_elem.endInsertions();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshUtils::buildNode2ElementsElementTypeMap(const Mesh & mesh,
			CSR<UInt> & node_to_elem,
			ElementType type,
			GhostType ghost_type) {
			AKANTU_DEBUG_IN();
			UInt nb_nodes = mesh.getNbNodes();

			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			UInt nb_elements = mesh.getConnectivity(type, ghost_type).size();

			UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();

			/// array for the node-element list
			node_to_elem.resizeRows(nb_nodes);
			node_to_elem.clearRows();

			/// count number of occurrence of each node
			for (UInt el = 0; el < nb_elements; ++el) {
			UInt el_offset = el * nb_nodes_per_element;
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			++node_to_elem.rowOffset(conn_val[el_offset + n]);
			}
			}

			/// convert the occurrence array in a csr one
			node_to_elem.countToCSR();

			node_to_elem.resizeCols();
			node_to_elem.beginInsertions();

			/// save the element index in the node-element list
			for (UInt el = 0; el < nb_elements; ++el) {
			UInt el_offset = el * nb_nodes_per_element;
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			node_to_elem.insertInRow(conn_val[el_offset + n], el);
			}
			}

			node_to_elem.endInsertions();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshUtils::buildFacets(Mesh & mesh) {
			AKANTU_DEBUG_IN();

			UInt spatial_dimension = mesh.getSpatialDimension();

			for (auto ghost_type : ghost_types) {
			for (const auto & type :
			mesh.elementTypes(spatial_dimension - 1, ghost_type)) {
			mesh.getConnectivity(type, ghost_type).resize(0);
			// \todo inform the mesh event handler
			}
			}

			buildFacetsDimension(mesh, mesh, true, spatial_dimension);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
			UInt to_dimension) {
			AKANTU_DEBUG_IN();

			UInt spatial_dimension = mesh.getSpatialDimension();

			buildAllFacets(mesh, mesh_facets, spatial_dimension, to_dimension);

			AKANTU_DEBUG_OUT();
			}
			/* -------------------------------------------------------------------------- */
			void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
			UInt from_dimension, UInt to_dimension) {
			AKANTU_DEBUG_IN();

			to_dimension = std::max(to_dimension, UInt(0));

			AKANTU_DEBUG_ASSERT(
			mesh_facets.isMeshFacets(),
			"The mesh_facets should be initialized with initMeshFacets");

			/// generate facets
			buildFacetsDimension(mesh, mesh_facets, false, from_dimension);

			/// sort facets and generate sub-facets
			for (UInt i = from_dimension - 1; i > to_dimension; --i) {
			buildFacetsDimension(mesh_facets, mesh_facets, false, i);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshUtils::buildFacetsDimension(const Mesh & mesh, Mesh & mesh_facets,
			bool boundary_only, UInt dimension) {
			AKANTU_DEBUG_IN();

			// save the current parent of mesh_facets and set it temporarly to mesh since
			// mesh is the one containing the elements for which mesh_facets has the
			// sub-elements
			// example: if the function is called with mesh = mesh_facets
			const Mesh * mesh_facets_parent = nullptr;
			try {
			mesh_facets_parent = &mesh_facets.getMeshParent();
			} catch (...) {
			}

			mesh_facets.defineMeshParent(mesh);
			MeshAccessor mesh_accessor(mesh_facets);

			UInt spatial_dimension = mesh.getSpatialDimension();

			const Array<Real> & mesh_facets_nodes = mesh_facets.getNodes();
			const auto mesh_facets_nodes_it = mesh_facets_nodes.begin(spatial_dimension);

			CSR<Element> node_to_elem;
			buildNode2Elements(mesh, node_to_elem, dimension);

			Array<UInt> counter;
			std::vector<Element> connected_elements;

			NewElementsEvent event(AKANTU_CURRENT_FUNCTION);

