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mesh_partition.cc
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			/**
			* @file mesh_partition.cc
			*
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Tue Aug 17 2010
			* @date last modification: Fri Jan 22 2016
			*
			* @brief implementation of common part of all partitioner
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2012, 2014, 2015 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 "mesh_partition.hh"
			#include "aka_iterators.hh"
			#include "aka_types.hh"
			#include "mesh_accessor.hh"
			#include "mesh_utils.hh"
			/* -------------------------------------------------------------------------- */
			#include <algorithm>
			#include <numeric>
			#include <unordered_map>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			MeshPartition::MeshPartition(const Mesh & mesh, UInt spatial_dimension,
			const ID & id, const MemoryID & memory_id)
			: Memory(id, memory_id), mesh(mesh), spatial_dimension(spatial_dimension),
			partitions("partition", id, memory_id),
			ghost_partitions("ghost_partition", id, memory_id),
			ghost_partitions_offset("ghost_partition_offset", id, memory_id),
			saved_connectivity("saved_connectivity", id, memory_id) {
			AKANTU_DEBUG_IN();

			UInt nb_total_element = 0;
			for (auto && type :
			mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
			linearized_offsets.push_back(std::make_pair(type, nb_total_element));
			nb_total_element += mesh.getConnectivity(type).size();
			}

			AKANTU_DEBUG_OUT();
			}

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

			/* -------------------------------------------------------------------------- */
			UInt MeshPartition::linearized(const Element & element) {
			auto it =
			std::find_if(linearized_offsets.begin(), linearized_offsets.end(),
			[&element](auto & a) { return a.first == element.type; });
			AKANTU_DEBUG_ASSERT(it != linearized_offsets.end(),
			"A bug might be crawling around this corner...");
			return (it->second + element.element);
			}

			/* -------------------------------------------------------------------------- */
			Element MeshPartition::unlinearized(UInt lin_element) {
			ElementType type{_not_defined};
			UInt offset{0};
			for (auto & pair : linearized_offsets) {
			if (lin_element < pair.second)
			continue;
			std::tie(type, offset) = pair;
			}

			return Element{type, lin_element - offset, _not_ghost};
			}

			/* -------------------------------------------------------------------------- */
			/**
			* TODO this function should most probably be rewritten in a more modern way
			* conversion in c++ of the GENDUALMETIS (mesh.c) function wrote by George in
			* Metis (University of Minnesota)
			*/
			void MeshPartition::buildDualGraph(Array<Int> & dxadj, Array<Int> & dadjncy,
			Array<Int> & edge_loads,
			const EdgeLoadFunctor & edge_load_func) {
			AKANTU_DEBUG_IN();

			std::map<ElementType, std::tuple<const Array<UInt> *, UInt, UInt>>
			connectivities;
			UInt spatial_dimension = mesh.getSpatialDimension();
			UInt nb_total_element{0};

			for (auto & type :
			mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
			auto type_p1 = mesh.getP1ElementType(type);
			auto nb_nodes_per_element_p1 = mesh.getNbNodesPerElement(type_p1);
			auto magic_number = mesh.getNbNodesPerElement(mesh.getFacetType(type_p1));

			const auto & conn = mesh.getConnectivity(type, _not_ghost);
			connectivities[type] = std::make_tuple(
			&conn, nb_nodes_per_element_p1, magic_number);
			nb_total_element += conn.size();
			}

			CSR<Element> node_to_elem;
			MeshUtils::buildNode2Elements(mesh, node_to_elem);

			dxadj.resize(nb_total_element + 1);
			/// initialize the dxadj array
			auto dxadj_it = dxadj.begin();
			for (auto & pair : connectivities) {
			const auto & connectivity = *std::get<0>(pair.second);
			auto nb_nodes_per_element_p1 = std::get<1>(pair.second);

			std::fill_n(dxadj_it, connectivity.size(), nb_nodes_per_element_p1);
			dxadj_it += connectivity.size();
			}

			/// convert the dxadj_val array in a csr one
			for (UInt i = 1; i < nb_total_element; ++i)
			dxadj(i) += dxadj(i - 1);
			for (UInt i = nb_total_element; i > 0; --i)
			dxadj(i) = dxadj(i - 1);
			dxadj(0) = 0;

			dadjncy.resize(2 * dxadj(nb_total_element));
			edge_loads.resize(2 * dxadj(nb_total_element));

			/// weight map to determine adjacency
			std::unordered_map<UInt, UInt> weight_map;

			for (auto & pair : connectivities) {
			auto type = pair.first;
			const auto & connectivity = *std::get<0>(pair.second);
			auto nb_nodes_per_element = std::get<1>(pair.second);
			auto magic_number = std::get<2>(pair.second);

			Element element{type, 0, _not_ghost};

			for (const auto & conn :
			make_view(connectivity, connectivity.getNbComponent())) {
			auto linearized_el = linearized(element);

