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group_manager.cc
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			/**
			* @file group_manager.cc
			*
			* @author Dana Christen <dana.christen@gmail.com>
			* @author Marco Vocialta <marco.vocialta@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			* @author David Simon Kammer <david.kammer@epfl.ch>
			*
			* @date creation: Fri May 03 2013
			* @date last modification: Tue Sep 02 2014
			*
			* @brief Stores information about ElementGroup and NodeGroup
			*
			* @section LICENSE
			*
			* Copyright (©) 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 "group_manager.hh"
			#include "mesh.hh"
			#include "aka_csr.hh"
			#include "mesh_utils.hh"

			#include "element_group.hh"
			#include "node_group.hh"
			#include "data_accessor.hh"
			#include "distributed_synchronizer.hh"

			/* -------------------------------------------------------------------------- */
			#include <sstream>
			#include <algorithm>
			#include <iterator>
			#include <list>
			#include <queue>
			#include <numeric>
			/* -------------------------------------------------------------------------- */

			__BEGIN_AKANTU__

			/* -------------------------------------------------------------------------- */
			GroupManager::GroupManager(const Mesh & mesh,
			const ID & id,
			const MemoryID & mem_id) : id(id),
			memory_id(mem_id),
			mesh(mesh) {

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			GroupManager::~GroupManager() {
			ElementGroups::iterator eit = element_groups.begin();
			ElementGroups::iterator eend = element_groups.end();
			for(; eit != eend ; ++eit) delete (eit->second);

			NodeGroups::iterator nit = node_groups.begin();
			NodeGroups::iterator nend = node_groups.end();
			for(; nit != nend ; ++nit) delete (nit->second);
			}

			/* -------------------------------------------------------------------------- */
			NodeGroup & GroupManager::createNodeGroup(const std::string & group_name,
			bool replace_group) {
			AKANTU_DEBUG_IN();

			NodeGroups::iterator it = node_groups.find(group_name);

			if(it != node_groups.end()) {
			if (replace_group) {
			it->second->empty();
			AKANTU_DEBUG_OUT();
			return *(it->second);
			}
			else
			AKANTU_EXCEPTION("Trying to create a node group that already exists:" << group_name);
			}

			NodeGroup * node_group = new NodeGroup(group_name, id + ":" + group_name + "_node_group",
			memory_id);

			node_groups[group_name] = node_group;

			AKANTU_DEBUG_OUT();

			return *node_group;
			}

			/* -------------------------------------------------------------------------- */
			template<typename T>
			NodeGroup & GroupManager::createFilteredNodeGroup(const std::string & group_name,
			const NodeGroup & source_node_group,
			T & filter) {
			AKANTU_DEBUG_IN();

			NodeGroup & node_group = this->createNodeGroup(group_name);
			node_group.append(source_node_group);
			if (T::type == FilterFunctor::_node_filter_functor) {
			node_group.applyNodeFilter(filter);
			}
			else {
			AKANTU_DEBUG_ERROR("ElementFilter cannot be applied to NodeGroup yet."
			<< " Needs to be implemented.");
			}

			AKANTU_DEBUG_OUT();
			return node_group;
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::destroyNodeGroup(const std::string & group_name) {
			AKANTU_DEBUG_IN();

			NodeGroups::iterator nit = node_groups.find(group_name);
			NodeGroups::iterator nend = node_groups.end();
			if (nit != nend) {
			delete (nit->second);
			node_groups.erase(nit);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
			UInt dimension,
			bool replace_group) {
			AKANTU_DEBUG_IN();

			NodeGroup & new_node_group = createNodeGroup(group_name + "_nodes", replace_group);

			ElementGroups::iterator it = element_groups.find(group_name);

			if(it != element_groups.end()) {
			if (replace_group) {
			it->second->empty();
			AKANTU_DEBUG_OUT();
			return *(it->second);
			}
			else
			AKANTU_EXCEPTION("Trying to create a element group that already exists:" << group_name);
			}

			ElementGroup * element_group = new ElementGroup(group_name, mesh, new_node_group,
			dimension,
			id + ":" + group_name + "_element_group",
			memory_id);

			node_groups[group_name + "_nodes"] = &new_node_group;
			element_groups[group_name] = element_group;