			// init the SubelementToElement data to improve performance
			for (auto && ghost_type : ghost_types) {
			for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
			auto & subelement_to_element =
			mesh_accessor.getSubelementToElement(type, ghost_type);
			subelement_to_element.resize(mesh.getNbElement(type, ghost_type),
			ElementNull);

			auto facet_types = mesh.getAllFacetTypes(type);

			for (auto && ft : arange(facet_types.size())) {
			auto facet_type = facet_types(ft);
			mesh_accessor.getElementToSubelement(facet_type, ghost_type);
			mesh_accessor.getConnectivity(facet_type, ghost_type);
			}
			}
			}

			const ElementSynchronizer * synchronizer = nullptr;
			if (mesh.isDistributed()) {
			synchronizer = &(mesh.getElementSynchronizer());
			}

			Element current_element;
			for (auto && ghost_type : ghost_types) {
			GhostType facet_ghost_type = ghost_type;
			current_element.ghost_type = ghost_type;

			for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
			auto facet_types = mesh.getAllFacetTypes(type);
			current_element.type = type;

			for (auto && ft : arange(facet_types.size())) {
			auto facet_type = facet_types(ft);
			auto nb_element = mesh.getNbElement(type, ghost_type);

			auto && element_to_subelement =
			&mesh_accessor.getElementToSubelementNC(facet_type, ghost_type);
			auto && connectivity_facets =
			&mesh_accessor.getConnectivity(facet_type, ghost_type);

			auto nb_nodes_per_facet = connectivity_facets->getNbComponent();
			// Vector<UInt> facet(nb_nodes_per_facet);

			for (UInt el = 0; el < nb_element; ++el) {
			current_element.element = el;

			auto && facets =
			mesh.getFacetConnectivity(current_element, ft).transpose();

			for (auto facet : facets) {
			// facet = facets(f);

			UInt first_node_nb_elements = node_to_elem.getNbCols(facet(0));
			counter.resize(first_node_nb_elements);
			counter.zero();

			// loop over the other nodes to search intersecting elements,
			// which are the elements that share another node with the
			// starting element after first_node
			for (auto && data : enumerate(node_to_elem.getRow(facet(0)))) {
			auto && local_el = std::get<0>(data);
			auto && first_node = std::get<1>(data);
			for (auto n : arange(1, nb_nodes_per_facet)) {
			auto && node_elements = node_to_elem.getRow(facet(n));
			counter(local_el) += std::count(
			node_elements.begin(), node_elements.end(), first_node);
			}
			}

			// counting the number of elements connected to the facets and
			// taking the minimum element number, because the facet should
			// be inserted just once
			UInt nb_element_connected_to_facet = 0;
			Element minimum_el = ElementNull;
			connected_elements.clear();
			for (auto && data : enumerate(node_to_elem.getRow(facet(0)))) {

			if (not(counter(std::get<0>(data)) == nb_nodes_per_facet - 1)) {
			continue;
			}

			auto && real_el = std::get<1>(data);

			++nb_element_connected_to_facet;
			minimum_el = std::min(minimum_el, real_el);
			connected_elements.push_back(real_el);
			}

			if (minimum_el != current_element) {
			continue;
			}

			bool full_ghost_facet = false;

			UInt n = 0;
			while (n < nb_nodes_per_facet and mesh.isPureGhostNode(facet(n))) {
			++n;
			}
			if (n == nb_nodes_per_facet) {
			full_ghost_facet = true;
			}

			if (full_ghost_facet) {
			continue;
			}

			if (boundary_only and nb_element_connected_to_facet != 1) {
			continue;
			}

			std::vector<Element> elements;

