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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: Mon Jul 21 2014
			*
			* @brief implementation of common part of all partitioner
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2012, 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 "mesh_partition.hh"
			#include "mesh_utils.hh"
			#include "aka_types.hh"
			/* -------------------------------------------------------------------------- */

			__BEGIN_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();

			AKANTU_DEBUG_OUT();
			}

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

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/**
			* 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();

			// tweak mesh;
			const Mesh::ConnectivityTypeList & type_list = mesh.getConnectivityTypeList();
			UInt nb_types = type_list.size();
			UInt nb_good_types = 0;

			UInt nb_nodes_per_element_p1[nb_types];

			UInt magic_number[nb_types];

			// UInt * conn_val[nb_types];
			UInt nb_element[nb_types];

			Array<UInt> * conn[nb_types];

			Array<Element> lin_to_element;

			Element elem;
			elem.ghost_type = _not_ghost;

			const_cast<Mesh &>(mesh).updateTypesOffsets(_not_ghost);
			const_cast<Mesh &>(mesh).updateTypesOffsets(_ghost);

			Mesh::ConnectivityTypeList::const_iterator it;
			for(it = type_list.begin(); it != type_list.end(); ++it) {
			ElementType type = *it;
			if(Mesh::getSpatialDimension(type) != mesh.getSpatialDimension()) continue;
			elem.type = type;

			ElementType type_p1 = Mesh::getP1ElementType(type);

			nb_nodes_per_element_p1[nb_good_types] = Mesh::getNbNodesPerElement(type_p1);
			nb_element[nb_good_types] = mesh.getConnectivity(type, _not_ghost).getSize();
			magic_number[nb_good_types] =
			Mesh::getNbNodesPerElement(Mesh::getFacetType(type_p1));

			conn[nb_good_types] = &const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost));

			for (UInt i = 0; i < nb_element[nb_good_types]; ++i) {
			elem.element = i;
			lin_to_element.push_back(elem);
			}

			nb_good_types++;
			}

			CSR<UInt> node_to_elem;

			MeshUtils::buildNode2Elements(mesh, node_to_elem);

			UInt nb_total_element = 0;
			UInt nb_total_node_element = 0;
			for (UInt t = 0; t < nb_good_types; ++t) {
			nb_total_element += nb_element[t];
			nb_total_node_element += nb_element[t]*nb_nodes_per_element_p1[t];
			}

			dxadj.resize(nb_total_element + 1);

			/// initialize the dxadj array
			for (UInt t = 0, linerized_el = 0; t < nb_good_types; ++t)
			for (UInt el = 0; el < nb_element[t]; ++el, ++linerized_el)
			dxadj(linerized_el) = nb_nodes_per_element_p1[t];

			/// 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
			unordered_map<UInt, UInt>::type weight_map;

			for (UInt t = 0, linerized_el = 0; t < nb_good_types; ++t) {
			for (UInt el = 0; el < nb_element[t]; ++el, ++linerized_el) {
			/// fill the weight map
			for (UInt n = 0; n < nb_nodes_per_element_p1[t]; ++n) {
			UInt node = (*conn[t])(el, n);
			CSR<UInt>::iterator k;
			for (k = node_to_elem.rbegin(node); k != node_to_elem.rend(node); --k) {
			UInt current_el = *k;
			if(current_el <= linerized_el) break;

			unordered_map<UInt, UInt>::type::iterator it_w;
			it_w = weight_map.find(current_el);

			if(it_w == weight_map.end()) {
			weight_map[current_el] = 1;
			} else {
			it_w->second++;
			}
			}
			}
			/// each element with a weight of the size of a facet are adjacent
			unordered_map<UInt, UInt>::type::iterator it_w;
			for(it_w = weight_map.begin(); it_w != weight_map.end(); ++it_w) {
			if(it_w->second == magic_number[t]) {
			UInt adjacent_el = it_w->first;