			AKANTU_DEBUG_OUT();

			return *element_group;
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::destroyElementGroup(const std::string & group_name,
			bool destroy_node_group) {
			AKANTU_DEBUG_IN();

			ElementGroups::iterator eit = element_groups.find(group_name);
			ElementGroups::iterator eend = element_groups.end();
			if (eit != eend) {
			if (destroy_node_group)
			destroyNodeGroup(eit->second->getNodeGroup().getName());
			delete (eit->second);
			element_groups.erase(eit);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::destroyAllElementGroups(bool destroy_node_groups) {
			AKANTU_DEBUG_IN();

			ElementGroups::iterator eit = element_groups.begin();
			ElementGroups::iterator eend = element_groups.end();
			for(; eit != eend ; ++eit) {
			if (destroy_node_groups)
			destroyNodeGroup(eit->second->getNodeGroup().getName());
			delete (eit->second);
			}
			element_groups.clear();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
			UInt dimension,
			NodeGroup & node_group) {
			AKANTU_DEBUG_IN();

			if(element_groups.find(group_name) != element_groups.end())
			AKANTU_EXCEPTION("Trying to create a element group that already exists:" << group_name);

			ElementGroup * element_group = new ElementGroup(group_name, mesh, node_group,
			dimension,
			id + ":" + group_name + "_element_group",
			memory_id);

			element_groups[group_name] = element_group;

			AKANTU_DEBUG_OUT();

			return *element_group;
			}

			/* -------------------------------------------------------------------------- */
			template <typename T>
			ElementGroup & GroupManager::createFilteredElementGroup(const std::string & group_name,
			UInt dimension,
			const NodeGroup & node_group,
			T & filter) {
			AKANTU_DEBUG_IN();

			ElementGroup * element_group = NULL;

			if (T::type == FilterFunctor::_node_filter_functor) {
			NodeGroup & filtered_node_group = this->createFilteredNodeGroup(group_name + "_nodes",
			node_group,
			filter);
			element_group = &(this->createElementGroup(group_name,
			dimension,
			filtered_node_group));
			}
			else if (T::type == FilterFunctor::_element_filter_functor) {
			AKANTU_DEBUG_ERROR("Cannot handle an ElementFilter yet. Needs to be implemented.");
			}

			AKANTU_DEBUG_OUT();

			return *element_group;
			}

			/* -------------------------------------------------------------------------- */
			class ClusterSynchronizer : public DataAccessor {
			typedef std::set< std::pair<UInt, UInt> > DistantIDs;

			public:
			ClusterSynchronizer(GroupManager & group_manager,
			UInt element_dimension,
			std::string cluster_name_prefix,
			ElementTypeMapArray<UInt> & element_to_fragment,
			DistributedSynchronizer & distributed_synchronizer,
			UInt nb_cluster) :
			group_manager(group_manager),
			element_dimension(element_dimension),
			cluster_name_prefix(cluster_name_prefix),
			element_to_fragment(element_to_fragment),
			distributed_synchronizer(distributed_synchronizer),
			nb_cluster(nb_cluster) { }

			UInt synchronize() {
			StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
			UInt rank = comm.whoAmI();
			UInt nb_proc = comm.getNbProc();

			/// find starting index to renumber local clusters
			Array<UInt> nb_cluster_per_proc(nb_proc);
			nb_cluster_per_proc(rank) = nb_cluster;
			comm.allGather(nb_cluster_per_proc.storage(), 1);

			starting_index = std::accumulate(nb_cluster_per_proc.begin(),
			nb_cluster_per_proc.begin() + rank,
			0);

			UInt global_nb_fragment = std::accumulate(nb_cluster_per_proc.begin() + rank,
			nb_cluster_per_proc.end(),
			starting_index);

			/// create the local to distant cluster pairs with neighbors
			distributed_synchronizer.computeBufferSize(*this, _gst_gm_clusters);
			distributed_synchronizer.asynchronousSynchronize(*this, _gst_gm_clusters);
			distributed_synchronizer.waitEndSynchronize(*this, _gst_gm_clusters);

			/// count total number of pairs
			Array<Int> nb_pairs(nb_proc);
			nb_pairs(rank) = distant_ids.size();
			comm.allGather(nb_pairs.storage(), 1);