			// build elements_on_facets: linearized_el must come first
			// in order to store the facet in the correct direction
			// and avoid to invert the sign in the normal computation
			elements.reserve(elements.size() + connected_elements.size());
			for (auto && connected_element : connected_elements) {
			elements.push_back(connected_element);
			}

			if (nb_element_connected_to_facet == 1) { /// boundary facet
			elements.push_back(ElementNull);
			} else if (nb_element_connected_to_facet == 2) { /// internal facet
			/// check if facet is in between ghost and normal
			/// elements: if it's the case, the facet is either
			/// ghost or not ghost. The criterion to decide this
			/// is arbitrary. It was chosen to check the processor
			/// id (prank) of the two neighboring elements. If
			/// prank of the ghost element is lower than prank of
			/// the normal one, the facet is not ghost, otherwise
			/// it's ghost
			GhostType gt[2] = {_not_ghost, _not_ghost};

			for (UInt el = 0; el < connected_elements.size(); ++el) {
			gt[el] = connected_elements[el].ghost_type;
			}

			if ((gt[0] == _not_ghost) xor (gt[1] == _not_ghost)) {
			UInt prank[2];
			for (UInt el = 0; el < 2; ++el) {
			prank[el] = synchronizer->getRank(connected_elements[el]);
			}

			// ugly trick from Marco detected :P
			bool ghost_one = (gt[0] != _ghost);
			if (prank[ghost_one] > prank[!ghost_one]) {
			facet_ghost_type = _not_ghost;
			} else {
			facet_ghost_type = _ghost;
			}

			connectivity_facets = &mesh_accessor.getConnectivity(
			facet_type, facet_ghost_type);
			element_to_subelement = &mesh_accessor.getElementToSubelementNC(
			facet_type, facet_ghost_type);
			}
			}

			element_to_subelement->push_back(elements);
			connectivity_facets->push_back(facet);

			/// current facet index
			UInt current_facet = connectivity_facets->size() - 1;
			Element facet_element{facet_type, current_facet, facet_ghost_type};
			event.getList().push_back(facet_element);
			/// loop on every element connected to current facet and
			/// insert current facet in the first free spot of the
			/// subelement_to_element vector
			for (auto & loc_el : elements) {
			if (loc_el == ElementNull) {
			continue;
			}

			auto && subelements =
			mesh_accessor.getSubelementToElement(loc_el);

			for (auto & el : subelements) {
			if (el != ElementNull) {
			continue;
			}

			el = facet_element;
			break;
			}
			}

			/// reset connectivity in case a facet was found in
			/// between ghost and normal elements
			if (facet_ghost_type != ghost_type) {
			facet_ghost_type = ghost_type;
			connectivity_facets =
			&mesh_accessor.getConnectivity(facet_type, facet_ghost_type);
			element_to_subelement = &mesh_accessor.getElementToSubelement(
			facet_type, facet_ghost_type);
			}
			}
			}
			}
			}
			}

			mesh_facets.sendEvent(event);

			// restore the parent of mesh_facet
			if (mesh_facets_parent != nullptr) {
			mesh_facets.defineMeshParent(*mesh_facets_parent);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshUtils::renumberMeshNodes(Mesh & mesh,
			Array<UInt> & local_connectivities,
			UInt nb_local_element, UInt nb_ghost_element,
			ElementType type,
			Array<UInt> & old_nodes_numbers) {
			AKANTU_DEBUG_IN();

			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			std::map<UInt, UInt> renumbering_map;
			for (UInt i = 0; i < old_nodes_numbers.size(); ++i) {
			renumbering_map[old_nodes_numbers(i)] = i;
			}

			/// renumber the nodes
			renumberNodesInConnectivity(local_connectivities,
			(nb_local_element + nb_ghost_element) *
			nb_nodes_per_element,
			renumbering_map);

			old_nodes_numbers.resize(renumbering_map.size());
			for (auto & renumber_pair : renumbering_map) {
			old_nodes_numbers(renumber_pair.second) = renumber_pair.first;
			}
			renumbering_map.clear();

			MeshAccessor mesh_accessor(mesh);