			/// fill the weight map
			for (UInt n : arange(nb_nodes_per_element)) {
			auto && node = conn(n);
			for (auto k = node_to_elem.rbegin(node); k != node_to_elem.rend(node);
			--k) {
			auto & current_element = *k;
			auto current_el = linearized(current_element);
			AKANTU_DEBUG_ASSERT(current_el != UInt(-1),
			"Linearized element not found");
			if (current_el <= linearized_el)
			break;

			auto weight_map_insert =
			weight_map.insert(std::make_pair(current_el, 1));
			if (not weight_map_insert.second)
			(weight_map_insert.first->second)++;
			}
			}

			/// each element with a weight of the size of a facet are adjacent
			for (auto & weight_pair : weight_map) {
			auto & adjacent_el = weight_pair.first;
			auto magic = weight_pair.second;
			if (magic != magic_number)
			continue;

			#if defined(AKANTU_COHESIVE_ELEMENT)
			/// Patch in order to prevent neighboring cohesive elements
			/// from detecting each other
			auto adjacent_element = unlinearized(adjacent_el);

			auto el_kind = element.kind();
			auto adjacent_el_kind = adjacent_element.kind();

			if (el_kind == adjacent_el_kind && el_kind == _ek_cohesive)
			continue;
			#endif
			UInt index_adj = dxadj(adjacent_el)++;
			UInt index_lin = dxadj(linearized_el)++;

			dadjncy(index_lin) = adjacent_el;
			dadjncy(index_adj) = linearized_el;
			}

			element.element++;
			weight_map.clear();
			}
			}

			Int k_start = 0, linerized_el = 0, j = 0;
			for (auto & pair : connectivities) {
			const auto & connectivity = *std::get<0>(pair.second);
			auto nb_nodes_per_element_p1 = std::get<1>(pair.second);
			auto nb_element = connectivity.size();

			for (UInt el = 0; el < nb_element; ++el, ++linerized_el) {
			for (Int k = k_start; k < dxadj(linerized_el); ++k, ++j)
			dadjncy(j) = dadjncy(k);
			dxadj(linerized_el) = j;
			k_start += nb_nodes_per_element_p1;
			}
			}

			for (UInt i = nb_total_element; i > 0; --i)
			dxadj(i) = dxadj(i - 1);
			dxadj(0) = 0;

			UInt adj = 0;
			for (UInt i = 0; i < nb_total_element; ++i) {
			UInt nb_adj = dxadj(i + 1) - dxadj(i);
			for (UInt j = 0; j < nb_adj; ++j, ++adj) {
			Int el_adj_id = dadjncy(dxadj(i) + j);
			Element el = unlinearized(i);
			Element el_adj = unlinearized(el_adj_id);

			Int load = edge_load_func(el, el_adj);
			edge_loads(adj) = load;
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshPartition::fillPartitionInformation(
			const Mesh & mesh, const Int * linearized_partitions) {
			AKANTU_DEBUG_IN();

			CSR<Element> node_to_elem;

			MeshUtils::buildNode2Elements(mesh, node_to_elem);

			UInt linearized_el = 0;
			for (auto & type :
			mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
			UInt nb_element = mesh.getNbElement(type);
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			partitions.alloc(nb_element, 1, type, _not_ghost);
			auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
			ghost_part_csr.resizeRows(nb_element);

			ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
			ghost_partitions.alloc(0, 1, type, _ghost);

			const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);

			for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
			UInt part = linearized_partitions[linearized_el];

			partitions(type, _not_ghost)(el) = part;
			std::list<UInt> list_adj_part;
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			UInt node = connectivity.storage()[el * nb_nodes_per_element + n];
			CSR<Element>::iterator ne;
			for (ne = node_to_elem.begin(node); ne != node_to_elem.end(node);
			++ne) {
			const Element & adj_element = *ne;
			UInt adj_el = linearized(adj_element);
			UInt adj_part = linearized_partitions[adj_el];
			if (part != adj_part) {
			list_adj_part.push_back(adj_part);
			}
			}
			}

			list_adj_part.sort();
			list_adj_part.unique();

			for (auto & adj_part : list_adj_part) {
			ghost_part_csr.getRows().push_back(adj_part);
			ghost_part_csr.rowOffset(el)++;

			ghost_partitions(type, _ghost).push_back(adj_part);
			ghost_partitions_offset(type, _ghost)(el)++;
			}
			}

			ghost_part_csr.countToCSR();

			/// convert the ghost_partitions_offset array in an offset array
			Array<UInt> & ghost_partitions_offset_ptr =
			ghost_partitions_offset(type, _ghost);
			for (UInt i = 1; i < nb_element; ++i)
			ghost_partitions_offset_ptr(i) += ghost_partitions_offset_ptr(i - 1);
			for (UInt i = nb_element; i > 0; --i)
			ghost_partitions_offset_ptr(i) = ghost_partitions_offset_ptr(i - 1);
			ghost_partitions_offset_ptr(0) = 0;
			}