			UInt total_nb_pairs = std::accumulate(nb_pairs.begin(), nb_pairs.end(), 0);

			/// generate pairs global array
			UInt local_pair_index = std::accumulate(nb_pairs.storage(),
			nb_pairs.storage() + rank, 0);

			Array<UInt> total_pairs(total_nb_pairs, 2);

			DistantIDs::iterator ids_it = distant_ids.begin();
			DistantIDs::iterator ids_end = distant_ids.end();

			for (; ids_it != ids_end; ++ids_it, ++local_pair_index) {
			total_pairs(local_pair_index, 0) = ids_it->first;
			total_pairs(local_pair_index, 1) = ids_it->second;
			}

			/// communicate pairs to all processors
			nb_pairs *= 2;
			comm.allGatherV(total_pairs.storage(), nb_pairs.storage());

			/// renumber clusters

			/// generate fragment list
			std::vector< std::set<UInt> > global_clusters;
			UInt total_nb_cluster = 0;

			Array<bool> is_fragment_in_cluster(global_nb_fragment, 1, false);
			std::queue<UInt> fragment_check_list;

			while (total_pairs.getSize() != 0) {
			/// create a new cluster
			++total_nb_cluster;
			global_clusters.resize(total_nb_cluster);
			std::set<UInt> & current_cluster = global_clusters[total_nb_cluster - 1];

			UInt first_fragment = total_pairs(0, 0);
			UInt second_fragment = total_pairs(0, 1);
			total_pairs.erase(0);

			fragment_check_list.push(first_fragment);
			fragment_check_list.push(second_fragment);

			while (!fragment_check_list.empty()) {
			UInt current_fragment = fragment_check_list.front();

			UInt * total_pairs_end = total_pairs.storage() + total_pairs.getSize() * 2;

			UInt * fragment_found = std::find(total_pairs.storage(),
			total_pairs_end,
			current_fragment);

			if (fragment_found != total_pairs_end) {
			UInt position = fragment_found - total_pairs.storage();
			UInt pair = position / 2;
			UInt other_index = (position + 1) % 2;
			fragment_check_list.push(total_pairs(pair, other_index));
			total_pairs.erase(pair);
			}
			else {
			fragment_check_list.pop();
			current_cluster.insert(current_fragment);
			is_fragment_in_cluster(current_fragment) = true;
			}
			}
			}

			/// add to FragmentToCluster all local fragments
			for (UInt c = 0; c < global_nb_fragment; ++c) {
			if (!is_fragment_in_cluster(c)) {
			++total_nb_cluster;
			global_clusters.resize(total_nb_cluster);
			std::set<UInt> & current_cluster = global_clusters[total_nb_cluster - 1];

			current_cluster.insert(c);
			}
			}

			/// reorganize element groups to match global clusters
			for (UInt c = 0; c < global_clusters.size(); ++c) {

			/// create new element group corresponding to current cluster
			std::stringstream sstr;
			sstr << cluster_name_prefix << "_" << c;
			ElementGroup & cluster = group_manager.createElementGroup(sstr.str(),
			element_dimension,
			true);

			std::set<UInt>::iterator it = global_clusters[c].begin();
			std::set<UInt>::iterator end = global_clusters[c].end();

			/// append to current element group all fragments that belong to
			/// the same cluster if they exist
			for (; it != end; ++it) {
			Int local_index = *it - starting_index;

			if (local_index < 0 \|\| local_index >= Int(nb_cluster)) continue;

			std::stringstream tmp_sstr;
			tmp_sstr << "tmp_" << cluster_name_prefix << "_" << local_index;
			GroupManager::element_group_iterator eg_it
			= group_manager.element_group_find(tmp_sstr.str());

			AKANTU_DEBUG_ASSERT(eg_it != group_manager.element_group_end(),
			"Temporary fragment \""<< tmp_sstr.str() << "\" not found");

			cluster.append(*(eg_it->second));
			group_manager.destroyElementGroup(tmp_sstr.str(), true);
			}
			}

			return total_nb_cluster;
			}

			private:
			/// functions for parallel communications
			inline UInt getNbDataForElements(const Array<Element> & elements,
			SynchronizationTag tag) const {
			if (tag == _gst_gm_clusters)
			return elements.getSize() * sizeof(UInt);

			return 0;
			}

			inline void packElementData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			SynchronizationTag tag) const {
			if (tag != _gst_gm_clusters) return;