			/// copy the renumbered connectivity to the right place
			auto & local_conn = mesh_accessor.getConnectivity(type);
			local_conn.resize(nb_local_element);

			if (nb_local_element > 0) {
			memcpy(local_conn.storage(), local_connectivities.storage(),
			nb_local_element * nb_nodes_per_element * sizeof(UInt));
			}

			auto & ghost_conn = mesh_accessor.getConnectivity(type, _ghost);
			ghost_conn.resize(nb_ghost_element);

			if (nb_ghost_element > 0) {
			std::memcpy(ghost_conn.storage(),
			local_connectivities.storage() +
			nb_local_element * nb_nodes_per_element,
			nb_ghost_element * nb_nodes_per_element * sizeof(UInt));
			}

			auto & ghost_counter = mesh_accessor.getGhostsCounters(type, _ghost);
			ghost_counter.resize(nb_ghost_element, 1);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshUtils::renumberNodesInConnectivity(
			Array<UInt> & list_nodes, UInt nb_nodes,
			std::map<UInt, UInt> & renumbering_map) {
			AKANTU_DEBUG_IN();

			UInt * connectivity = list_nodes.storage();
			UInt new_node_num = renumbering_map.size();
			for (UInt n = 0; n < nb_nodes; ++n, ++connectivity) {
			UInt & node = *connectivity;
			auto it = renumbering_map.find(node);
			if (it == renumbering_map.end()) {
			UInt old_node = node;
			renumbering_map[old_node] = new_node_num;
			node = new_node_num;
			++new_node_num;
			} else {
			node = it->second;
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshUtils::purifyMesh(Mesh & mesh) {
			AKANTU_DEBUG_IN();

			std::map<UInt, UInt> renumbering_map;

			RemovedNodesEvent remove_nodes(mesh, AKANTU_CURRENT_FUNCTION);
			Array<UInt> & nodes_removed = remove_nodes.getList();

			for (auto ghost_type : ghost_types) {
			for (auto type :
			mesh.elementTypes(_all_dimensions, ghost_type, _ek_not_defined)) {
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
			UInt nb_element(connectivity.size());

			renumberNodesInConnectivity(
			connectivity, nb_element * nb_nodes_per_element, renumbering_map);
			}
			}

			Array<UInt> & new_numbering = remove_nodes.getNewNumbering();
			std::fill(new_numbering.begin(), new_numbering.end(), UInt(-1));

			for (auto && pair : renumbering_map) {
			new_numbering(std::get<0>(pair)) = std::get<1>(pair);
			}

			for (UInt i = 0; i < new_numbering.size(); ++i) {
			if (new_numbering(i) == UInt(-1)) {
			nodes_removed.push_back(i);
			}
			}

			mesh.sendEvent(remove_nodes);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshUtils::flipFacets(
			Mesh & mesh_facets,
			const ElementTypeMapArray<UInt> & remote_global_connectivities,
			GhostType gt_facet) {
			AKANTU_DEBUG_IN();

			UInt spatial_dimension = mesh_facets.getSpatialDimension();

			/// get global connectivity for local mesh
			ElementTypeMapArray<UInt> local_global_connectivities(
			"local_global_connectivity", mesh_facets.getID(),
			mesh_facets.getMemoryID());

			local_global_connectivities.initialize(
			mesh_facets, _spatial_dimension = spatial_dimension - 1,
			_ghost_type = gt_facet, _with_nb_nodes_per_element = true,
			_with_nb_element = true);

			mesh_facets.getGlobalConnectivity(local_global_connectivities);
			MeshAccessor mesh_accessor(mesh_facets);