			#if defined(AKANTU_COHESIVE_ELEMENT)
			/// Patch in order to prevent neighboring cohesive elements
			/// from detecting each other
			ElementKind linearized_el_kind = mesh.linearizedToElement(linerized_el).kind;
			ElementKind adjacent_el_kind = mesh.linearizedToElement(adjacent_el).kind;

			if (linearized_el_kind == adjacent_el_kind &&
			linearized_el_kind == _ek_cohesive) continue;
			#endif

			UInt index_adj = dxadj(adjacent_el )++;
			UInt index_lin = dxadj(linerized_el)++;

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

			weight_map.clear();
			}
			}

			Int k_start = 0;
			for (UInt t = 0, linerized_el = 0, j = 0; t < nb_good_types; ++t)
			for (UInt el = 0; el < nb_element[t]; ++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[t];
			}

			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 = lin_to_element(i);
			Element el_adj = lin_to_element(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<UInt> node_to_elem;

			MeshUtils::buildNode2Elements(mesh, node_to_elem);

			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);

			UInt linearized_el = 0;
			for(; it != end; ++it) {
			ElementType type = *it;

			UInt nb_element = mesh.getNbElement(type);
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			partitions .alloc(nb_element, 1, type, _not_ghost);
			CSR<UInt> & 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<UInt>::iterator ne;
			for (ne = node_to_elem.begin(node); ne != node_to_elem.end(node); ++ne) {
			UInt adj_el = *ne;
			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(std::list<UInt>::iterator adj_it = list_adj_part.begin();
			adj_it != list_adj_part.end();
			++adj_it) {
			ghost_part_csr.getRows().push_back(*adj_it);
			ghost_part_csr.rowOffset(el)++;

			ghost_partitions(type, _ghost).push_back(*adj_it);
			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) {
			Mesh::type_iterator fit = mesh.firstType(sp,
			_not_ghost,
			_ek_not_defined);
			Mesh::type_iterator fend = mesh.lastType(sp,
			_not_ghost,
			_ek_not_defined);

			for(; fit != fend; ++fit) {
			ElementType type = *fit;

			UInt nb_element = mesh.getNbElement(type);

			partitions .alloc(nb_element, 1, type, _not_ghost);
			AKANTU_DEBUG_INFO("Allocating partitions for " << type);
			CSR<UInt> & 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;
			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;

			CSR<UInt>::iterator git = ghost_partitions_csr(min_elem.type, _not_ghost).begin(min_elem.element);
			CSR<UInt>::iterator gend = ghost_partitions_csr(min_elem.type, _not_ghost).end(min_elem.element);
			for(; git != gend; ++git) {
			adjacent_parts.insert(*git);
			}
			adjacent_parts.erase(min_part);
			std::set<UInt>::const_iterator pit = adjacent_parts.begin();
			std::set<UInt>::const_iterator pend = adjacent_parts.end();
			for(; pit != pend; ++pit) {
			ghost_part_csr.getRows().push_back(*pit);
			ghost_part_csr.rowOffset(i)++;
			ghost_partitions(type, _ghost).push_back(*pit);
			}

			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.getSize() == 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.getSize();

			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.getSize(); ++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();

			ElementTypeMapArray<UInt>::type_iterator it = saved_connectivity.firstType(spatial_dimension,
			_not_ghost,
			_ek_not_defined);
			ElementTypeMapArray<UInt>::type_iterator end = saved_connectivity.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));
			Array<UInt> & saved_conn = saved_connectivity(type, _not_ghost);
			conn.copy(saved_conn);
			}

			AKANTU_DEBUG_OUT();
			}

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

			__END_AKANTU__

rAKA/src/mesh_utils/mesh_partition.cc1a2d9c66bba6bugfixes/32-python…

mesh_partition.ccView Options

rAKA/src/mesh_utils/mesh_partition.cc
1a2d9c66bba6bugfixes/32-python…

mesh_partition.cc
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