			Array<Element>::const_iterator<> el_it = elements.begin();
			Array<Element>::const_iterator<> el_end = elements.end();

			for (; el_it != el_end; ++el_it) {

			const Element & el = *el_it;

			/// for each element pack its global cluster index
			buffer << element_to_fragment(el.type, el.ghost_type)(el.element) + starting_index;
			}
			}

			inline void unpackElementData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			SynchronizationTag tag) {
			if (tag != _gst_gm_clusters) return;

			Array<Element>::const_iterator<> el_it = elements.begin();
			Array<Element>::const_iterator<> el_end = elements.end();

			for (; el_it != el_end; ++el_it) {
			UInt distant_cluster;

			buffer >> distant_cluster;

			const Element & el = *el_it;
			UInt local_cluster = element_to_fragment(el.type, el.ghost_type)(el.element) + starting_index;

			distant_ids.insert(std::make_pair(local_cluster, distant_cluster));
			}
			}

			private:
			GroupManager & group_manager;
			UInt element_dimension;
			std::string cluster_name_prefix;
			ElementTypeMapArray<UInt> & element_to_fragment;
			DistributedSynchronizer & distributed_synchronizer;

			UInt nb_cluster;
			DistantIDs distant_ids;

			UInt starting_index;
			};

			/* -------------------------------------------------------------------------- */
			/// \todo this function doesn't work in 1D
			UInt GroupManager::createBoundaryGroupFromGeometry() {
			UInt spatial_dimension = mesh.getSpatialDimension();

			return createClusters(spatial_dimension - 1, "boundary");
			}

			/* -------------------------------------------------------------------------- */
			//// \todo if needed element list construction can be optimized by
			//// templating the filter class
			UInt GroupManager::createClusters(UInt element_dimension,
			std::string cluster_name_prefix,
			const GroupManager::ClusteringFilter & filter,
			DistributedSynchronizer * distributed_synchronizer,
			Mesh * mesh_facets) {
			AKANTU_DEBUG_IN();

			UInt nb_proc = StaticCommunicator::getStaticCommunicator().getNbProc();
			std::string tmp_cluster_name_prefix = cluster_name_prefix;

			ElementTypeMapArray<UInt> * element_to_fragment = NULL;

			if (nb_proc > 1 && distributed_synchronizer) {
			element_to_fragment = new ElementTypeMapArray<UInt>;
			mesh.initElementTypeMapArray(*element_to_fragment, 1, element_dimension,
			false, _ek_not_defined, true);
			tmp_cluster_name_prefix = "tmp_" + tmp_cluster_name_prefix;
			}

			/// Get facets
			bool mesh_facets_created = false;

			if (!mesh_facets && element_dimension > 0) {
			mesh_facets = new Mesh(mesh.getSpatialDimension(),
			mesh.getNodes().getID(),
			"mesh_facets_for_clusters");

			mesh_facets->defineMeshParent(mesh);

			MeshUtils::buildAllFacets(mesh, *mesh_facets,
			element_dimension,
			element_dimension - 1,
			distributed_synchronizer);
			}

			ElementTypeMapArray<bool> seen_elements("seen_elements");
			mesh.initElementTypeMapArray(seen_elements, 1, element_dimension,
			false, _ek_not_defined, true);

			for (ghost_type_t::iterator gt = ghost_type_t::begin();
			gt != ghost_type_t::end(); ++gt) {

			GhostType ghost_type = *gt;
			Element el;
			el.ghost_type = ghost_type;

			Mesh::type_iterator type_it = mesh.firstType(element_dimension,
			ghost_type, _ek_not_defined);
			Mesh::type_iterator type_end = mesh.lastType (element_dimension,
			ghost_type, _ek_not_defined);

			for (; type_it != type_end; ++type_it) {
			el.type = *type_it;
			el.kind = Mesh::getKind(*type_it);
			UInt nb_element = mesh.getNbElement(*type_it, ghost_type);
			Array<bool> & seen_elements_array = seen_elements(el.type, ghost_type);

			for (UInt e = 0; e < nb_element; ++e) {
			el.element = e;
			if (!filter(el))
			seen_elements_array(e) = true;
			}
			}
			}