			/// loop on every facet
			for (auto type_facet :
			mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {

			auto & connectivity = mesh_accessor.getConnectivity(type_facet, gt_facet);
			auto & local_global_connectivity =
			local_global_connectivities(type_facet, gt_facet);
			const auto & remote_global_connectivity =
			remote_global_connectivities(type_facet, gt_facet);

			auto & element_per_facet =
			mesh_accessor.getElementToSubelementNC(type_facet, gt_facet);
			auto & subfacet_to_facet =
			mesh_accessor.getSubelementToElementNC(type_facet, gt_facet);

			auto nb_nodes_per_facet = connectivity.getNbComponent();
			auto nb_nodes_per_P1_facet =
			Mesh::getNbNodesPerElement(Mesh::getP1ElementType(type_facet));

			for (auto && data :
			zip(make_view(connectivity, nb_nodes_per_facet),
			make_view(local_global_connectivity, nb_nodes_per_facet),
			make_view(remote_global_connectivity, nb_nodes_per_facet),
			make_view(subfacet_to_facet, subfacet_to_facet.getNbComponent()),
			make_view(element_per_facet))) {

			auto & conn = std::get<0>(data);
			auto & local_gconn = std::get<1>(data);
			const auto & remote_gconn = std::get<2>(data);

			/// skip facet if connectivities are the same
			if (local_gconn == remote_gconn) {
			continue;
			}

			/// re-arrange connectivity
			auto conn_tmp = conn;
			auto begin = local_gconn.begin();
			auto end = local_gconn.end();

			AKANTU_DEBUG_ASSERT(std::is_permutation(begin, end, remote_gconn.begin()),
			"This facets are not just permutation of each other, "
			<< local_gconn << " and " << remote_gconn);

			for (auto && data : enumerate(remote_gconn)) {
			auto it = std::find(begin, end, std::get<1>(data));
			AKANTU_DEBUG_ASSERT(it != end, "Node not found");
			UInt new_position = it - begin;
			conn(new_position) = conn_tmp(std::get<0>(data));
			;
			}
			// std::transform(remote_gconn.begin(), remote_gconn.end(), conn.begin(),
			// [&](auto && gnode) {
			// auto it = std::find(begin, end, gnode);
			// AKANTU_DEBUG_ASSERT(it != end, "Node not found");
			// return conn_tmp(it - begin);
			// });

			/// if 3D, check if facets are just rotated
			if (spatial_dimension == 3) {
			auto begin = remote_gconn.begin();
			/// find first node
			auto it = std::find(begin, remote_gconn.end(), local_gconn(0));

			UInt n;
			UInt start = it - begin;
			/// count how many nodes in the received connectivity follow
			/// the same order of those in the local connectivity
			for (n = 1; n < nb_nodes_per_P1_facet &&
			local_gconn(n) ==
			remote_gconn((start + n) % nb_nodes_per_P1_facet);
			++n) {
			;
			}

			/// skip the facet inversion if facet is just rotated
			if (n == nb_nodes_per_P1_facet) {
			continue;
			}
			}

			/// update data to invert facet
			auto & element_per_facet = std::get<4>(data);
			if (element_per_facet[1] !=
			ElementNull) { // by convention the first facet
			// cannot be a ElementNull
			std::swap(element_per_facet[0], element_per_facet[1]);
			}

			auto & subfacets_of_facet = std::get<3>(data);
			std::swap(subfacets_of_facet(0), subfacets_of_facet(1));
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshUtils::fillElementToSubElementsData(Mesh & mesh) {
			AKANTU_DEBUG_IN();

			if (mesh.getNbElement(mesh.getSpatialDimension() - 1) == 0) {
			AKANTU_DEBUG_INFO("There are not facets, add them in the mesh file or call "
			"the buildFacet method.");
			return;
			}

			UInt spatial_dimension = mesh.getSpatialDimension();
			ElementTypeMapArray<Real> barycenters("barycenter_tmp", mesh.getID(),
			mesh.getMemoryID());
			barycenters.initialize(mesh, _nb_component = spatial_dimension,
			_spatial_dimension = _all_dimensions);

			Element element;
			for (auto ghost_type : ghost_types) {
			element.ghost_type = ghost_type;
			for (const auto & type : mesh.elementTypes(_all_dimensions, ghost_type)) {
			element.type = type;