			// All Facets
			for (Int sp = spatial_dimension - 1; sp >= 0; --sp) {
			for (auto & type : mesh.elementTypes(sp, _not_ghost, _ek_not_defined)) {
			UInt nb_element = mesh.getNbElement(type);

			partitions.alloc(nb_element, 1, type, _not_ghost);
			AKANTU_DEBUG_INFO("Allocating partitions for " << type);
			auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
			ghost_part_csr.resizeRows(nb_element);

			ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
			ghost_partitions.alloc(0, 1, type, _ghost);
			AKANTU_DEBUG_INFO("Allocating ghost_partitions for " << type);
			const Array<std::vector<Element>> & elem_to_subelem =
			mesh.getElementToSubelement(type, _not_ghost);
			for (UInt i(0); i < mesh.getNbElement(type, _not_ghost);
			++i) { // Facet loop

			const std::vector<Element> & adjacent_elems = elem_to_subelem(i);
			if (!adjacent_elems.empty()) {
			Element min_elem{_max_element_type, std::numeric_limits<UInt>::max(),
			*ghost_type_t::end()};
			UInt min_part(std::numeric_limits<UInt>::max());
			std::set<UInt> adjacent_parts;

			for (UInt j(0); j < adjacent_elems.size(); ++j) {
			UInt adjacent_elem_id = adjacent_elems[j].element;
			UInt adjacent_elem_part =
			partitions(adjacent_elems[j].type,
			adjacent_elems[j].ghost_type)(adjacent_elem_id);
			if (adjacent_elem_part < min_part) {
			min_part = adjacent_elem_part;
			min_elem = adjacent_elems[j];
			}
			adjacent_parts.insert(adjacent_elem_part);
			}
			partitions(type, _not_ghost)(i) = min_part;

			auto git = ghost_partitions_csr(min_elem.type, _not_ghost)
			.begin(min_elem.element);
			auto gend = ghost_partitions_csr(min_elem.type, _not_ghost)
			.end(min_elem.element);
			for (; git != gend; ++git) {

			adjacent_parts.insert(min_part);
			}
			adjacent_parts.erase(min_part);
			for (auto & part : adjacent_parts) {
			ghost_part_csr.getRows().push_back(part);
			ghost_part_csr.rowOffset(i)++;
			ghost_partitions(type, _ghost).push_back(part);
			}

			ghost_partitions_offset(type, _ghost)(i + 1) =
			ghost_partitions_offset(type, _ghost)(i + 1) +
			adjacent_elems.size();
			} else {
			partitions(type, _not_ghost)(i) = 0;
			}
			}
			ghost_part_csr.countToCSR();
			}
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshPartition::tweakConnectivity(const Array<UInt> & pairs) {
			AKANTU_DEBUG_IN();

			if (pairs.size() == 0)
			return;

			Mesh::type_iterator it =
			mesh.firstType(spatial_dimension, _not_ghost, _ek_not_defined);
			Mesh::type_iterator end =
			mesh.lastType(spatial_dimension, _not_ghost, _ek_not_defined);

			for (; it != end; ++it) {
			ElementType type = *it;

			Array<UInt> & conn =
			const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost));
			UInt nb_nodes_per_element = conn.getNbComponent();
			UInt nb_element = conn.size();

			Array<UInt> & saved_conn = saved_connectivity.alloc(
			nb_element, nb_nodes_per_element, type, _not_ghost);
			saved_conn.copy(conn);

			for (UInt i = 0; i < pairs.size(); ++i) {
			for (UInt el = 0; el < nb_element; ++el) {
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			if (pairs(i, 1) == conn(el, n))
			conn(el, n) = pairs(i, 0);
			}
			}
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshPartition::restoreConnectivity() {
			AKANTU_DEBUG_IN();
			MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
			for (auto && type : saved_connectivity.elementTypes(
			spatial_dimension, _not_ghost, _ek_not_defined)) {
			auto & conn = mesh_accessor.getConnectivity(type, _not_ghost);
			auto & saved_conn = saved_connectivity(type, _not_ghost);
			conn.copy(saved_conn);
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			bool MeshPartition::hasPartitions(const ElementType & type,
			const GhostType & ghost_type) {
			return partitions.exists(type, ghost_type);
			}

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

			} // namespace akantu

rAKA/src/mesh_utils/mesh_partition.cc41a559eaea2cbugfixes/46-bug-in…

mesh_partition.ccView Options

rAKA/src/mesh_utils/mesh_partition.cc
41a559eaea2cbugfixes/46-bug-in…

mesh_partition.cc
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