			Array<bool> checked_node(mesh.getNbNodes(), 1, false);

			UInt nb_cluster = 0;

			/// keep looping until all elements are seen
			for (ghost_type_t::iterator gt = ghost_type_t::begin();
			gt != ghost_type_t::end(); ++gt) {

			GhostType ghost_type = *gt;
			Element uns_el;
			uns_el.ghost_type = ghost_type;

			Mesh::type_iterator type_it = mesh.firstType(element_dimension,
			ghost_type,
			_ek_not_defined);
			Mesh::type_iterator type_end = mesh.lastType(element_dimension,
			ghost_type,
			_ek_not_defined);

			for (; type_it != type_end; ++type_it) {
			uns_el.type = *type_it;
			Array<bool> & seen_elements_vec = seen_elements(uns_el.type, uns_el.ghost_type);

			for (UInt e = 0; e < seen_elements_vec.getSize(); ++e) {
			// skip elements that have been already seen
			if (seen_elements_vec(e) == true) continue;

			// set current element
			uns_el.element = e;
			seen_elements_vec(e) = true;

			/// create a new cluster
			std::stringstream sstr;
			sstr << tmp_cluster_name_prefix << "_" << nb_cluster;
			ElementGroup & cluster = createElementGroup(sstr.str(),
			element_dimension,
			true);
			++nb_cluster;

			// point element are cluster by themself
			if(element_dimension == 0) {
			cluster.add(uns_el);

			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(uns_el.type);
			Vector<UInt> connect =
			mesh.getConnectivity(uns_el.type, uns_el.ghost_type).begin(nb_nodes_per_element)[uns_el.element];
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			/// add element's nodes to the cluster
			UInt node = connect[n];
			if (!checked_node(node)) {
			cluster.addNode(node);
			checked_node(node) = true;
			}
			}

			continue;
			}

			std::queue<Element> element_to_add;
			element_to_add.push(uns_el);

			/// keep looping until current cluster is complete (no more
			/// connected elements)
			while(!element_to_add.empty()) {

			/// take first element and erase it in the queue
			Element el = element_to_add.front();
			element_to_add.pop();

			/// if parallel, store cluster index per element
			if (nb_proc > 1 && distributed_synchronizer)
			(*element_to_fragment)(el.type, el.ghost_type)(el.element) = nb_cluster - 1;

			/// add current element to the cluster
			cluster.add(el);

			const Array<Element> & element_to_facet
			= mesh_facets->getSubelementToElement(el.type, el.ghost_type);

			UInt nb_facet_per_element = element_to_facet.getNbComponent();

			for (UInt f = 0; f < nb_facet_per_element; ++f) {
			const Element & facet = element_to_facet(el.element, f);

			if (facet == ElementNull) continue;

			const std::vector<Element> & connected_elements
			= mesh_facets->getElementToSubelement(facet.type, facet.ghost_type)(facet.element);

			for (UInt elem = 0; elem < connected_elements.size(); ++elem) {
			const Element & check_el = connected_elements[elem];

			// check if this element has to be skipped
			if (check_el == ElementNull \|\| check_el == el) continue;

			Array<bool> & seen_elements_vec_current
			= seen_elements(check_el.type, check_el.ghost_type);

			if (seen_elements_vec_current(check_el.element) == false) {
			seen_elements_vec_current(check_el.element) = true;
			element_to_add.push(check_el);
			}
			}
			}


			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
			Vector<UInt> connect =
			mesh.getConnectivity(el.type, el.ghost_type).begin(nb_nodes_per_element)[el.element];
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			/// add element's nodes to the cluster
			UInt node = connect[n];
			if (!checked_node(node)) {
			cluster.addNode(node, false);
			checked_node(node) = true;
			}
			}
			}
			}
			}
			}

			if (nb_proc > 1 && distributed_synchronizer) {
			ClusterSynchronizer cluster_synchronizer(*this, element_dimension,
			cluster_name_prefix,
			*element_to_fragment,
			*distributed_synchronizer,
			nb_cluster);
			nb_cluster = cluster_synchronizer.synchronize();
			delete element_to_fragment;
			}

			if (mesh_facets_created)
			delete mesh_facets;

			if(mesh.isDistributed())
			this->synchronizeGroupNames();