			UInt nb_element = mesh.getNbElement(type, ghost_type);
			Array<Real> & barycenters_arr = barycenters(type, ghost_type);
			barycenters_arr.resize(nb_element);
			auto bary = barycenters_arr.begin(spatial_dimension);
			auto bary_end = barycenters_arr.end(spatial_dimension);

			for (UInt el = 0; bary != bary_end; ++bary, ++el) {
			element.element = el;
			mesh.getBarycenter(element, *bary);
			}
			}
			}

			MeshAccessor mesh_accessor(mesh);
			for (Int sp(spatial_dimension); sp >= 1; --sp) {
			if (mesh.getNbElement(sp) == 0) {
			continue;
			}

			for (auto ghost_type : ghost_types) {
			for (auto & type : mesh.elementTypes(sp, ghost_type)) {
			auto & subelement_to_element =
			mesh_accessor.getSubelementToElement(type, ghost_type);
			subelement_to_element.resize(mesh.getNbElement(type, ghost_type));
			subelement_to_element.set(ElementNull);
			}

			for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
			auto & element_to_subelement =
			mesh_accessor.getElementToSubelement(type, ghost_type);
			element_to_subelement.resize(mesh.getNbElement(type, ghost_type));
			element_to_subelement.clear();
			}
			}

			CSR<Element> nodes_to_elements;
			buildNode2Elements(mesh, nodes_to_elements, sp);

			Element facet_element;

			for (auto ghost_type : ghost_types) {
			facet_element.ghost_type = ghost_type;
			for (const auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
			facet_element.type = type;

			auto & element_to_subelement =
			mesh_accessor.getElementToSubelement(type, ghost_type);

			const auto & connectivity = mesh.getConnectivity(type, ghost_type);
			//element_to_subelement.resize(connectivity.size());

			for (auto && data : enumerate(
			make_view(connectivity, mesh.getNbNodesPerElement(type)))) {
			const auto & facet = std::get<1>(data);
			facet_element.element = std::get<0>(data);

			std::map<Element, UInt> element_seen_counter;
			auto nb_nodes_per_facet =
			mesh.getNbNodesPerElement(Mesh::getP1ElementType(type));

			// count the number of node in common between the facet and the
			// other element connected to the nodes of the facet
			for (auto node : arange(nb_nodes_per_facet)) {
			for (auto & elem : nodes_to_elements.getRow(facet(node))) {
			auto cit = element_seen_counter.find(elem);
			if (cit != element_seen_counter.end()) {
			cit->second++;
			} else {
			element_seen_counter[elem] = 1;
			}
			}
			}

			// check which are the connected elements
			std::vector<Element> connected_elements;
			for (auto && cit : element_seen_counter) {
			if (cit.second == nb_nodes_per_facet) {
			connected_elements.push_back(cit.first);
			}
			}

			// add the connected elements as sub-elements
			for (auto & connected_element : connected_elements) {
			element_to_subelement(facet_element.element)
			.push_back(connected_element);
			}

			// add the element as sub-element to the connected elements
			for (auto & connected_element : connected_elements) {
			Vector<Element> subelements_to_element =
			mesh.getSubelementToElement(connected_element);

			// find the position where to insert the element
			auto it = std::find(subelements_to_element.begin(),
			subelements_to_element.end(), ElementNull);

			AKANTU_DEBUG_ASSERT(
			it != subelements_to_element.end(),
			"The element "
			<< connected_element << " seems to have too many facets!! ("
			<< (it - subelements_to_element.begin()) << " < "
			<< mesh.getNbFacetsPerElement(connected_element.type)
			<< ")");

			*it = facet_element;
			}
			}
			}
			}
			}

			AKANTU_DEBUG_OUT();
			}

			} // namespace akantu

rAKA/src/mesh_utils/mesh_utils.ccb56858367c28bugfixes/39-the-python…

mesh_utils.ccView Options

rAKA/src/mesh_utils/mesh_utils.cc
b56858367c28bugfixes/39-the-python…

mesh_utils.cc
View Options