			AKANTU_DEBUG_OUT();
			return nb_cluster;
			}

			/* -------------------------------------------------------------------------- */
			template<typename T>
			void GroupManager::createGroupsFromMeshData(const std::string & dataset_name) {
			std::set<std::string> group_names;
			const ElementTypeMapArray<T> & datas = mesh.getData<T>(dataset_name);
			typedef typename ElementTypeMapArray<T>::type_iterator type_iterator;

			std::map<std::string, UInt> group_dim;

			for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
			type_iterator type_it = datas.firstType(_all_dimensions, *gt);
			type_iterator type_end = datas.lastType(_all_dimensions, *gt);
			for (; type_it != type_end; ++type_it) {
			const Array<T> & dataset = datas(type_it, gt);
			UInt nb_element = mesh.getNbElement(type_it, gt);
			AKANTU_DEBUG_ASSERT(dataset.getSize() == nb_element,
			"Not the same number of elements ("<< type_it << ":" << gt <<
			") in the map from MeshData (" << dataset.getSize() << ") "
			<< dataset_name <<" and in the mesh (" << nb_element << ")!");
			for(UInt e(0); e < nb_element; ++e) {
			std::stringstream sstr; sstr << dataset(e);
			std::string gname = sstr.str();
			group_names.insert(gname);

			std::map<std::string, UInt>::iterator it = group_dim.find(gname);
			if(it == group_dim.end()) {
			group_dim[gname] = mesh.getSpatialDimension(*type_it);
			} else {
			it->second = std::max(it->second, mesh.getSpatialDimension(*type_it));
			}
			}
			}
			}

			std::set<std::string>::iterator git = group_names.begin();
			std::set<std::string>::iterator gend = group_names.end();
			for (;git != gend; ++git) createElementGroup(git, group_dim[git]);

			if(mesh.isDistributed())
			this->synchronizeGroupNames();

			Element el;
			for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
			el.ghost_type = *gt;

			type_iterator type_it = datas.firstType(_all_dimensions, *gt);
			type_iterator type_end = datas.lastType(_all_dimensions, *gt);
			for (; type_it != type_end; ++type_it) {
			el.type = *type_it;

			const Array<T> & dataset = datas(type_it, gt);
			UInt nb_element = mesh.getNbElement(type_it, gt);
			AKANTU_DEBUG_ASSERT(dataset.getSize() == nb_element,
			"Not the same number of elements in the map from MeshData and in the mesh!");

			UInt nb_nodes_per_element = mesh.getNbNodesPerElement(el.type);

			Array<UInt>::const_iterator< Vector<UInt> > cit =
			mesh.getConnectivity(type_it, gt).begin(nb_nodes_per_element);

			for(UInt e(0); e < nb_element; ++e, ++cit) {
			el.element = e;
			std::stringstream sstr; sstr << dataset(e);
			ElementGroup & group = getElementGroup(sstr.str());
			group.add(el, false, false);

			const Vector<UInt> & connect = *cit;
			for (UInt n = 0; n < nb_nodes_per_element; ++n) {
			UInt node = connect[n];
			group.addNode(node, false);
			}

			}
			}
			}

			git = group_names.begin();
			for (;git != gend; ++git) {
			getElementGroup(*git).optimize();
			}
			}

			template void GroupManager::createGroupsFromMeshData<std::string>(const std::string & dataset_name);
			template void GroupManager::createGroupsFromMeshData<UInt>(const std::string & dataset_name);

			/* -------------------------------------------------------------------------- */
			void GroupManager::createElementGroupFromNodeGroup(const std::string & name,
			const std::string & node_group_name,
			UInt dimension) {
			NodeGroup & node_group = getNodeGroup(node_group_name);
			ElementGroup & group = createElementGroup(name, dimension, node_group);

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

			std::set<Element> seen;

			Array<UInt>::const_iterator<> itn = node_group.begin();
			Array<UInt>::const_iterator<> endn = node_group.end();
			for (;itn != endn; ++itn) {
			CSR<Element>::iterator ite = node_to_elem.begin(*itn);
			CSR<Element>::iterator ende = node_to_elem.end(*itn);
			for (;ite != ende; ++ite) {
			const Element & elem = *ite;
			if(dimension != _all_dimensions && dimension != Mesh::getSpatialDimension(elem.type)) continue;
			if(seen.find(elem) != seen.end()) continue;

			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(elem.type);
			Array<UInt>::const_iterator< Vector<UInt> > conn_it =
			mesh.getConnectivity(elem.type, elem.ghost_type).begin(nb_nodes_per_element);
			const Vector<UInt> & conn = conn_it[elem.element];

			UInt count = 0;
			for (UInt n = 0; n < conn.size(); ++n) {
			count += (node_group.getNodes().find(conn(n)) != -1 ? 1 : 0);
			}

			if(count == nb_nodes_per_element) group.add(elem);

			seen.insert(elem);
			}
			}

			group.optimize();
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::printself(std::ostream & stream, int indent) const {
			std::string space;
			for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);

			stream << space << "GroupManager [" << std::endl;

			std::set<std::string> node_group_seen;
			for(const_element_group_iterator it(element_group_begin()); it != element_group_end(); ++it) {
			it->second->printself(stream, indent + 1);
			node_group_seen.insert(it->second->getNodeGroup().getName());
			}

			for(const_node_group_iterator it(node_group_begin()); it != node_group_end(); ++it) {
			if(node_group_seen.find(it->second->getName()) == node_group_seen.end())
			it->second->printself(stream, indent + 1);
			}

			stream << space << "]" << std::endl;
			}

			/* -------------------------------------------------------------------------- */
			UInt GroupManager::getNbElementGroups(UInt dimension) const {
			if(dimension == _all_dimensions) return element_groups.size();

			ElementGroups::const_iterator it = element_groups.begin();
			ElementGroups::const_iterator end = element_groups.end();
			UInt count = 0;
			for(;it != end; ++it) count += (it->second->getDimension() == dimension);
			return count;
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::checkAndAddGroups(CommunicationBuffer & buffer) {
			AKANTU_DEBUG_IN();

			UInt nb_node_group; buffer >> nb_node_group;
			AKANTU_DEBUG_INFO("Received " << nb_node_group << " node group names");

			for (UInt ng = 0; ng < nb_node_group; ++ng) {
			std::string node_group_name;
			buffer >> node_group_name;

			if(node_groups.find(node_group_name) == node_groups.end()) {
			this->createNodeGroup(node_group_name);
			}

			AKANTU_DEBUG_INFO("Received node goup name: " << node_group_name);
			}


			UInt nb_element_group; buffer >> nb_element_group;
			AKANTU_DEBUG_INFO("Received " << nb_element_group << " element group names");
			for (UInt eg = 0; eg < nb_element_group; ++eg) {
			std::string element_group_name; buffer >> element_group_name;
			std::string node_group_name; buffer >> node_group_name;
			UInt dim; buffer >> dim;

			AKANTU_DEBUG_INFO("Received element group name: " << element_group_name
			<< " corresponding to a "
			<< Int(dim) << "D group with node group "
			<< node_group_name);

			NodeGroup & node_group = *node_groups[node_group_name];

			if(element_groups.find(element_group_name) == element_groups.end()) {
			this->createElementGroup(element_group_name, dim, node_group);
			}

			}


			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void GroupManager::fillBufferWithGroupNames(DynamicCommunicationBuffer & comm_buffer) const {
			AKANTU_DEBUG_IN();

			// packing node group names;
			UInt nb_groups = this->node_groups.size();
			comm_buffer << nb_groups;
			AKANTU_DEBUG_INFO("Sending " << nb_groups << " node group names");

			NodeGroups::const_iterator nnames_it = node_groups.begin();
			NodeGroups::const_iterator nnames_end = node_groups.end();
			for (; nnames_it != nnames_end; ++nnames_it) {
			std::string node_group_name = nnames_it->first;
			comm_buffer << node_group_name;
			AKANTU_DEBUG_INFO("Sending node goupe name: " << node_group_name);
			}

			// packing element group names with there associated node group name
			nb_groups = this->element_groups.size();
			comm_buffer << nb_groups;
			AKANTU_DEBUG_INFO("Sending " << nb_groups << " element group names");
			ElementGroups::const_iterator gnames_it = this->element_groups.begin();
			ElementGroups::const_iterator gnames_end = this->element_groups.end();
			for (; gnames_it != gnames_end; ++gnames_it) {
			ElementGroup & element_group = *(gnames_it->second);
			std::string element_group_name = gnames_it->first;
			std::string node_group_name = element_group.getNodeGroup().getName();
			UInt dim = element_group.getDimension();

			comm_buffer << element_group_name;
			comm_buffer << node_group_name;
			comm_buffer << dim;

			AKANTU_DEBUG_INFO("Sending element group name: " << element_group_name
			<< " corresponding to a "
			<< Int(dim) << "D group with the node group "
			<< node_group_name);
			}

			AKANTU_DEBUG_OUT();
			}


			/* -------------------------------------------------------------------------- */
			void GroupManager::synchronizeGroupNames() {
			AKANTU_DEBUG_IN();

			StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
			UInt nb_proc = comm.getNbProc();
			UInt my_rank = comm.whoAmI();

			if(nb_proc == 1) return;

			if(my_rank == 0) {
			for (UInt p = 1; p < nb_proc; ++p) {
			CommunicationStatus status;
			comm.probe<char>(p, p, status);
			AKANTU_DEBUG_INFO("Got " << printMemorySize<char>(status.getSize()) << " from proc " << p);

			CommunicationBuffer recv_buffer(status.getSize());
			comm.receive(recv_buffer.storage(), recv_buffer.getSize(), p, p);

			this->checkAndAddGroups(recv_buffer);
			}

			DynamicCommunicationBuffer comm_buffer;
			this->fillBufferWithGroupNames(comm_buffer);

			UInt buffer_size = comm_buffer.getSize();

			comm.broadcast(&buffer_size, 1, 0);

			AKANTU_DEBUG_INFO("Initiating broadcast with " << printMemorySize<char>(comm_buffer.getSize()));
			comm.broadcast(comm_buffer.storage(), buffer_size, 0);

			} else {
			DynamicCommunicationBuffer comm_buffer;
			this->fillBufferWithGroupNames(comm_buffer);

			AKANTU_DEBUG_INFO("Sending " << printMemorySize<char>(comm_buffer.getSize()) << " to proc " << 0);
			comm.send(comm_buffer.storage(), comm_buffer.getSize(), 0, my_rank);

			UInt buffer_size = 0;
			comm.broadcast(&buffer_size, 1, 0);

			AKANTU_DEBUG_INFO("Receiving broadcast with " << printMemorySize<char>(comm_buffer.getSize()));
			CommunicationBuffer recv_buffer(buffer_size);
			comm.broadcast(recv_buffer.storage(), recv_buffer.getSize(), 0);

			this->checkAndAddGroups(recv_buffer);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			const ElementGroup & GroupManager::getElementGroup(const std::string & name) const {
			const_element_group_iterator it = element_group_find(name);
			if(it == element_group_end()) {
			AKANTU_EXCEPTION("There are no element groups named " << name
			<< " associated to the group manager: " << id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			ElementGroup & GroupManager::getElementGroup(const std::string & name) {
			element_group_iterator it = element_group_find(name);
			if(it == element_group_end()) {
			AKANTU_EXCEPTION("There are no element groups named " << name
			<< " associated to the group manager: " << id);
			}

			return *(it->second);
			}


			/* -------------------------------------------------------------------------- */
			const NodeGroup & GroupManager::getNodeGroup(const std::string & name) const {
			const_node_group_iterator it = node_group_find(name);
			if(it == node_group_end()) {
			AKANTU_EXCEPTION("There are no node groups named " << name
			<< " associated to the group manager: " << id);
			}

			return *(it->second);
			}

			/* -------------------------------------------------------------------------- */
			NodeGroup & GroupManager::getNodeGroup(const std::string & name) {
			node_group_iterator it = node_group_find(name);
			if(it == node_group_end()) {
			AKANTU_EXCEPTION("There are no node groups named " << name
			<< " associated to the group manager: " << id);
			}

			return *(it->second);
			}


			__END_AKANTU__

rAKA/src/mesh/group_manager.ccfc32600c244bbugfixes/python_interfa…

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rAKA/src/mesh/group_manager.cc
fc32600c244bbugfixes/python_interfa…

group_manager.cc
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